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Gene Summary Type AAO1 ARABIDOPSIS ALDEHYDE OXIDASE 1 aldehyde oxidase/ indole-3acetaldehyde oxidase Process: Auxin biosynthetic process (Seo et al. 1998). AGI: AT5G20960. Pop. Ort.: POPTRDRAFT_767106 (AAO1) - fgenesh4_pg.C_LG_IX000157 AAO3 ABSCISIC ALDEHYDE OXIDASE 3: Encodes the aldehyde oxidase delta isoform catalyzing the final step in abscisic acid biosynthesis. AGI: AT2G27150. Pop. Ort.: POPTRDRAFT_767106 (AAO1) - fgenesh4_pg.C_LG_IX000157 AAO4 ARABIDOPSIS ALDEHYDE OXIDASE 4: Encodes aldehyde oxidase AAO4 preferentially expressed in developing seeds. AGI: AT1G04580. Pop. Ort.: POPTRDRAFT_767106 (AAO1) - fgenesh4_pg.C_LG_IX000157 ACL5 ACAULIS 5: Encodes a spermine synthase. Required for internode elongation and vascular development, specifically in the mechanism that defines the boundaries between veins and nonvein regions. This mechanism may be mediated by polar auxin transport. Though ACL5 has been shown to function as a spermine synthase in E. coli, an ACL5 knockout has no effect on the endogenous levels of free and conjugated polyamines in Arabidopsis, suggesting that ACL5 may have a very specific or altogether different in vivo function. Process: Auxin polar transport, phloem or xylem histogenesis (Clay and Nelson 2005) and vessel member cell differentiation (Hanzawa et al. 1997). AGI: AT5G19530. Pop. Ort.: POPTRDRAFT_717791 - estExt_Genewise1_v1.C_LG_VI2502 abscisic aldehyde oxidase/ aldehyde oxidase/ indole-3acetaldehyde oxidase aldehyde oxidase/ aryl-aldehyde oxidase spermine synthase/ thermospermine synthase References (Seo et al. 1998) (Jensen et al. 2008) (Ibdah et al. 2009) (Clay and Nelson 2005; Imai et al. 2006; Muniz et al. 2008; Kakehi et al. 2008; Baucher et al. 2007) Gene Summary Type ACR4 ARABIDOPSIS CRINKLY4: Encodes a membrane localized protein with similarity to receptor kinases which is involved in epidermal cell differentiation. Flowers of mutants have disorganized ovule integument growth and abnormal sepal margins. In the roots, mutants initiate more lateral roots but fewer laterals actually emerge due to defects in lateral root formation. Mutants also display disorganized columella. The root phenotypes can be traced to abnormalities in asymmetric divisions in the pericycle and root apex. Conflicting data regarding the role of the kinase domain- which may or may not be required for function. Complementation studies indicate that the C-terminal domain is also not required for signalling function. May be regulated by protein turnover which is mediated by endocytic processes. kinase/ transmembrane receptor protein kinase References (De Smet et al. 2008; Tanaka et al. 2007) Process: Embryonic development ending in seed dormancy (Tanaka et al. 2002), lateral root formation, regulation of asymmetric cell division and root cap development (De Smet et al. 2008). AGI: AT3G59420. Pop. Ort.: POPTRDRAFT_562238 - eugene3.00070176 AG AGAMOUS: encoding a MADS domain transcription factor. Specifies floral meristem and carpel and stamen identity. Binds CArG box sequences. It is the only C function gene. It interacts genetically with the other homeotic genes to specify the floral organs. DNA binding / transcription factor (Bao et al. 2004; Zhao et al. 2007) Process: stamen and carpel development (Gomez-Mena et al. 2005), leaf development (Doyle and Amasino 2009) and maintenance of floral organ identity (Mizukami and Ma 1997) AGI: AT4G18960. Pop. Ort.: POPTRDRAFT_758707 (PTAG1) - fgenesh4_pg.C_LG_IV000335 AHK2 ARABIDOPSIS HISTIDINE KINASE 2: Important regulator of vascular tissue development in Arabidopsis thaliana shoots. Process: Regulation of shoot development (Riefler et al. 2006). AGI: AT5G35750. Pop. Ort.: POPTRDRAFT_775135 - fgenesh4_pg.C_LG_XIV001045 cytokinin receptor/ osmosensor/ protein histidine kinase (Hejatko et al. 2009; Riefler et al. 2006; Nishimura et al. 2004) Gene Summary Type AHK3 ARABIDOPSIS HISTIDINE KINASE 3: Important regulator of vascular tissue development in Arabidopsis thaliana shoots. Encodes a histidine kinases, a cytokinin receptor that controls cytokinin-mediated leaf longevity through a specific phosphorylation of the response regulator, ARR2. cytokinin receptor/ osmosensor/ protein histidine kinase Process: Regulation of shoot development (Riefler et al. 2006). AGI: AT1G27320. Pop. Ort.: POPTRDRAFT_554773 (PHK4) - eugene3.00031406 AHP6 ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN 6: AHP6 lacks the conserved histidine residue (Asn83 in AHP6b), which is required for phosphotransfer, present in the other AHPs. AHP6 does not appear to have phosphotransfer activity. Acts as an inhibitor of cytokinin signalling by interacting with the phosphorelay machinery. Expressed in developing protoxylem and associated pericycle cell files. Negative regulator of cytokinin signalling. Expression is down-regulated by cytokinins. There are two alternatively spliced genes for this locus, AHP6a and AHP6b, differing in the length of the first exon. In ahp6-2 seedlings, only the AHP6a transcript is present. Members of the AHP gene family include: AT3G21510 (AHP1), AT3G29350 (AHP2), AT5G39340 (AHP3), AT3G16360 (AHP4), AT1G03430 (AHP5) and AT1G80100 (AHP6). histidine phosphotransfer kinase/ transferase, transferring phosphoruscontaining groups References (Spichal et al. 2004; FrancoZorrilla et al. 2005; Hejatko et al. 2009; Riefler et al. 2006; Nishimura et al. 2004; Romanov et al. 2006) (Mähönen et al. 2006) Process: Cytokinin mediated signalling pathway, response to cytokinin stimulus and xylem development (Mähönen et al. 2006). AGI: AT1G80100. Pop. Ort.: POPTRDRAFT_815256 - estExt_fgenesh4_pg.C_LG_I1468 AMI1 AMIDASE 1: Encodes an enzyme with similarity to bacterial acylamidohydrolases and exhibits indole-3-acetamide amidohydrolase activity in vitro. This enzyme may be involved in the in vivo biosynthesis of indole-acetic acid from indole-3-acetamide, a native metabolite of A. thaliana. It appears to exist as a monomer. Process: Indoleacetic acid biosynthetic process (Pollmann et al. 2003). AGI: AT1G08980. Pop. Ort.: POPTRDRAFT_662772 (AMI1) - grail3.0016020901 amidase/ hydrolase, acting on carbonnitrogen (but not peptide) bonds / indoleacetamide hydrolase (Neu et al. 2007) Gene Summary Type ANAC012 ARABIDOPSIS NAC DOMAIN CONTAINING PROTEIN 12: NAM (no apical meristem) family member. Negatively regulates xylary fiber development. Encodes SND1, a NAC Domain transcription factor involved in secondary wall biosynthesis in fibers. Expressed specifically in interfascicular fibers and xylary fibers in stems. Expressed in the procambium of stem inflorescences and root. May act as a negative regulator of secondary wall thickening in xylary fibers. Acts redundantly with NST1 to control development of secondary walls in siliques. transcription factor Process: Lignin biosynthetic process (Mitsuda et al. 2007) and secondary cell wall biogenesis (Mitsuda et al. 2007; Zhong et al. 2006a). AGI: AT1G32770. Pop. Ort.: POPTRDRAFT_569285 (NAC068) - eugene3.00111299 ANAC101 ARABIDOPSIS NAC-DOMAIN PROTEIN 101: Encodes a NAC-domain transcription factor involved in xylem formation. Induces transdifferentiation of various cells into metaxylem vessel elements. Located in the nucleus. Expression induced in the presence of auxin, cytokinin and brassinosteroids. Process: Response to brassinosteroid stimulus, response to cytokinin stimulus and xylem development (Kubo et al. 2005). transcription activator/ transcription factor/ transcription regulator References (Ko et al. 2007; Mitsuda et al. 2007; Zhong et al. 2007a; Zhong et al. 2006b; Zhong et al. 2007b; Mitsuda and OhmeTakagi 2008; McCarthy et al. 2009) (Soyano et al. 2008; Baucher et al. 2007; Kubo et al. 2005) AGI: AT5G62380. Pop. Ort.: POPTRDRAFT_773505 (NAC037) - fgenesh4_pg.C_LG_XII001280 AO2 ALDEHYDE OXIDASE 2 aldehyde oxidase (Koiwai et al. 2000) AGI: AT3G43600. Pop. Ort.: POPTRDRAFT_767106 (AAO1) - fgenesh4_pg.C_LG_IX000157 APL ALTERED PHLOEM DEVELOPMENT: MYB family transcription factor member. Encodes gene product that is required for several aspects of phloem development in the root: a) the specific divisions organizing the phloem pole, b) sieve element differentiation and c) the expression of a companion-specific gene. Mutant has a defect in the organization of phloem poles in the root. apl seedlings have a short, determinate root with only occasional lateral branches. Process: Xylem and phloem development (Bonke et al. 2003). AGI: AT1G79430. Pop. Ort.: POPTRDRAFT_765696 - fgenesh4_pg.C_LG_VIII000710 transcription factor/ transcription regulator (Baucher et al. 2007) Gene Summary Type ARR15 RESPONSE REGULATOR 15: Encodes a nuclear response regulator that acts as a negative regulator in cytokininmediated signal transduction. Transcript accumulates in leaves and roots in response to cytokinin treatment. transcription regulator/ twocomponent response regulator Process: Cytokinin mediated signaling pathway (Hwang et al. 2002; Kiba et al. 2003) and response to cytokinin stimulus (D'Agostino et al. 2000; Kiba et al. 2002; Kim et al. 2006). References (Kiba et al. 2002; Kiba et al. 2003) AGI: AT1G74890. Pop. Ort.: POPTRDRAFT_824636 (ARR3) - estExt_fgenesh4_pg.C_LG_XV0454 ARR5 ARABIDOPSIS RESPONSE REGULATOR 5: Encodes a transcription repressor that mediates a negative feedback loop in cytokinin signaling. ARR5 expression is upregulated by Class I KNOX genes. Arr5 protein is stabilized by cytokinin in a two-component phosphorelay. Process: Cytokinin mediated signaling pathway (Hwang et al. 2002; To et al. 2007) and response to cytokinin stimulus (Brandstatter and Kieber 1998; D'Agostino et al. 2000; Kim et al. 2006). transcription regulator/ twocomponent response regulator (D'Agostino et al. 2000; Spichal et al. 2004) AGI: AT3G48100. Pop. Ort.: POPTRDRAFT_824636 (ARR3) - estExt_fgenesh4_pg.C_LG_XV0454 ARR6 RESPONSE REGULATOR 6: Encodes a Type-A response regulator that is responsive to cytokinin treatment. Its C-ter domain is very short in comparison to other Arabidopsis ARRs (17 total). Arr6 protein is stabilized by cytokinin. Process: Cytokinin mediated signaling pathway (Hwang et al. 2002; To et al. 2007) and response to cytokinin stimulus (Brandstatter and Kieber 1998; D'Agostino et al. 2000; Kim et al. 2006). transcription regulator/ twocomponent response regulator (Ren et al. 2009) AGI: AT5G62920. Pop. Ort.: POPTRDRAFT_824636 (ARR3) - estExt_fgenesh4_pg.C_LG_XV0454 ARR7 RESPONSE REGULATOR 7: Encodes a member of the Arabidopsis response regulator (ARR) family, most closely related to ARR15. A two-component response regulator protein containing a phosphate accepting domain in the receiver domain but lacking a DNA binding domain in the output domain. Involved in response to cytokinin and meristem stem cell maintenance. Arr7 protein is stabilized by cytokinin. Process: Cytokinin mediated signaling pathway (To et al. 2007; Hwang et al. 2002), response to cytokinin stimulus (Kim et al. 2006) and stem cell maintenance (Leibfried et al. 2005). AGI: AT1G19050. Pop. Ort.: POPTRDRAFT_824636 (ARR3) - estExt_fgenesh4_pg.C_LG_XV0454 transcription regulator/ twocomponent response regulator (Ren et al. 2009; Lee et al. 2008) Gene Summary Type ASA1 ANTHRANILATE SYNTHASE ALPHA SUBUNIT 1: ASA1 encodes the alpha subunit of anthranilate synthase, which catalyzes the rate-limiting step of tryptophan synthesis. ASA1 is induced by ethylene, and forms a link between ethylene signaling and auxin synthesis in roots. anthranilate synthase References (Sun et al. 2009) Process: Auxin biosynthetic process (Stepanova et al. 2005). AGI: AT5G05730. Pop. Ort.: POPTRDRAFT_227100 (ASA1) - gw1.X.1797.1 ASB1 ANTHRANILATE SYNTHASE BETA SUBUNIT 1: Catalyzes the first step of tryptophan biosynthesis: Chorismate L-Glutamine = Anthranilate Pyruvate L-Glutamate. Functions as a heterocomplex with anthranilate synthase alpha subunit (ASA1 or ASA2). anthranilate synthase (Stepanova et al. 2005) Process: Auxin biosynthetic process (Stepanova et al. 2005). AGI: AT1G25220. Pop. Ort.: POPTRDRAFT_566399 (ASB1) - eugene3.00100957 ASB1-like A AGI: AT1G25155. Pop. Ort.: POPTRDRAFT_419417 (ASB2) - gw1.VIII.845.1 anthranilate synthase beta subunit, putative ASB1-like B AGI: AT1G24807. Pop. Ort.: POPTRDRAFT_419417 (ASB2) - gw1.VIII.845.1 anthranilate synthase beta subunit, putative ASB1-like C AGI: AT1G24909. Pop. Ort.: POPTRDRAFT_419417 (ASB2) - gw1.VIII.845.1 anthranilate synthase beta subunit, putative ASB1-like D AGI: AT1G25083. Pop. Ort.: POPTRDRAFT_419417 (ASB2) - gw1.VIII.845.1 anthranilate synthase beta subunit, putative ASB2 ANTHRANILATE SYNTHASE BETA SUBUNIT 2 anthranilate synthase beta subunit, putative AGI: AT5G57890. Pop. Ort.: POPTRDRAFT_566399 (ASB1) - eugene3.00100957 (Zhong et al. 1999) Gene Summary Type AT2G34590 AGI: AT2G34590. Pop. Ort.: POPTRDRAFT_668506 - grail3.0080008401 transketolase family protein AT3G25660 AGI: AT3G25660. Pop. Ort.: POPTRDRAFT_558478 - eugene3.00050093 glutamyltRNA(Gln) amidotransferase, putative ATE1_ALPHA Encodes the e1 alpha subunit of the pyruvate dehydrogenase complex (PDC) oxidoreductase, acting on the aldehyde or oxo group of donors, disulfide as acceptor / pyruvate dehydrogenase (acetyl-transferring) ATHB15/C NA/ICU4 CORONA: Member of the III HD-Zip family. Critical for vascular development and negatively regulates vascular cell differentiation. AGI: AT1G59900. Pop. Ort.: POPTRDRAFT_657555 - grail3.0009040502 DNA binding / transcription factor Process: Meristem initiation (Prigge et al. 2005), organ morphogenesis and regulation of meristem growth (Green et al. 2005) and phloem or xylem histogenesis (Kim et al. 2005). AGI: AT1G52150. Pop. Ort.: POPTRDRAFT_797557 (HB5) - fgenesh4_pm.C_LG_I000560 ATHB8 HOMEOBOX GENE 8: Member of the III HD-Zip family. Acting as a differentiation-promoting transcription factor of the vascular meristems. Process: Meristem initiation (Prigge et al. 2005), xylem development and positive regulation of cell differentiation and cell proliferation (Baima et al. 2001) and response to auxin stimulus (Baima et al. 1995; Mattsson et al. 2003). AGI: AT4G32880. Pop. Ort.: POPTRDRAFT_832118 (HB8) - estExt_fgenesh4_pm.C_LG_VI0713 DNA binding / transcription factor References (Hawker and Bowman 2004; Baucher et al. 2007; Kim et al. 2005; Ochando et al. 2008) (Hawker and Bowman 2004; Baucher et al. 2007) Gene Summary Type ATIPT1 ISOPENTENYLTRANSFERASE 1: Encodes a putative adenylate isopentenyltransferase which catalyzes the formation of isopentenyladenosine 5'-monophosphate (iPMP) from AMP and dimethylallylpyrophosphate (DMAPP). Involved in cytokinin biosynthesis. adenylate dimethylallyltransfe rase References (Kuderova et al. 2008) Process: Secondary growth: Increase in plant girth due to the activity of lateral meristems (vascular and cork cambium) (Matsumoto-Kitano et al. 2008). AGI: AT1G68460. Pop. Ort.: POPTRDRAFT_564538 - eugene3.00081133 ATIPT14 AB061402 Arabidopsis thaliana AtIPT4 mRNA for cytokinin synthase. Process: Cytokinin biosynthetic process (Miyawaki et al. 2006; Kakimoto 2001). adenylate dimethylallyltransfe rase (Kakimoto 2001; Li et al. 2010) AGI: AT4G24650. Pop. Ort.: POPTRDRAFT_564538 - eugene3.00081133 ATIPT6 AB061404 Arabidopsis thaliana AtIPT6 mRNA for cytokinin synthase, complete cds Process: Cytokinin biosynthetic process (Miyawaki et al. 2006). AGI: AT1G25410. Pop. Ort.: POPTRDRAFT_564538 - eugene3.00081133 ATIPT8 ATP/ADP ISOPENTENYLTRANSFERASES: Encodes cytokinin synthase. Process: Cytokinin biosynthetic process (Miyawaki et al. 2006; Takei et al. 2001). ATP binding / adenylate dimethylallyltransfe rase/ tRNA isopentenyltransfera se ATP/ADP ISOPENTENYLTR ANSFERASES AGI: AT3G19160. Pop. Ort.: POPTRDRAFT_564538 - eugene3.00081133 ATPAO2 POLYAMINE OXIDASE 2 AGI: AT2G43020. Pop. Ort.: POPTRDRAFT_831582 - estExt_fgenesh4_pm.C_LG_V0482 ATR1 ARABIDOPSIS P450 REDUCTASE 1: Encodes a cyp450 reductase likely to be involved in phenylpropanoid metabolism. AGI: AT4G24520. POPTRDRAFT_818445 (ATR1) - estExt_fgenesh4_pg.C_LG_V0696 (Miyawaki et al. 2006) (Miyawaki et al. 2006; Takei et al. 2001) amine oxidase/ electron carrier/ oxidoreductase NADPHhemoprotein reductase (Celenza et al. 2005; Bender and Fink 1998) Gene Summary Type ATR1-like AGI: AT3G02280. Pop. Ort.: POPTRDRAFT_714013 (ATR3) - estExt_Genewise1_v1.C_LG_IV3209 flavodoxin protein ATR2 ARABIDOPSIS P450 REDUCTASE 2: Encodes NADPH-cytochrome P450 reductase that catalyzes the first oxidative step of the phenylpropanoid general pathway. NADPHhemoprotein reductase AGI: AT4G30210. Pop. Ort.: POPTRDRAFT_825890 - estExt_fgenesh4_pg.C_LG_XVIII0790 AUX1 AUXIN RESISTANT 1: Encodes an auxin influx transporter. AUX1 resides at the apical plasma membrane of protophloem cells and at highly dynamic subpopulations of Golgi apparatus and endosomes in all cell types. AUX1 action in the lateral root cap and/or epidermal cells influences lateral root initiation and positioning. Process: Auxin polar transport (Kramer and Bennett 2006), establishment of planar polarity (Fischer et al. 2006) and positive gravitropism (Bennett et al. 1996). AGI: AT2G38120. Pop. Ort.: POPTRDRAFT_653103 (PtrAUX1) - grail3.0023028402 BAM1 BARELY ANY MERISTEM 1: Encodes a CLAVATA1-related receptor kinase-like protein required for both shoot and flower meristem function. Very similar to BAM2,with more than 85% a.a. identity. It has a broad expression pattern and is involved in vascular strand development in the leaf, control of leaf shape, size and symmetry, male gametophyte development and ovule specification and function. Anthers of double mutants (bam1bam2) appeared abnormal at a very early stage and lack the endothecium, middle, and tapetum layers. Further analyses revealed that cells interior to the epidermis (in anther tissue) acquire some characteristics of pollen mother cells (PMCs), suggesting defects in cell fate specification. The pollen mother-like cells degenerate before the completion of meiosis, suggesting that these cells are defective. In addition, the BAM1 expression pattern supports both an early role in promoting somatic cell fates and a subsequent function in the PMCs. Process: Regulation of meristem growth (DeYoung et al. 2006) and regulation of meristem structural organization (Deyoung and Clark 2008). AGI: AT5G65700. Pop. Ort.: POPTRDRAFT_717990 - estExt_Genewise1_v1.C_LG_VII0023 References family amino acid transmembrane transporter/ auxin binding / auxin influx transmembrane transporter/ transporter ATP binding / kinase/ protein serine/threonine kinase (Smolen et al. 2002) (KleineVehn et al. 2006; Belin et al. 2009; Carrier et al. 2008; De Smet et al. 2007) (Deyoung and Clark 2008; Hord et al. 2006) Gene Summary Type BAM2 BARELY ANY MERISTEM 2: Encodes a CLAVATA1-related receptor kinase-like protein required for both shoot and flower meristem function. Very similar to BAM1, with more than 85% a.a. identity. It has a broad expression pattern and is involved in vascular strand development in the leaf, control of leaf shape, size and symmetry, male gametophyte development and ovule specification and function. Anthers of double mutants (bam1bam2) appeared abnormal at a very early stage and lack the endothecium, middle, and tapetum layers. Further analyses revealed that cells interior to the epidermis (in anther tissue) acquire some characteristics of pollen mother cells (PMCs), suggesting defects in cell fate specification. The pollen mother-like cells degenerate before the completion of meiosis, suggesting that these cells are defective. In addition, the BAM2 expression pattern supports both an early role in promoting somatic cell fates and a subsequent function in the PMCs. ATP binding / protein binding / protein kinase/ protein serine/threonine References (Deyoung and Clark 2008; Hord et al. 2006) Process: Regulation of meristem growth (DeYoung et al. 2006) and regulation of meristem structural organization (Deyoung and Clark 2008). AGI: AT3G49670. Pop. Ort.: POPTRDRAFT_717990 - estExt_Genewise1_v1.C_LG_VII0023 BP/KNAT1 KNOTTED-LIKE FROM ARABIDOPSIS THALIANA: A member of class I knotted1-like homeobox gene family (together with KNAT2). Similar to the knotted1 (kn1) homeobox gene of maize. Normally expressed in the peripheral and rib zone of shoot apical meristem but not in the leaf primordia. It is also expressed in the fourth floral whorl, in the region that would become style, particularly in the cell surrounding the transmitting tissue. No expression was detected in the first three floral whorls. Expression is repressed by auxin and AS1 which results in the promotion of leaf fate. transcription factor (Baucher et al. 2007; Kanrar et al. 2006; Ragni et al. 2008) Process: Cell fate commitment (Venglat et al. 2002), cell fate specification (Lincoln et al. 1994) and xylem and phloem pattern formation (Douglas and Riggs 2005). AGI: AT4G08150. Pop. Ort.: POPTRDRAFT_710537 (KNOX) - estExt_Genewise1_v1.C_LG_II1820 BP/KNAT2 KNOTTED-LIKE FROM ARABIDOPSIS THALIANA 2: A member of class I knotted1-like homeobox gene family (together with KNAT1). Similar to the knotted1 (kn1) homeobox gene of maize. KNAT2 acts synergistically with cytokinins and antagonistically with ethylene based on ectopic expression studies in different mutant backgrounds and hormone treatments. In addition, KNAT2 is negatively regulated by AS and YABBY genes. KNAT2 is strongly expressed in the shoot apex of seedlings, while in mature plants the gene is primarily expressed in flowers and inflorescence stems. Process: Cytokinin mediated signaling pathway (Hamant et al. 2002). AGI: AT1G70510. Pop. Ort.: POPTRDRAFT_658310 - grail3.0036024801 transcription factor (Ikezaki et al. 2010; Ragni et al. 2008) Gene Summary Type BP/KNAT6 Homeodomain transcription factor KNAT6, belonging to class I of KN transcription factor family (which also includes KNAT1 and KNAT2). Expression is increased in as and bop1 leaf mutants. DNA binding / transcription activator/ transcription factor Process: Contributes to SAM maintenance and boundary establishment in the embryo via the SHOOT MERISTEMLESS(STM)/CUP-SHAPED COTYLEDON (CUC) pathway (Belles-Boix et al. 2006). References (Ragni et al. 2008; BellesBoix et al. 2006) AGI: AT1G23380. Pop. Ort.: POPTRDRAFT_658310 - grail3.0036024801 BRL1 BRI 1 LIKE: mutant has Altered vascular cell differentiation; LRR Receptor Kinase kinase (Baucher et al. 2007) AGI: AT1G55610. Pop. Ort.: POPTRDRAFT_844734 - e_gw1.I.6306.1 BRL2 BRI1-LIKE 2: Encodes a leucine rich repeat receptor kinase and associated with provascular/procambial cells. Similar to BRI, brassinosteroid receptor protein. Process: Auxin mediated signaling pathway and brassinosteroid mediated signaling pathway (Ceserani et al. 2009), phloem transport and xylem and phloem pattern formation (Clay and Nelson 2002). AGI: AT2G01950. Pop. Ort.: POPTRDRAFT_657034 - grail3.0010068301 BRL3 BRI1-LIKE 3: Similar to BRI, brassinosteroid receptor protein. AGI: AT3G13380. Pop. Ort.: POPTRDRAFT_672125 - grail3.0140000501 CKI1 CYTOKININ-INDEPENDENT 1: Important regulators of vascular tissue development in Arabidopsis thaliana shoots. Encodes a putative plasma membrane-bound hybrid histidine kinase and cytokinin sensor that is expressed within the female gametophyte. Process: Cytokinin mediated signaling pathway (Hwang et al. 2002). AGI: AT2G47430. Pop. Ort.: POPTRDRAFT_898811 - e_gw1.XIV.2340.1 ATP binding / protein serine/threonine kinase/ transmembrane receptor protein serine/threonine kinase ATP binding / protein binding / protein kinase/ protein serine/threonine kinase protein histidine kinase/ twocomponent response regulator (Baucher et al. 2007; Ceserani et al. 2009) (CanoDelgado al. 2004) et (Glover et al. 2008; Hejatko et al. 2009) Gene Summary Type CLE40 CLAVATA3/ESR-RELATED 40: Member of a large family of putative ligands homologous to the Clavata3 gene. Consists of a single exon. protein binding / receptor binding References (Fiers et al. 2005) AGI: AT5G12990. Pop. Ort.: POPTRDRAFT_750766 - fgenesh4_pg.C_LG_I000369 CLE41 CLAVATA3/ESR-RELATED 41: Belongs to a large gene family, called CLE for CLAVATA3/ESR-related, encoding small peptides with conserved carboxyl termini. The C-terminal 12 amino acid sequence of CLE41 is identical to that of a dodeca peptide (TDIF, tracheary element differentiation inhibitory factor) isolated from Arabidopsis and functions as a suppressor of plant stem cell differentiation. TDIF sequence is also identical to the C-terminal 12 amino acids of CLE44 (AT4G13195). TDIF/CLE41/44/42 was shown to act as ligand for PXY. protein binding / receptor binding (Hirakawa et al. 2008; Lehesranta et al. 2009) Process: Phloem or xylem histogenesis (Ito et al. 2006). AGI: AT3G24770. Pop. Ort.: POPTRDRAFT_569594 - eugene3.00120247 CLE42 (Ito et al. 2006) CLAVATA3/ESR-RELATED 42: Belongs to a large gene family, called CLE for CLAVATA3/ESR-related, encoding small peptides with conserved carboxyl termini. AGI: AT2G34925. Pop. Ort.: POPTRDRAFT_751056 - fgenesh4_pg.C_LG_I000659 CLE44 (Hirakawa et al. 2008; Lehesranta et al. 2009) CLAVATA3/ESR-RELATED 44: Belongs to a large gene family, called CLE for CLAVATA3/ESR-related, encoding small peptides with conserved carboxyl termini. The C-terminal 12 amino acid sequence of CLE44 is identical to that of a dodeca peptide (TDIF, tracheary element differentiation inhibitory factor) isolated from Arabidopsis and functions as a suppressor of plant stem cell differentiation. TDIF sequence is also identical to the C-terminal 12 amino acids of CLE41 (AT3G24770). TDIF/CLE41/44/42 was shown to act as ligand for PXY. Process: Phloem or xylem histogenesis (Ito et al. 2006). AGI: AT4G13195. Pop. Ort.: POPTRDRAFT_569594 - eugene3.00120247 CLE6 CLAVATA3/ESR-RELATED 6: Member of a large family of putative ligands homologous to the Clavata3 gene. Consists of a single exon. Can replace CLV3 function in vivo. AGI: AT2G31085. Pop. Ort.: POPTRDRAFT_574352 - eugene3.00190826 protein binding / receptor binding (Cock and McCormick 2001) Gene Summary Type CLV1 CLAVATA 1: Putative receptor kinase with an extracellular leucine-rich domain. Controls shoot and floral meristem size, and contributes to establish and maintain floral meristem identity. Negatively regulated by KAPP (kinaseassociated protein phosphatase) (Williams et al. 1997; Trotochaud et al. 1999). CLV3 peptide binds directly CLV1 ectodomain. ATP binding / kinase/ protein serine/threonine kinase/ receptor signaling protein serine/threonine kinase Process: Cell differentiation (Williams et al. 1999) and regulation of meristem structural organization (Clark et al. 1997). References (Ogawa et al. 2008) AGI: AT1G75820. Pop. Ort.: POPTRDRAFT_583546 - eugene3.15140001 CLV2 CLAVATA2: Receptor-like protein containing leucine-rich repeats. Regulates both meristem and organ development in Arabidopsis. Process: Anatomical structure morphogenesis, regulation of flower development and growth (Kayes and Clark 1998) and meristem development (Wang et al. 2008). protein binding / receptor signaling protein (Wang et al. 2010) AGI: AT1G65380. Pop. Ort.: POPTRDRAFT_596988 - eugene3.00870064 CLV3 CLAVATA3: One of the three CLAVATA genes controlling the size of the shoot apical meristem (SAM) in Arabidopsis. Belongs to a large gene family called CLE for CLAVATA3/ESR-related. Encodes a stem cell-specific protein CLV3 presumed to be a precursor of a secreted peptide hormone. The deduced ORF encodes a 96-amino acid protein with an 18-amino acid N-terminal signal peptide. The functional form of CLV3 (MCLV3) is a posttranscriptionally modified 12-amino acid peptide, in which two of the three prolines were modified to hydroxyproline. CLV3 binds the ectodomain of the CLAVATA1 (CLV1) receptor-kinase. Regulates shoot and floral meristem development. Required for CLAVATA1 receptor-like kinase assembly into a signaling complex that includes KAPP and a Rho-related protein. It restricts its own domain of expression, the central zone (CZ) of the shoot apical meristem (SAM), by preventing differentiation of peripheral zone cells, which surround the CZ, into CZ cells and restricts overall SAM size by a separate, long-range effect on cell division rate. CLE domain of CLV3 is sufficient for function. Process: Cell differentiation (Brand et al. 2000), meristem development (Muller et al. 2006) and regulation of meristem structural organization (Kondo et al. 2006). AGI: AT2G27250. Pop. Ort.: POPTRDRAFT_821595 - estExt_fgenesh4_pg.C_LG_IX1351 kinase activator/ protein binding / receptor binding (Ogawa et al. 2008; Fiers et al. 2005; Reddy and Meyerowitz 2005; Muller et al. 2006; Kondo et al. 2006) Gene Summary Type References COV1 CONTINUOUS VASCULAR RING: Encodes an integral membrane protein of unknown function, highly conserved between plants and bacteria; is likely to be involved in a mechanism that negatively regulates the differentiation of vascular tissue in the stem. Mutants display a dramatic increase in vascular tissue development in the stem in place of the interfascicular region that normally separates the vascular bundles. membrane protein (Baucher et al. 2007) Process: Stem vascular tissue pattern formation and auxin mediated signaling pathway (Parker et al. 2003). AGI: AT2G20120. Pop. Ort.: POPTRDRAFT_669317 - grail3.0020005701 CYP79B2 CYTOCHROME P450 79B2: Belongs to cytochrome P450 and is involved in tryptophan metabolism. Converts Trp to indo-3-acetaldoxime (IAOx), a precursor to IAA and indole glucosinolates. Process: Indoleacetic acid biosynthetic process (Ljung et al. 2005; Zhao et al. 2002). AGI: AT4G39950. Pop. Ort.: POPTRDRAFT_555694 (CYP79D8) - eugene3.00040407 CYP79B3 CYTOCHROME P450 79B3: Encodes a cytochrome P450. Involved in tryptophan metabolism. Converts Trp to indole-3-acetaldoxime (IAOx), a precursor to IAA and indole glucosinolates. Process: Indoleacetic acid biosynthetic process (Ljung et al. 2005; Zhao et al. 2002). AGI: AT2G22330. Pop. Ort.: POPTRDRAFT_584081 (CYP79D6v2) - eugene3.15850001 CYP83A1 CYTOCHROME P450 83A1: Encodes a cytochrome p450 enzyme that catalyzes the initial conversion of aldoximes to thiohydroximates in the synthesis of glucosinolates not derived from tryptophan. Also has a role in auxin homeostasis. AGI: AT4G13770. Pop. Ort.: POPTRDRAFT_346721 (CYP83F1) - fgenesh1_pg.C_LG_II000227 electron carrier/ heme binding / iron ion binding / monooxygenase/ oxygen binding electron carrier/ heme binding / iron ion binding / monooxygenase/ oxygen binding oxidoreductase, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen / oxygen binding (Mikkelsen et al. 2009) (Mikkelsen et al. 2009) (Naur et al. 2003; Bak and Feyereisen 2001) Gene Summary Type CYP83B1 SUR2 CYTOCHROME P450 MONOOXYGENASE 83B1: Encodes an oxime-metabolizing enzyme in the biosynthetic pathway of glucosinolates. Is required for phytochrome signal transduction in red light. Mutation confers auxin overproduction. oxidoreductase, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen / oxygen binding AGI: AT4G31500. Pop. Ort.: POPTRDRAFT_346721 (CYP83F1) - fgenesh1_pg.C_LG_II000227 Dof5.6/HC A2 Preferentially expressed in the vasculature of all the organs, particularly in the cambium, phloem, and interfascicular parenchyma cells of inflorescence stems. Process: Phloem or xylem histogenesis and procambium histogenesis (Guo et al. 2009). Dof-type zinc finger domaincontaining protein References (Naur et al. 2003; Bak and Feyereisen 2001) (Guo et al. 2009) AGI: AT5G62940. Pop. Ort.: POPTRDRAFT_570095 - eugene3.00120748 ELF5A-1 EUKARYOTIC ELONGATION FACTOR 5A-1: Xylem abundance. In mammalian cells it functions as a shuttle protein that translocates mRNA from the nucleus to cytoplasmic ribosomes. Overexpression results in an increase in both primary and secondary xylem formation. In RNAi suppressed lines, xylem formation is reduced. translation initiation factor Process: Xylem development (Liu et al. 2008). AGI: AT1G13950. Pop. Ort.: POPTRDRAFT_717121 - estExt_Genewise1_v1.C_LG_VI0968 F11A3.11 AGI: AT2G20340. Pop. Ort.: POPTRDRAFT_816969 - estExt_fgenesh4_pg.C_LG_II2533 tyrosine decarboxylase, putative F17M19.7 AGI: AT1G71920. Pop. Ort.: POPTRDRAFT_287731 - gw1.41.216.1 histidinolphosphate aminotransferase, putative (Liu et al. 2008) Gene Summary Type F23N19.18 AGI: AT1G62810. Pop. Ort.: POPTRDRAFT_744008 - estExt_Genewise1_v1.C_1270098 copper amine oxidase, putative F4I10.4 AGI: AT4G33070. Pop. Ort.: POPTRDRAFT_835585 - estExt_fgenesh4_pm.C_LG_XVI0442 pyruvate decarboxylase, putative GH3.6/DFL 1 DWARF IN LIGHT 1: Encodes an IAA-amido synthase that conjugates Ala, Asp, Phe, and Trp to auxin. Lines overexpressing this gene accumulate IAA-ASP and are hypersensitive to several auxins. Identified as a dominant mutation that displays shorter hypocotyls in light grown plants when compared to wild type siblings. Protein is similar to auxin inducible gene from pea (GH3). indole-3-acetic acid amido synthetase References (Nakazawa et al. 2001) Process: Auxin homeostasis and response to auxin stimulus (Staswick et al. 2005) and auxin mediated signaling pathway (Nakazawa et al. 2001). AGI: AT5G54510. Pop. Ort.: POPTRDRAFT_571444 (GH3-6) - eugene3.00130808 GN GNOM: Encodes a GDP/GTP exchange factor for small G-proteins of the ADP ribosylation factor (RAF) class, and as regulator of intracellular trafficking. Homologous to Sec7p and YEC2 from yeast. Involved in the specification of apical-basal pattern formation. Essential for cell division, expansion and adhesion. It appears that heteotypic binding between the DCB and C-terminal domains of two GNOM proteins is required for membrane association, however, GNOM appears to exist predominantly as a heterodimer formed through DCB-DCB interactions. GTP:GDP antiporter/ protein homodimerization (Helariutta and Bhalerao 2003) Process: Basipetal auxin transport (Kleine-Vehn et al. 2008), cytokinesis by cell plate formation (Shevell et al. 1994), establishment of planar polarity (Fischer et al. 2006) and phloem or xylem histogenesis (Koizumi et al. 2000). AGI: AT1G13980. Pop. Ort.: POPTRDRAFT_578433 - eugene3.00180657 HPA1 HISTIDINOL PHOSPHATE AMINOTRANSFERASE 1: Encodes histidinol-phosphate aminotransferase that catalyzes the eighth step in histidine biosynthesis. Loss of function mutations are embryo lethal. AGI: AT5G10330. Pop. Ort.: POPTRDRAFT_287731 - gw1.41.216.1 IAGLU INDOLE-3-ACETATE BETA-D-GLUCOSYLTRANSFERASE AGI: AT4G15550. Pop. Ort.: POPTRDRAFT_645347 - grail3.0021016401 histidinolphosphate transaminase UDPglycosyltransferase/ transferase, transferring glycosyl groups (Mo et al. 2006) Gene Summary Type IAR1 IAA-ALANINE RESISTANT 1: member of IAA-alanine resistance protein 1 metal ion transmembrane transporter AGI: AT1G68100. Pop. Ort.: POPTRDRAFT_720768 - estExt_Genewise1_v1.C_LG_VIII2016 IAR3 IAA-ALANINE RESISTANT 3: encodes a member of the six Arabidopsis IAA-amino acid conjugate hydrolase subfamily and conjugates and conjugates IAA-Ala in vitro. Gene is expressed most strongly in roots, stems, and flowers. References IAA-Ala conjugate hydrolase/ metallopeptidase AGI: AT1G51760. Pop. Ort.: POPTRDRAFT_711792 (ILL11) - estExt_Genewise1_v1.C_LG_III0403 IAR4 IAA-ALANINE RESISTANT 4: Arabidopsis thaliana pyruvate dehydrogenase E1a-like subunit. 81% identical to a previously characterized Arabidopsis mitochondrial PDH E1a-subunit, AT1G59900. AGI: AT1G24180. Pop. Ort.: POPTRDRAFT_1090032 - estExt_Genewise1Plus.C_LG_X1893 oxidoreductase, acting on the aldehyde or oxo group of donors, disulfide as acceptor / pyruvate dehydrogenase (acetyl-transferring) IGS-like AGI: AT2G04400. Pop. Ort.: POPTRDRAFT_834976 - estExt_fgenesh4_pm.C_LG_XIV0483 indole-3-glycerol phosphate synthase (IGPS) ILL5 Encodes a member of the six Arabidopsis IAA-amino acid conjugate hydrolase subfamily and conjugates and is very similar to IAR3. IAA-amino acid conjugate hydrolase/ metallopeptidase AGI: AT1G51780. Pop. Ort.: POPTRDRAFT_711792 (ILL11) - estExt_Genewise1_v1.C_LG_III0403 ILR1 IAA-LEUCINE RESISTANT 1: Hydrolyzes amino acid conjugates of the plant growth regulator indole-3-acetic acid (IAA), including IAA-Leu and IAA-Phe. Uses Mg and Co ions as cofactors. Process: Auxin metabolic process (Bartel and Fink 1995). AGI: AT3G02875. Pop. Ort.: POPTRDRAFT_763045 (ILL1) - fgenesh4_pg.C_LG_VI001355 IAA-Leu conjugate hydrolase/ IAA-Phe conjugate hydrolase/ metallopeptidase (Quint et al. 2009) (Bartel and Fink 1995) Gene Summary Type IRX3 IRREGULAR XYLEM 3: Encodes a xylem-specific cellulose synthase that is phosphorylated on one or more serine residues (on either S185 or one of S180 or S181). cellulose synthase Process: Cellulose synthase activity (Taylor et al. 1999). References (Atanassov et al. 2009; Zhong et al. 2006b) AGI: AT5G17420. Pop. Ort.: POPTRDRAFT_717644 - estExt_Genewise1_v1.C_LG_VI2188 KAN1 KANADI: GARP family member. Encodes a KANADI protein (KAN) that regulates organ polarity in Arabidopsis. KAN is required for abaxial identity in both leaves and carpels, and encodes a nuclear-localized protein in the GARP family of putative transcription factors. Together with KAN2, this gene appears to be involved in the development of the carpel and the outer integument of the ovule. Along with KAN2 and KAN4, KAN1 appears to be required for proper regulation of PIN1 in early embryogenesis. transcription factor (Baucher et al. 2007; Pekker et al. 2005; Wu et al. 2008) Process: Abaxial cell fate specification (Pekker et al. 2005), adaxial/abaxial axis specification (Wu et al. 2008), polarity specification of adaxial/abaxial axis (Ha et al. 2007), radial pattern formation and xylem and phloem pattern formation (Emery et al. 2003). AGI: AT5G16560. Pop. Ort.: POPTRDRAFT_755990 - fgenesh4_pg.C_LG_II002170 KAN2 KANADI 2: MYB family transcription factor member. Encodes a KANADI protein (KAN) that regulates organ polarity in Arabidopsis. KAN is required for abaxial identity in both leaves and carpels, and encodes a nuclearlocalized protein in the GARP family of putative transcription factors. Together with KAN2, this gene appears to be involved in the development of the carpel and the outer integument of the ovule. Along with KAN2 and KAN4, KAN1 appears to be required for proper regulation of PIN1 in early embryogenesis. DNA binding / transcription factor (Baucher et al. 2007; Pekker et al. 2005; Wu et al. 2008) DNA binding / transcription factor (Baucher et al. 2007; Pekker et al. 2005; Wu et al. 2008) Process: Polarity specification of adaxial/abaxial axis (Ha et al. 2007). AGI: AT1G32240. Pop. Ort.: POPTRDRAFT_590054 - eugene3.00290237 KAN3 KANADI 3: GARP family member. Encodes a KANADI protein (KAN) that regulates organ polarity in Arabidopsis. KAN is required for abaxial identity in both leaves and carpels, and encodes a nuclear-localized protein in the GARP family of putative transcription factors. Together with KAN2, this gene appears to be involved in the development of the carpel and the outer integument of the ovule. Along with KAN2 and KAN4, KAN1 appears to be required for proper regulation of PIN1 in early embryogenesis. AGI: AT4G17695. Pop. Ort.: POPTRDRAFT_590054 - eugene3.00290237 Gene Summary Type KAN4/ATS ABERRANT TESTA SHAPE: Encodes a member of the KANADI family of putative transcription factors. Involved in integument formation during ovule development and expressed at the boundary between the inner and outer integuments. It is essential for directing laminar growth of the inner integument. Along with KAN1 and KAN2, KAN4 is involved in proper localization of PIN1 in early embryogenesis. DNA binding / transcription factor References (McAbee et al. 2006) Process: Integument development (Kelley et al. 2009) and ovule development (Leon-Kloosterziel et al. 1994). AGI: AT5G42630. Pop. Ort.: POPTRDRAFT_917686 - e_gw1.40.547.1 KAPP KINASE ASSOCIATED PROTEIN PHOSPHATASE: kinase associated protein phosphatase composed of three domains: an amino-terminal signal anchor, a kinase interaction (KI) domain, and a type 2C protein phosphatase catalytic region. Process: Regulation of meristem structural organization (Stone et al. 1998) and negative regulator of CLV1 signaling (Trotochaud et al. 1999). phosphoprotein phosphatase/ protein kinase binding / protein serine/threonine phosphatase (Williams et al. 1997) AGI: AT5G19280. Pop. Ort.: POPTRDRAFT_805045 - fgenesh4_pm.C_LG_X000351 LAS Lateral Suppressor: GRAS transcription factor family member. It is involved in the initiation of axillary meristems during both the vegetative and reproductive growth phases and functions upstream of REV and AXR1 in the regulation of shoot branching. transcription factor (Raman et al. 2008) Process: Regulation of transcription (Riechmann et al. 2000) and secondary shoot formation (Greb et al. 2003). AGI: AT1G55580. Pop. Ort.: POPTRDRAFT_550683 (GRAS44) - eugene3.00013124 LAX3 LIKE AUX1 3: Encodes an auxin influx carrier LAX3 (Like Aux1) that promotes lateral root emergence. Auxininduced expression of LAX3 in turn induces a selection of cell-wall-remodelling enzymes, which are likely to promote cell separation in advance of developing lateral root primordia. Process: Auxin polar transport (Swarup et al. 2008). AGI: AT1G77690. Pop. Ort.: POPTRDRAFT_643656 (PtrAUX8) - grail3.0003074001 LCV1 LIKE COV 1 AGI: AT2G20130. Pop. Ort.: POPTRDRAFT_669317 - grail3.0020005701 amino acid transmembrane transporter/ auxin influx transmembrane transporter/ transporter (Vandenbuss che et al. 2010) Gene Summary Type MAB1 MACCI-BOU catalytic/ pyruvate dehydrogenase (acetyl-transferring) AGI: AT5G50850. Pop. Ort.: POPTRDRAFT_829373 - estExt_fgenesh4_pm.C_LG_I0194 MAX1/CYP 711A1 Encodes a protein with similarity to thromboxane-A synthase, member of the CYP711A cytochrome P450 family. MAX1 is a specific repressor of vegetative axillary buds generated by the axillary meristem. Expressed in vascular traces in the rosette stem and axillary buds throughout plant development. Mutants have increased axillary branches. Along with MAX3,4 thought to mediate control of shoot branching via synthesis of a signal molecule which is transported over long distance mediated by MAX2. cDNA supports the existence of the longer transcript predicted for this locus, no cDNA isolated for shorter transcript. MAX1 downregulates 11 genes involved in flavonoid pathway (CHS, CHI, F3H, F3'H, FLS, DFR, ANS, UFGT, RT, AAC and GST). electron carrier/ heme binding / iron ion binding / monooxygenase/ oxygen binding References (Lazar and Goodman 2006) Process: Auxin polar transport (Bennett et al. 2006), positive regulation of flavonoid biosynthetic process (Lazar and Goodman 2006), regulation of meristem structural organization (Stirnberg et al. 2002) and secondary shoot formation (Booker et al. 2005). AGI: AT2G26170. Pop. Ort.: POPTRDRAFT_352660 (CYP711A8) - fgenesh1_pg.C_LG_VI001581 MAX2 MORE AXILLARY BRANCHES 2: ORE9 family member. The mutations at MAX2 cause increased hypocotyl and petiole elongation in light-grown seedlings. Positional cloning identifies MAX2 as a member of the F-box leucine-rich repeat family of proteins. MAX2 is identical to ORE9, a proposed regulator of leaf senescence. Involved in positive regulation of light responses. ubiquitin-protein ligase (Stirnberg et al. 2007; Shen et al. 2007) Process: Auxin polar transport (Bennett et al. 2006), regulation of meristem structural organization (Stirnberg et al. 2002) and shoot morphogenesis (Stirnberg et al. 2007). AGI: AT2G42620. Pop. Ort.: POPTRDRAFT_1099491 - estExt_Genewise1Plus.C_LG_XIV2555 MAX3/CC D7 CAROTENOID CLEAVAGE DIOXYGENASE 7: MAX3 encodes a plastidic dioxygenase that can cleave multiple carotenoids. AGI: AT2G44990. Pop. Ort.: POPTRDRAFT_781295 - fgenesh4_pg.C_scaffold_40000045 CAROTENOID CLEAVAGE DIOXYGENASE 7 (Schwartz et al. 2004; Zou et al. 2006; Booker et al. 2004) Gene Summary Type MAX4/CC D8 CAROTENOID CLEAVAGE DIOXYGENASE 8: Encodes a protein with similarity to carotenoid cleaving deoxygenases, the enzymes that cleave beta-carotene. Involved in the production of a graft transmissable signal to suppress axillary branching. Protein is localized to chloroplast stroma and expressed primarily in root tip. Mutants in the gene exhibit increased shoot branching, and light-dependent defects in hook opening and hypocotyl/root elongation. Only upregulated by auxin in the root and hypocotyl, and this is not required for the inhibition of shoot branching. oxidoreductase, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen Process: Auxin metabolic process (Auldridge et al. 2006), auxin polar transport (Bennett et al. 2006), response to auxin stimulus (Sorefan et al. 2003) and secondary shoot formation (Auldridge et al. 2006; Sorefan et al. 2003). References (Schwartz et al. 2004; Alder et al. 2008) AGI: AT4G32810. Pop. Ort.: POPTRDRAFT_561749 - eugene3.00061708 miR156A Encodes a microRNA that targets several SPL family members, including SPL3,4, and 5. By regulating the expression of SPL3 (and probably also SPL4 and SPL5), this microRNA regulates vegetative phase change. misc_RNA (Martin et al. 2010; Wu et al. 2009) AGI: AT2G25095. Pop. Ort.: POPTRDRAFT_576281 - eugene3.00160416, POPTRDRAFT_769294 fgenesh4_pg.C_LG_X000784, POPTRDRAFT_793900 fgenesh4_pg.C_scaffold_9189000001, POPTRDRAFT_656548 - grail3.0010026801, POPTRDRAFT_733659 - estExt_Genewise1_v1.C_LG_XV2187, POPTRDRAFT_755123 - fgenesh4_pg.C_LG_II001303, POPTRDRAFT_769914 - fgenesh4_pg.C_LG_X001404 miR156B Encodes a microRNA that targets several SPL family members, including SPL3,4, and 5. By regulating the expression of SPL3 (and probably also SPL4 and SPL5), this microRNA regulates vegetative phase change. misc_RNA (Martin et al. 2010; Wu et al. 2009) AGI: AT4G30972. Pop. Ort.: POPTRDRAFT_755123 - fgenesh4_pg.C_LG_II001303, POPTRDRAFT_793900 fgenesh4_pg.C_scaffold_9189000001 miR156C Encodes a microRNA that targets several SPL family members, including SPL3,4, and 5. By regulating the expression of SPL3 (and probably also SPL4 and SPL5), this microRNA regulates vegetative phase change. AGI: AT4G31877. Pop. Ort.: POPTRDRAFT_769914 - fgenesh4_pg.C_LG_X001404, POPTRDRAFT_656548 grail3.0010026801, POPTRDRAFT_754682 - fgenesh4_pg.C_LG_II000862, POPTRDRAFT_646571 grail3.0018026401 misc_RNA (Martin et al. 2010; Wu et al. 2009) Gene Summary Type miR156D Encodes a microRNA that targets several SPL family members, including SPL3,4, and 5. By regulating the expression of SPL3 (and probably also SPL4 and SPL5), this microRNA regulates vegetative phase change. misc_RNA References (Martin et al. 2010; Wu et al. 2009) AGI: AT5G10945. Pop. Ort.: POPTRDRAFT_576281 - eugene3.00160416, POPTRDRAFT_769914 fgenesh4_pg.C_LG_X001404, POPTRDRAFT_755123 - fgenesh4_pg.C_LG_II001303, POPTRDRAFT_733659 estExt_Genewise1_v1.C_LG_XV2187, POPTRDRAFT_656548 - grail3.0010026801, POPTRDRAFT_793900 fgenesh4_pg.C_scaffold_9189000001 miR156E Encodes a microRNA that targets several SPL family members, including SPL3,4, and 5. By regulating the expression of SPL3 (and probably also SPL4 and SPL5), this microRNA regulates vegetative phase change. AGI: AT5G11977. Pop. Ort.: POPTRDRAFT_576281 - eugene3.00160416, POPTRDRAFT_769914 fgenesh4_pg.C_LG_X001404, POPTRDRAFT_755123 - fgenesh4_pg.C_LG_II001303, POPTRDRAFT_575458 eugene3.00150853, POPTRDRAFT_733659 - estExt_Genewise1_v1.C_LG_XV2187, POPTRDRAFT_656548 grail3.0010026801, POPTRDRAFT_770592 - fgenesh4_pg.C_LG_X002082, POPTRDRAFT_793900 fgenesh4_pg.C_scaffold_9189000001 miR156F misc_RNA (Martin et al. 2010; Wu et al. 2009) - Encodes a microRNA that targets several SPL family members, including SPL3,4, and 5. By regulating the expression of SPL3 (and probably also SPL4 and SPL5), this microRNA regulates vegetative phase change. misc_RNA (Martin et al. 2010; Wu et al. 2009) AGI: AT5G26147. Pop. Ort.: POPTRDRAFT_576281 - eugene3.00160416, POPTRDRAFT_947685 e_gw1.9962.5.1, POPTRDRAFT_813446 - fgenesh4_pm.C_scaffold_57000049, POPTRDRAFT_769914 fgenesh4_pg.C_LG_X001404, POPTRDRAFT_764848 - fgenesh4_pg.C_LG_VII001193, POPTRDRAFT_755123 fgenesh4_pg.C_LG_II001303, POPTRDRAFT_733659 estExt_Genewise1_v1.C_LG_XV2187, POPTRDRAFT_656548 - grail3.0010026801, POPTRDRAFT_793900 - fgenesh4_pg.C_scaffold_9189000001 miR156G Encodes a microRNA that targets several SPL family members, including SPL3,4, and 5. By regulating the expression of SPL3 (and probably also SPL4 and SPL5), this microRNA regulates vegetative phase change. misc_RNA (Martin et al. 2010; Wu et al. 2009) AGI: AT2G19425. Pop. Ort.: POPTRDRAFT_1117116 - estExt_Genewise1Plus.C_1520155 miR156H Encodes a microRNA that targets several SPL family members, including SPL3,4, and 5. By regulating the expression of SPL3 (and probably also SPL4 and SPL5), this microRNA regulates vegetative phase change. AGI: AT5G55835. Pop. Ort.: POPTRDRAFT_576281 estExt_Genewise1_v1.C_LG_XV2187 - eugene3.00160416, POPTRDRAFT_733659 - misc_RNA (Martin et al. 2010; Wu et al. 2009) Gene Summary Type miR165A Regulation of vascular development in inflorescence stems, that targets several III HD-Zip family members including PHV, PHB, REV, ATHB8, and ATHB15/CNA/ICU4. misc_RNA AGI: AT1G01183. Pop. Ort.: POPTRDRAFT_778882 (HB7) - fgenesh4_pg.C_LG_XVIII000250, POPTRDRAFT_832118 (HB8) - estExt_fgenesh4_pm.C_LG_VI0713, POPTRDRAFT_292259 - gw1.6326.1.1 miR165B Regulation of vascular development in inflorescence stems, that targets several III HD-Zip family members including PHV, PHB, REV, ATHB8, and ATHB15/CNA/ICU4. misc_RNA AGI: AT4G00885. Pop. Ort.: POPTRDRAFT_778882 (HB7) - fgenesh4_pg.C_LG_XVIII000250, POPTRDRAFT_832118 (HB8) - estExt_fgenesh4_pm.C_LG_VI0713, POPTRDRAFT_292259 - gw1.6326.1.1 miR166A Regulation of vascular development in inflorescence stems, that targets several III HD-Zip family members including PHV, PHB, REV, ATHB8, and ATHB15/CNA/ICU4. misc_RNA AGI: AT2G46685. Pop. Ort.: POPTRDRAFT_562548 - eugene3.00070486 miR166B Regulation of vascular development in inflorescence stems, that targets several III HD-Zip family members including PHV, PHB, REV, ATHB8, and ATHB15/CNA/ICU4. misc_RNA AGI: AT3G61897. Pop. Ort.: POPTRDRAFT_562548 - eugene3.00070486 miR166C Regulation of vascular development in inflorescence stems, that targets several III HD-Zip family members including PHV, PHB, REV, ATHB8, and ATHB15/CNA/ICU4. misc_RNA AGI: AT5G08712. Pop. Ort.: POPTRDRAFT_562548 - eugene3.00070486 miR166D Regulation of vascular development in inflorescence stems, that targets several III HD-Zip family members including PHV, PHB, REV, ATHB8, and ATHB15/CNA/ICU4. misc_RNA AGI: AT5G08717. Pop. Ort.: POPTRDRAFT_562548 - eugene3.00070486 miR166E Regulation of vascular development in inflorescence stems, that targets several III HD-Zip family members including PHV, PHB, REV, ATHB8, and ATHB15/CNA/ICU4. AGI: AT5G41905. Pop. Ort.: POPTRDRAFT_562548 - eugene3.00070486 misc_RNA References (Kim et al. 2005; Mallory et al. 2004; Yao et al. 2009) (Kim et al. 2005; Mallory et al. 2004; Yao et al. 2009) (Kim et al. 2005; Mallory et al. 2004; Yao et al. 2009) (Kim et al. 2005; Mallory et al. 2004; Yao et al. 2009) (Kim et al. 2005; Mallory et al. 2004; Yao et al. 2009) (Kim et al. 2005; Mallory et al. 2004; Yao et al. 2009) (Kim et al. 2005; Mallory et al. 2004; Yao et al. 2009) Gene Summary Type miR166F Regulation of vascular development in inflorescence stems, that targets several III HD-Zip family members including PHV, PHB, REV, ATHB8, and ATHB15/CNA/ICU4. misc_RNA AGI: AT5G43603. Pop. Ort.: POPTRDRAFT_768574 - fgenesh4_pg.C_LG_X000064, POPTRDRAFT_763035 fgenesh4_pg.C_LG_VI001345 miR166G Dominant gain of function alleles have enlarged meristems, fasciated stems and radialized leaves. During early embryo development expression is reciprocal to target mRNAs but then changes to overlapping expression with targets. Regulation of vascular development in inflorescence stems, that targets several III HD-Zip family members including PHV, PHB, REV, ATHB8, and ATHB15/CNA/ICU4. misc_RNA References (Kim et al. 2005; Mallory et al. 2004; Yao et al. 2009) (Kim et al. 2005; Mallory et al. 2004; Yao et al. 2009) AGI: AT5G63715. Pop. Ort.: POPTRDRAFT_562548 - eugene3.00070486 miR172A Encodes a microRNA that targets several genes containing AP2 domains including AP2. misc_RNA AGI: AT2G28056. Pop. Ort.: POPTRDRAFT_743690 - estExt_Genewise1_v1.C_1230150 miR172B Encodes a microRNA that targets several genes containing AP2 domains including AP2. misc_RNA AGI: AT5G04275. Pop. Ort.: POPTRDRAFT_565769 (DHQD4) - eugene3.00100327, POPTRDRAFT_820288 (RAP3) - estExt_fgenesh4_pg.C_LG_VIII0359, POPTRDRAFT_770475 (RAP4) - fgenesh4_pg.C_LG_X001965, POPTRDRAFT_575387 - eugene3.00150782 MP MONOPTEROS: Encodes a transcription factor (auxin-responsive protein (IAA24) / auxin response factor 5 (ARF5)) mediating embryo axis formation and vascular development. Similar to AUXIN RESPONSIVE FACTOR 1 (ARF1) shown to bind to auxin responsive elements (AREs), and to the maize transcriptional activator VIVIPAROUS 1 (VP1). In situ hybridization shows expression in provascular tissue of embryos, the emerging shoot primordia, then is restricted to provascular tissue, and in the root central vascular cylinder. Process: meristem development and root development (Vidaurre et al. 2007), response to auxin stimulus (Ouellet et al. 2001), xylem and phloem pattern formation and longitudinal axis specification (Przemeck et al. 1996). AGI: AT1G19850. Pop. Ort.: POPTRDRAFT_652033 - grail3.0002064402 transcription factor (Lee et al. 2010; Held et al. 2008; Wu et al. 2009) (Lee et al. 2010; Held et al. 2008; Wu et al. 2009) (Johnson and Douglas 2007; Wenzel et al. 2007) Gene Summary Type References NIT1 NITRILASE 1: Mutants are resistant to indole-3-acetonitrile (IAN). NIT1 catalyzes the terminal activation step in indole-acetic acid biosynthesis. Predominantly expressed isoform of nitrilase isoenzyme family. Aggregation of NIT1 in cells directly abutting wound sites is one of the earliest events associated with wound and herbicide-induced cell death. The protein undergoes thiolation following treatment with the oxidant tert-butylhydroperoxide. It is also involved in the conversion of IAN to IAM (indole-3-acetamide) and other non-auxin-related metabolic processes. indole-3acetonitrile nitrilase/ indole-3acetonitrile nitrile hydratase/ nitrilase (Vorwerk et al. 2001; Hillebrand et al. 1998; Normanly et al. 1997) Process: Indoleacetic acid biosynthetic process (Muller et al. 1998). AGI: AT3G44310. Pop. Ort.: POPTRDRAFT_782522 (NIT1) - fgenesh4_pg.C_scaffold_66000137 NIT2 NITRILASE 2: Encodes an enzyme that catalyzes the hydrolysis of indole-3-acetonitrile (IAN) to indole-3-acetic acid (IAA) (nitrile aminohydrolase, EC 3.5.5.1) and IAN to indole-3-acetamide (IAM) at lower levels. Mutants have reduced sensitivity to IAN and are sensitive to IAA. This enzyme likely participates in other non-auxin-related metabolic pathways. Process: Indoleacetic acid biosynthetic process (Muller et al. 1998). indole-3acetonitrile nitrilase/ indole-3acetonitrile nitrile hydratase/ nitrilase (Vorwerk et al. 2001; Hillebrand et al. 1998) AGI: AT3G44300. Pop. Ort.: POPTRDRAFT_782522 (NIT1) - fgenesh4_pg.C_scaffold_66000137 NIT4 NITRILASE 4: encodes a nitrilase isomer. The purified enzyme shows a strong substrate specificity for beta-cyano-Lalanine, a intermediate product of the cyanide detoxification pathway. AGI: AT5G22300. Pop. Ort.: POPTRDRAFT_782522 (NIT1) - fgenesh4_pg.C_scaffold_66000137 PAI1 PHOSPHORIBOSYLANTHRANILATE ISOMERASE 1: Encodes phosphoribosylanthranilate isomerase which catalyzes the third step of the tryptophan biosynthetic pathway. Member of gene family. 3-cyanoalanine hydratase/ cyanoalanine nitrilase/ indole-3acetonitrile nitrilase/ nitrilase/ nitrile hydratase phosphoribosylanth ranilate isomerase (Piotrowski et al. 2001) (Li et al. 1995) AGI: AT1G07780. Pop. Ort.: POPTRDRAFT_564037 - eugene3.00080632 PAI2 PHOSPHORIBOSYLANTHRANILATE ISOMERASE 2: Encodes phosphoribosylanthranilate isomerase which catalyzes the third step in the tryptophan biosynthetic pathway. AGI: AT5G05590. Pop. Ort.: POPTRDRAFT_564037 - eugene3.00080632 phosphoribosylanth ranilate isomerase (Li et al. 1995) Gene Summary Type PAI3 PHOSPHORIBOSYLANTHRANILATE ISOMERASE 3: Encodes phosphoribosylanthranilate isomerase which catalyzes the third step in tryptophan biosynthesis. phosphoribosylanth ranilate isomerase References (Li et al. 1995) AGI: AT1G29410. Pop. Ort.: POPTRDRAFT_564037 - eugene3.00080632 PAT1/TRP1 TRYPTOPHAN BIOSYNTHESIS 1: Encodes the tryptophan biosynthetic enzyme phosphoribosylanthranilate transferase (PAT1, called trpD in bacteria). Converts anthranilate and phosphoribosylpyrophosphate into phosphoribosylanthranilate and inorganic pyrophosphate. anthranilate phosphoribosyltrans ferase (Rose et al. 1997) AGI: AT5G17990. Pop. Ort.: POPTRDRAFT_423398 - gw1.XII.1858.1 PDC2 PYRUVATE DECARBOXYLASE-2 AGI: AT5G54960. Pop. Ort.: POPTRDRAFT_835585 - estExt_fgenesh4_pm.C_LG_XVI0442 PDC3 PYRUVATE DECARBOXYLASE-3 AGI: AT5G01330. Pop. Ort.: POPTRDRAFT_835585 - estExt_fgenesh4_pm.C_LG_XVI0442 PDHE1_ALPHA PYRUVATE DEHYDROGENASE E1 ALPHA AGI: AT1G01090. Pop. Ort.: POPTRDRAFT_755473 - grail3.0080008401 carboxy-lyase/ catalytic/ magnesium ion binding / pyruvate decarboxylase/ thiamin pyrophosphate binding carboxy-lyase/ catalytic/ magnesium ion binding / pyruvate decarboxylase/ thiamin pyrophosphate binding / transferase pyruvate dehydrogenase (acetyl-transferring) (Klok et al. 2002) Gene Summary Type PDHE1_BETA PYRUVATE DEHYDROGENASE E1 BETA: Encodes a putative plastid pyruvate dehydrogenase E1 beta subunit that is distinct from the mitochondrial pyruvate dehydrogenase E1 beta subunit. pyruvate dehydrogenase (acetyl-transferring) AGI: AT1G30120. Pop. Ort.: POPTRDRAFT_668506 - fgenesh4_pg.C_LG_II001653 PHB PHABULOSA: Member of the III HD-Zip family. Dominant PHB mutations cause transformation of abaxial leaf fates into adaxial leaf fates. Has overlapping functions with PHAVOLUTA, REVOLUTA and CORONA. DNA binding / transcription factor Process: Adaxial/abaxial pattern formation (McConnell and Barton 1998), meristem initiation, polarity specification of adaxial/abaxial axis and primary shoot apical meristem specification (Prigge et al. 2005). AGI: AT2G34710. Pop. Ort.: POPTRDRAFT_815792 (HB4) - estExt_fgenesh4_pg.C_LG_I2905 PHV PHAVOLUTA: Member of the III HD-Zip family. Dominant PHV mutations cause transformation of abaxial leaf fates into adaxial leaf fates. Has overlapping functions with PHABULOSA, REVOLUTA and CORONA/ATHB15 in patterning the apical portion of the embryo. DNA binding / protein binding / transcription factor Process: Adaxial/abaxial axis specification (McConnell et al. 2001), meristem initiation, polarity specification of adaxial/abaxial axis and primary shoot apical meristem specification (Prigge et al. 2005). AGI: AT1G30490. Pop. Ort.: POPTRDRAFT_815792 (HB4) - estExt_fgenesh4_pg.C_LG_I2905 PIN1 PIN-FORMED 1: Encodes an auxin efflux carrier involved in shoot and root development. It is involved in the maintenance of embryonic auxin gradients. Loss of function severely affects organ initiation, pin1 mutants are characterised by an inflorescence meristem that does not initiate any flowers, resulting in the formation of a naked inflorescence stem. PIN1 is involved in the determination of leaf shape by actively promoting development of leaf margin serrations. In roots, the protein mainly resides at the basal end of the vascular cells, but weak signals can be detected in the epidermis and the cortex. Expression levels and polarity of this auxin efflux carrier change during primordium development suggesting that cycles of auxin build-up and depletion accompany, and may direct, different stages of primordium development. PIN1 action on plant development does not strictly require function of PGP1 and PGP19 proteins. Process: Auxin polar transport (Petrasek et al. 2006), root development (Galweiler et al. 1998), shoot development (Vernoux et al. 2000) and xylem and phloem pattern formation (Alonso-Peral et al. 2006). AGI: AT1G73590. Pop. Ort.: POPTRDRAFT_728847 (PIN7) (PIN7) - estExt_Genewise1_v1.C_LG_XII1068 transporter References (Hawker and Bowman 2004; Mallory et al. 2004; Baucher et al. 2007; Ochando et al. 2008) (Hawker and Bowman 2004; Baucher et al. 2007; Chandler et al. 2007; Ochando et al. 2008) (Helariutta and Bhalerao 2003; Borghi et al. 2007; Wenzel et al. 2007; Weijers et al. 2005) Gene Summary Type PIN3 PIN-FORMED 3: A regulator of auxin efflux and involved in differential growth. PIN3 is expressed in gravity-sensing tissues, with PIN3 protein accumulating predominantly at the lateral cell surface. PIN3 localizes to the plasma membrane and to vesicles. In roots, PIN3 is expressed without pronounced polarity in tiers two and three of the columella cells, at the basal side of vascular cells, and to the lateral side of pericycle cells of the elongation zone. PIN3 overexpression inhibits root cell growth. Protein phosphorylation plays a role in PIN3 trafficking to the plasma membrane. auxin:hydrogen symporter/ transporter References (Harrison and Masson 2008) Process: Auxin polar transport (Friml et al. 2002b), root development and regulation of root meristem growth (Blilou et al. 2005) and root hair initiation and elongation (Lee and Cho 2006). AGI: AT1G70940. Pop. Ort.: POPTRDRAFT_803601 (PIN6) (PIN6) - fgenesh4_pm.C_LG_VIII000556 PIN4 PIN-FORMED 4: Encodes a putative auxin efflux carrier that is localized in developing and mature root meristems. It is involved in the maintenance of embryonic auxin gradients. A role for AtPIN4 in generating a sink for auxin below the quiescent center of the root meristem that is essential for auxin distribution and patterning is proposed. In the root, PIN4 is detected around the quiescent center and cells surrounding it, and localizes basally in provascular cells. PIN4 expression is upregulated in brassinosteroid-insensitive mutant (Li et al. 2005). auxin:hydrogen symporter/ transporter (Weijers et al. 2005) Process: Auxin polar transport (Petrasek et al. 2006; Friml et al. 2002a), root development (Friml et al. 2002a) and pattern specification process (Blilou et al. 2005). AGI: AT2G01420. Pop. Ort.: POPTRDRAFT_803601 (PIN6) (PIN6) - fgenesh4_pm.C_LG_VIII000556 PLT1 PLETHORA 1: Encodes a member of the AINTEGUMENTA-like (AIL) subclass of the AP2/EREBP family of transcription factors and is essential for quiescent center (QC) specification and stem cell activity. It is a key effector for establishment of the stem cell niche during embryonic pattern formation. It is transcribed in response to auxin accumulation and is dependent on auxin response transcription factors. Process: Stem cell maintenance (Aida et al. 2004). AGI: AT3G20840. Pop. Ort.: POPTRDRAFT_758079 (RAP23) (RAP23) - fgenesh4_pg.C_LG_III001621 transcription factor (Galinha et al. 2007) Gene Summary Type References PLT2 PLETHORA 2: Encodes a member of the AINTEGUMENTA-like (AIL) subclass of the AP2/EREBP family of transcription factors and is essential for quiescent center (QC) specification and stem cell activity. It is a key effector for establishment of the stem cell niche during embryonic pattern formation. It is transcribed in response to auxin accumulation and is dependent on auxin response transcription factors. transcription factor (Galinha et al. 2007) Process: Stem cell maintenance (Aida et al. 2004). AGI: AT1G51190. Pop. Ort.: POPTRDRAFT_758079 (RAP23) (RAP23) - fgenesh4_pg.C_LG_III001621 PXL2 AGI: AT4G28650. Pop. Ort.: POPTRDRAFT_553299 - eugene3.00002614 leucine-rich repeat transmembrane protein kinase, putative REV/IFL1 REVOLUTA: Member of the III HD-Zip family. REVOLUTA regulates meristem initiation at lateral positions. Has overlapping functions with PHAVOLUTA and PHABULOSA. DNA binding / lipid binding / transcription factor Process: Cell differentiation (Zhong and Ye 1999), meristem initiation (Otsuga et al. 2001), polarity specification of adaxial/abaxial axis (Prigge et al. 2005) and xylem and phloem pattern formation (Emery et al. 2003). AGI: AT5G60690. Pop. Ort.: POPTRDRAFT_741921 (HB2) - estExt_Genewise1_v1.C_660759 ROP1 RHO-RELATED PROTEIN FROM PLANTS 1: Expressed in the cambial zone and differentiating xylem in eucalyptus. Encodes a pollen-specific Rop GTPase, member of the Rho family of small GTP binding proteins that interacts with RIC3 and RIC4 to control tip growth in pollen tubes. These three proteins promote the proper targeting of exocytic vesicles in the pollen tube tip. ROP1 activity is regulated by the REN1 GTPase activator protein. AGI: AT3G51300. Pop. Ort.: POPTRDRAFT_827046 - estExt_fgenesh4_pg.C_570059 RPL REPLUMLESS: Encodes a homeodomain transcription factor. Has sequence similarity to the Arabidopsis ovule development regulator Bell1. Binds directly to the AGAMOUS cis-regulatory element. Its localization to the nucleus is dependent on the coexpression of either STM or BP. Mutant has additional lateral organs and phyllotaxy defect. Process: Internode patterning and xylem and phloem pattern formation (Smith and Hake 2003), vegetative to reproductive phase transition of meristem and maintenance of floral meristem identity (Smith et al. 2004), floral whorl morphogenesis (Bao et al. 2004), shoot development (Kanrar et al. 2006) and secondary shoot formation (Kanrar et al. 2008). AGI: AT5G02030. Pop. Ort.: POPTRDRAFT_218986 - gw1.VII.3291.1 GTP binding / GTPase activating protein binding / GTPase/ protein binding DNA binding / sequence-specific DNA binding / transcription factor (Hirakawa et al. 2010) (Hawker and Bowman 2004; Baucher et al. 2007; Ochando et al. 2008) (Foucart et al. 2009) (Bao et al. 2004; Rutjens et al. 2009) Gene Summary Type SCR SCARECROW: GRAS transcription factor family member. Encodes a member of a novel family having similarity to DNA binding proteins containing basic-leucine zipper regions; scr is expressed in cortex/endodermal initial cells and in the endodermal cell lineage. Regulates the radial organization of the root. Is required cell-autonomously for distal specification of the quiescent center, which in turn regulates stem cell fate of immediately surrounding cells. SCR appears to be a direct target of SHR. protein binding / protein homodimerization/ sequence-specific DNA binding / transcription factor Process: Asymmetric cell division (Di Laurenzio et al. 1996) and radial pattern formation (Wysocka-Diller et al. 2000). AGI: AT3G54220. Pop. Ort.: POPTRDRAFT_589585 (GRAS2) - eugene3.00280321 SHR SHORT ROOT: Involved in radial organization of the root and shoot axial organs. Essential for normal shoot gravitropism. The protein moves in a highly specific manner from the cells of the stele in which it is synthesized outward. Movement requires sequences within the GRAS and VHIID domains. Process: Asymmetric cell division and radial pattern formation (Helariutta et al. 2000). protein binding / sequence-specific DNA binding / transcription factor AGI: AT4G37650. Pop. Ort.: POPTRDRAFT_586010 (GRAS7) - eugene3.01860017 STM SHOOT MERISTEMLESS: Class I knotted-like homeodomain protein that is required for shoot apical meristem (SAM) formation during embryogenesis and for SAM function throughout the lifetime of the plant. Functions by preventing incorporation of cells in the meristem center into differentiating organ primordia. transcription factor Process: Cytokinin biosynthetic process (Yanai et al. 2005), regulation of meristem structural organization (Lenhard et al. 2002) and stem cell maintenance (Brand et al. 2002). References (Scheres et al. 1995; WysockaDiller et al. 2000; Cui et al. 2007; Paquette and Benfey 2005) (Gallagher and Benfey 2009; Cui et al. 2007; Paquette and Benfey 2005; Levesque et al. 2006) (Groover et al. 2006; Kanrar et al. 2006) AGI: AT1G62360. Pop. Ort.: POPTRDRAFT_811717 - fgenesh4_pm.C_scaffold_166000014 SUR1 SUPERROOT 1: Confers auxin overproduction. Mutants have an over-proliferation of lateral roots. Encodes a C-S lyase involved in converting S-alkylthiohydroximate to thiohydroximate in glucosinolate biosynthesis. Process: Indoleacetic acid biosynthetic process (Boerjan et al. 1995) and regulation of cell growth by extracellular stimulus (De Grauwe et al. 2005). Salkylthiohydroxima te lyase/ carbonsulfur lyase/ transaminase AGI: AT2G20610. Pop. Ort.: POPTRDRAFT_836654 (AMT1) - estExt_fgenesh4_pm.C_640067 T10O8.30 AGI: AT5G01320. Pop. Ort.: POPTRDRAFT_835585 - estExt_fgenesh4_pm.C_LG_XVI0442 pyruvate decarboxylase, putative (Seo et al. 1998; Stepanova et al. 2005) Gene Summary Type T14P4.22 AGI: AT1G02590. Pop. Ort.: POPTRDRAFT_588889 (AAO3) - eugene3.27080003 aldehyde putative T22N19.10 AGI: AT5G13360. Pop. Ort.: POPTRDRAFT_750995 (GH3-7) - fgenesh4_pg.C_LG_I000598 auxin-responsive GH3 family protein T22N19.20 AGI: AT5G13370. Pop. Ort.: POPTRDRAFT_750995 (GH3-7) - fgenesh4_pg.C_LG_I000598 auxin-responsive GH3 family protein T24P13.11 AGI: AT1G26730. Pop. Ort.: POPTRDRAFT_765774 - fgenesh4_pg.C_LG_VIII000788 EXS family protein / ERD1/XPR1/SYG1 family protein TDR/PXY AGI: AT5G61480. Pop. Ort.: POPTRDRAFT_1073831 - estExt_Genewise1Plus.C_LG_III1142 leucine-rich repeat transmembrane protein kinase, putative TGG1 THIOGLUCOSIDE GLUCOHYDROLASE 1: member of Glycoside Hydrolase Family 1. encodes one of two known functional myrosinase enzymes in Arabidopsis. The enzyme catalyzes the hydrolysis of glucosinolates into compounds that are toxic to various microbes and herbivores. hydrolase, hydrolyzing Oglycosyl compounds / thioglucosidase AGI: AT5G26000. Pop. Ort.: POPTRDRAFT_800515 - fgenesh4_pm.C_LG_IV000202 TGG2 GLUCOSIDE GLUCOHYDROLASE 2: Myrosinase (thioglucoside glucohydrolase) gene involved in glucosinoloate metabolism. AGI: AT5G25980. Pop. Ort.: POPTRDRAFT_800515 - fgenesh4_pm.C_LG_IV000202 TSA1 TRYPTOPHAN SYNTHASE ALPHA CHAIN: Catalyzes the conversion of indole-3-glycerolphosphate to indole, the penultimate reaction in the biosynthesis of tryptophan. Functions as a heterocomplex with tryptophan synthase beta subunit (TSA2). AGI: AT3G54640. Pop. Ort.: POPTRDRAFT_818693 - estExt_fgenesh4_pg.C_LG_V1322 References oxidase, hydrolase, hydrolyzing Oglycosyl compounds / thioglucosidase tryptophan synthase (Hirakawa et al. 2010; Etchells and Turner 2010) (Alvarez et al. 2008; Barth and Jander 2006) (Barth and Jander 2006) Gene Summary Type TSA-like AGI: AT4G02610. Pop. Ort.: POPTRDRAFT_818693 - estExt_fgenesh4_pg.C_LG_V1322 tryptophan synthase, alpha subunit, putative TSB1 TRP2 TRYPTOPHAN SYNTHASE BETA-SUBUNIT 1: A.thaliana tryptophan synthase beta subunit (trpB) tryptophan synthase References (Jing et al. 2009) Process: Indoleacetic acid biosynthetic process (Normanly et al. 1993). AGI: AT5G54810. Pop. Ort.: POPTRDRAFT_888009 - e_gw1.XI.471.1 TSB2 TRYPTOPHAN SYNTHASE BETA-SUBUNIT 2: Tryptophan synthase beta. Expressed at low levels in all tissues. tryptophan synthase AGI: AT4G27070. Pop. Ort.: POPTRDRAFT_888009 - e_gw1.XI.471.1 VND7 VASCULAR RELATED NAC-DOMAIN PROTEIN 7: NAM (no apical meristem) family member. Encodes a NACdomain transcription factor with transcriptional activation activity that is involved in xylem formation. Induces transdifferentiation of various cells into protoxylem vessel elements. Located in the nucleus. Expression induced in the presence of auxin, cytokinin and brassinosteroids. Process: Response to brassinosteroid stimulus, response to cytokinin stimulus and xylem development (Kubo et al. 2005). anscription activator/ transcription factor/ transcription regulator (Soyano et al. 2008; Baucher et al. 2007; Kubo et al. 2005) AGI: AT1G71930. Pop. Ort.: POPTRDRAFT_592235 (NAC055) - eugene3.00410078 WES1 Encodes an IAA-amido synthase that conjugates Asp and other amino acids to auxin in vitro. Lines carrying insertions in this gene are hypersensitive to auxin. indole-3-acetic acid amido synthetase (Park et al. 2007) Process: Auxin homeostasis and response to auxin stimulus (Staswick et al. 2005). AGI: AT4G27260. Pop. Ort.: POPTRDRAFT_571444 (GH3-6) - eugene3.00130808 WOL WOODEN LEG: Histidine kinase, cytokinin-binding receptor that transduces cytokinin signals across the plasma membrane. Process: Cytokinin mediated signaling pathway (Hwang et al. 2002), embryonic root morphogenesis (Mahonen et al. 2000) and regulation of shoot development (Riefler et al. 2006). AGI: AT2G01830. Pop. Ort.: POPTRDRAFT_766213 - fgenesh4_pg.C_LG_VIII001227 cytokinin receptor/ osmosensor/ phosphoprotein phosphatase/ protein histidine kinase (Kuroha et al. 2006; Nishimura et al. 2004; FrancoZorrilla et al. 2005; Baucher et al. 2007) Gene Summary Type References WOX4 WUSCHEL RELATED HOMEOBOX 4: Encodes a WUSCHEL-related homeobox gene family member with 65 amino acids in its homeodomain. Proteins in this family contain a sequence of eight residues (TLPLFPMH) downstream of the homeodomain called the WUS box. This protein also contains an acidic domain approximately 10 residues upstream of the WUS box. transcription factor (Ji et al. 2010) transcription factor (Gonzali et al. 2005) AGI: AT1G46480. Pop. Ort.: POPTRDRAFT_836454 - estExt_fgenesh4_pm.C_400124 WOX5 WUSCHEL RELATED HOMEOBOX 5: Response to auxin stimulus AGI: AT3G11260. Pop. Ort.: POPTRDRAFT_805455 - fgenesh4_pm.C_LG_X000761 WUS WUSCHEL: Homeobox gene controlling the stem cell pool. Expressed in the stem cell organizing center of meristems. Required to keep the stem cells in an undifferentiated state. Regulation of WUS transcription is a central checkpoint in stem cell control. The size of the WUS expression domain controls the size of the stem cell population through WUS indirectly activating the expression of CLAVATA3 (CLV3) in the stem cells and CLV3 repressing WUS transcription through the CLV1 receptor kinase signaling pathway. Repression of WUS transcription through AGAMOUS (AG) activity controls stem cell activity in the determinate floral meristem. Binds to TAAT element core motif. DNA binding / protein binding / transcription factor/ transcription regulator (Finlayson et al. 2010; Ikeda et al. 2009; Su et al. 2009) Process: Maintenance of shoot apical meristem identity (Sonoda et al. 2007) and stem cell maintenance (Laux et al. 1996). AGI: AT2G17950. Pop. Ort.: POPTRDRAFT_827060 - estExt_fgenesh4_pg.C_570090 ZPR3 LITTLE ZIPPER 3: ZPR3 is a small-leucine zipper containing protein that is involved in the establishment of leaf polarity. protein binding (Kim et al. 2008) Process: adaxial/abaxial axis specification, leaf shaping and vascular tissue pattern formation and meristem regulation and maintenance (Wenkel et al. 2007) and negative regulation of transcription factor activity (Kim et al. 2008). AGI: AT3G52770. Pop. Ort.: POPTRDRAFT_560740 - eugene3.00060699 ZPR4 AGI: AT2G36307. Pop. Ort.: POPTRDRAFT_567947 - eugene3.00102505 (Wenkel et al. 2007) Aida M, Beis D, Heidstra R, Willemsen V, Blilou I, Galinha C, Nussaume L, Noh YS, Amasino R, Scheres B (2004) The plethora genes mediate patterning of the arabidopsis root stem cell niche. 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