Download S1 - Genetics

S1. Loci derived from chicken Z chromosome-linked genes.
Cytogenetic
Accession
Gene
position
No.
Aldolase B,
Fructose biphosphate
(ALDOB)
p1.2
M10946
Reference
.
Locus
CHDZ15
CHDZ18
CHDZ20
CHDZ24
Primer
locations
Exon 4
Exon 5
Exon 6
Exon 7
Exon 7
Exon 8
Exon 12
Exon 13
Exon 15
Exon 16
Exon 15
Exon 16
Exon 18
Exon 19
Exon 20
Exon 21
Exon 24
Exon 25
[1]
ALDOB4
ALDOB6
ALDOB7
GHR-5.1
Intron 5b
GHR-5.2
Intron 5
BRM-12
Brahma protein (BRM)
p.1.2
X91638
[2]
BRM-15
Chromo-helicaseDNA-binding on the Z
chromosome
protein (CHDZ)
Growth hormone receptor
(GHR)
q1.6-2.1
p2.2
AF004397
D13154
[3]
[4]
GHR-exon9 Exon 9
Protein kinase C inhibitor
(PKCI)
q1.1
AB026676
[5]
PKCI-2
Exon 1
Intron 2
Prolactin receptor (PRLR)
p2.2
AJ011128
[6]
PRLRUN
UN
Patched (PTCH)
q1.2-1.6
U40074
[7]
PTCH-6
Spindlin (SPINZ)
q1.1
AB047853
[8]
SPINZ-2
[9]
VLDLR7
VLDLR8
Very low density
lipoprotein/
Vitellogenin receptor
(VLDLR)
p1.3
X80207
Exon 6
Exon 7
Exon 2
Exon 3
Exon 7
Exon 8
Exon 8
Exon 9
Primer sequences (5´-3´)
F:GGCAGGAACAAATGGAGAAACT
R:GCCAGAACCTGAAAACAGGAG
F:AGACCATGATCTCCAGCGCT
R:CCTTCCAGGTAGACATGATG
F:GTTCCTGGTGATTCCTGATTC
R:CAGATTCCTGCAAGAAAGAGG
F:CCCTATCTCATCATTGTTCC
R:CACAGAAGGAGCCCATTTGT
F:AGCACCTTTGAACAGTGGTT
R:TACTTTATGGAGACGACGGA
F:TAGAGAGATTGAGAACTACAGT
R:GACATCCTGGCAGAGTATCT
F:TACATACAGGCTCTACTCCT
R:CCCCTTCAGGTTCTTTAAAA
F:GAAGAGAGCTGAAACTCGG
R:TCATCTTCATCCATATTGG
F:CATTCACCTGCACTCCTGAG
R:GGCCTTTAAAGGACARTTCA
F:GCTTCCATTATGTATCTTACC
R:TTTGGCTTCTAGAGTTTTGCA
F:ATGTTATTGCTTGTTCAGAGTG
R:GAGTATTTGGAATAAAACAGCC
F:TGTTGTACTTTCTCCAGGGC
R:TCTGCCTCACAGAAATAGGTG
F:GATATCTCACCCCAAGCTCCAAC
R:CCCACTACTTCAGACAACATA
F:GGAAAAGATAAGCGAGATGGAG
R:CTTCTCAGCTTGACTGTCCTG
F:CCATTTTCTTCCAAGCAATA
R:TTTCTTGACAGTCCATAGCA
F:TATGGACTAGAACTGCACAAAG
R:AGACCATCCCCCTCCATTCATC
F:CAGAAGTGGAGAATGCATAG
R:ACAGTCACATTCATAGCCAA
F:GTTATTGGCTATGAATGTGA
R:GTTGATACAGATTTGGCTAC
PCR
conditionsa
58-35
56-37
61-40
55-35
60-35
50-35
60-5+
55-27
58-5+
50-30
50-35
58-35
58-35
52-39
47-35
58-39
53-40
51-40
60-35
57-35
VLDLR9
Exon 9
Exon 10
Exon 12
VLDLR-12
Exon 13
1.
2.
3.
4.
5.
6.
7.
8.
9.
a
F:AAGTGTGAATGTAGCCGTGG
R:TCGGTTGGTGAAAATCAGAC
F:GTTCCTTCCTCATCCTCTTG
R:ATAGACTGCCTCGTTCTCTC
62-35
55-35
Burgess, D.G. and E.E. Penhoet, Characterization of the chicken aldolase B gene. Journal of Biological Chemistry, 1985. 260(8): p. 4604-14.
Goodwin, G.H., Isolation of cDNAs encoding chicken homologues of the yeast SNF2 and Drosophila Brahma proteins. Gene, 1997. 184(1): p. 27-32.
Griffiths, R. and R.M. Korn, A CHD1 gene is Z chromosome linked in the chicken Gallus domesticus. Gene, 1997. 197(1-2): p. 225-229.
Tanaka, M., et al., Double antenna structure of chicken prolactin receptor deduced from the Cdna sequence. Biochemical and Biophysical Research
Communications, 1992. 188(2): p. 490-496.
Hori, T., et al., Wpkci, encoding an altered form of PKCI, is conserved widely on the avian W chromosome and expressed in early female embryos:
Implication of its role in female sex determination. Molecular Biology of the Cell, 2000. 11(10): p. 3645-3660.
Dunn, I.C., et al., Genetic mapping of the chicken prolactin receptor gene: a candidate gene for the control of broodiness. British Poultry Science, 1998.
39: p. S23-S24.
Marigo, V., et al., Conservation in hedgehog signaling: Induction of a chicken patched homolog by Sonic hedgehog in the developing limb.
Development, 1996. 122(4): p. 1225-1233.
Itoh, Y., et al., Chicken spindling genes on W and Z chromosomes: transcriptional expression of both genes and dynamic behavior of spindlin in
interphase and mitotic cells. Chromosome Research, 2001. 9(4): p. 283-299.
Bujo, H., et al., Chicken oocyte growth is mediated by an 8 ligand-binding repeat member of the Ldl receptor family. Embo Journal, 1994. 13(21): p.
5165-5175.
PCR conditions: Annealing temperature-number of cycles. All PCR reactions followed this three step format: (1:) 95 for 15 min/ 1 cycle; (2:) (94 for 30 sec,
annealing temp for 30 sec, 72 for 1 min) number of cycles; (3:) 72 for 10 min/one cycle. For some loci step two were run two times with different annealing
temperatures and number of cycles.
b
Primers designed in introns are flycatcher specific.