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Transcript
Conserve Fibroblast growth factor 8 (fgf 8) domains Ana Tomas Judith Paridaen Susana Domingues Fibroblast growth factor 8 Member of the FGF family Function: Mitogenic Chemotactic Angiogenic activity Promoting cell growth, differentiation and motility Some Fgf 8 characteristics N.º of a.a.: 233 Molecular weight: 26525.4 Theoretical p.i.: 10.44 Total n.º of negatively charged residues (Asp + Glu): 19 Total n.º of positively charged residues (Arg + Lys): 40 Formula: C1164H1877N363O330S9 Total n.º of atoms: 3743 Grand average of hydropathicity: -0.651 (soluble) Estimated half-life: The N-terminal of the sequence considered is M (Met) The estimated half-life is: 30 hours (mammalian) Instability index: The instability index (II) is computed to be 47.80 Unstable protein ProtParam tool - ExPASy Structure 6 chains present 913 residues Structure and active sites SP binding HBGF/FGF ProSAT - Protein Structure Annotation Tool Models Axolotl Ciona Chicken Ciona S. Cow Dog Drosophila Fugu Houseshrew Human Japanese lamprey Mouse Opossum Oryzias Rabbit Rat Rhesus macaque Shell turtle Tetraodon Zebrafish Phylogenetic tree Cluster algorithm Consensus domains ErkDD Kin_bind RDCIFTEIVLENNYT p85_SH2 SH2 KGAETGFYICMNKRG InsR_Kin Y_kin NARYEGWYMAFTRRG Multalin – Multi alignment program 3D structure and consensus domains ErkDD Kin_bind RDCIFTEIVLENNYT p85_SH2 SH2 KGAETGFYIC MNKRG InsR_Kin Y_kin NARYEGWYMAFTRRG Rasmol Fgf8 structure with receptor Receptor Fgf Rasmol Common regulatory elements in Fgf8 downstream targets Anna Ferrer-Vaquer Alisa Fuchs Fgf8 signaling pathway Elk Ets cJun Fos Myc ... Fgf8 inducible genes Sprouty1 > Mm, Gg, Dr Pax3 > Mm, Gg, Dr Otx2 > Mm, Gg, Dr Tbx2 > Mm, Gg, Dr Erm Pea3 Ptx1 Lhx6 Sef AP2 Flrt3 .... Many more Limitation: 1Kb of 5’UTR Alignment Alignment of sequences from different genes to find consensus blocks Not reliable Promoter analysis Sequence Position Family/ma trix Further Information Str. Opt. (red: ci-value > 60 Core sim. Matrix sim. from - to V$MZF1/MZ F1.02 V$HOMF/DL X1.01 V$TALE/TGI F.01 V$XBBF/RF X1.02 capitals: core sequence) Myeloid zinc finger protein MZF1 0.99 574 - 582 (-) 1.000 1.000 taGGGGaag DLX-1, -2, and -5 binding sites 0.91 720 - 732 (-) 1.000 1.000 ttgtatAATTaaa TG-interacting factor belonging to TALE class of homeodomain factors 1.00 904 - 914 (+) 1.000 1.000 atgtGTCAatc 0.90 952 - 970 (-) 1.000 0.904 gcgcctctctgGCAActtt 0.85 581 - 601 (+) 1.000 0.905 tagcttTGACttaaatatttt 0.84 941 - 957 (+) 1.000 0.909 gtttgcgtCAAAaagtt 0.83 109 - 123 (+) 1.000 0.914 gttCTTAagcacaaa X-box binding protein RFX1 cAMP-responsive V$CREB/CR element binding protein 1 EBP1.01 E2F, involved in cell cycle regulation, V$E2FF/E2 interacts with Rb p107 protein F.02 Hmx2/Nkx5-2 V$NKXH/HM homeodomain transcription factor X2.01 Results of promoter analysis Promotor/TF mSprouty1 mPax3 mOtx2 mTbx2 Elk vMyb ZBP-89 + + + + + + + + + + Conclusion Analysis of nucleotide sequences is much more difficult than amino acids
