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Supplementary material for the Web.

Estimation of Divergence Times from Multiple Protein Sequences (manuscript).

Table 3. 104 protein sequence data from 5 verterbrate species (data from Hovergen)

 
  Protein Estimate (a) of gamma parameter  Number of amino acids used  Accession numbera
 1 Insulin-like growth factor I  0.588  112  FAM00007 
 2 Prepro-insulin  0.811  106  FAM00008 
 3 Heparin cofactor II 1.139  453  FAM000037 
 4 Muscarinic acetylcholine receptor M1  0.454  459  FAM000059d 
 5 Angiotensin II receptor type I 0.994  354  FAM000084 
 6 Alcohol dehydrogenase-1 (Adh-1) 0.938  228  FAM000111 
 7 Gastric H+, K+ ATPase beta-subunit 1.144  281  FAM000133 
 8 Na+, K+ ATPase beta-subunit 0.718  301  FAM000135 
 9 Acetylcholine receptor delta-subunit 0.886  508  FAM000152a 
 10 Acetylcholine gamma-subunit 1.307  500  FAM000152b 
 11 Acetylcholine receptor alpha-subunit 0.409  456  FAM000152e 
 12 Serum albumin 4.916  596  FAM000192 
 13 Gap junction protein connexin-4 0.23  377  FAM000242 
 14 Alpha-A-crystallin 0.887  163  FAM000248a 
 15 Cu-Zn superoxide dismutase (SOD1) 0.853  150  FAM000256 
 16 Neural cadherin (N-cadherin) 0.355  900  FAM000258 
 17 Basic fibroblast growth factor (bFGF) 0.369  152  FAM000274 
 18 Preproglucagon 1.358  131  FAM000286 
 19 Bone morphogenetic protein-4 (BMP-4) 0.392  394  FAM000306a 
 20 Bone morphogenetic protein-2 (BMP-2) 0.581  351  FAM000306b 
 21 Tissue inhibitor of metalloproteinase-3 (TIMP-3) 0.512  209  FAM000330b 
 22 Aldehyde dehydrogenase I (ALDH-1) 0.595  499  FAM000337 
 23 Ornithine decarboxylase (ODC) 0.489  448  FAM000348 
 24 Osteonectin (Sparc)  0.367  292  FAM000350 
 25 Poly (ADP-ribose) synthetase 0.634  990  FAM000356 
 26 Phosphatase 2A-beta (PP2A-beta) 0.039  309  FAM000362 
 27 Preprosomatostatin 0.398  115  FAM000371 
 28 ABC transporter (TAP2) 2.661  656  FAM000385 
 29 Tryptophan hydroxylase (Tph) 0.668  437  FAM000388b 
 30 Iron binding protein (ferretin) heavy chain 0.403  176  FAM000533 
 31 Glutamine synthetase 0.46  368  FAM000534 
 32 Retinol-binding protein (RBP) 0.924  189  FAM000555 
 33 Type IIA activin receptor 0.286  513  FAM000561a 
 34 Alpha-enolase (2-phospho-D-glycerate hydrolase) 0.252  434  FAM000627 
 35 Cyclin D1  0.711  290  FAM000646a 
 36 Complement component C 1.96  1556  FAM000664 
 37 Zona pellucida glycoprotein-3 (ZP3) 3.254  397  FAM000667 
 38 Helix-loop-helix protein (Id-2) 0.243  133  FAM000769 
 39 Cardiac troponin 0.74  162  FAM000868a 
 40 Hepatic nuclear factor 1-alpha unit 0.608  585  FAM001004b 
 41 Retinal degeneration slow (RDS) protein 0.602  343  FAM001091 
 42 Hepatocyte growth factor (HGF) 0.883  706  FAM001247a 
 43 Hepatocyte growth factor-like protein 1.243  692  FAM001247c 
 44 Vimentin (intermediate filament) 0.365  455  FAM001327a 
 45 Middle weight neurofilament (NF-M) 0.838  748  FAM001328b 
 46 Cardiac calsequestrin 1.301  380  FAM001355 
 47 Steroidogenic factor-1 SF-1  0.505  451  FAM001365a 
 48 Thyroid hormone receptor alpha (c-erbA) 0.288  408  FAM001369a 
 49 Thyroid hormone receptor beta subunit 0.192  368  FAM001369b 
 50 Very low density lipoprotein receptor (VLDLR) 0.398  830  FAM001390b 
 51 Domain transcription factor LIM-1 0.187  401  FAM001396 
 52 Cyclin-dependent kinase (CDC2) 0.422  296  FAM001432b 
 53 Neural cell-adhesion molecule (N-CAM)  0.576  716  FAM001444 
 54 Neural cell surface protein F 0.665  991  FAM001446a 
 55 Focal adhesion kinase (FAK) 0.182  1051  FAM001463 
 56 Protein-tyrosine (src) kinase (CSK)  0.224  450  FAM001467 
 57 Neural receptor protein-tyrosine kinase (trkB) 0.508  797  FAM001471b 
 58 Insulin-like growth factor I receptor 0.434  1301  FAM001471e 
 59 c-met oncogene  0.881  1366  FAM001472 
 60 c-kit receptor tyrosine kinase 0.957  924  FAM001478b 
 61 Oocyte maturation factor Mos (c-mos)  1.456  324  FAM001493 
 62 Fibronectin (FN1)  0.839  1069  FAM001519 
 63 Zinc finger protein slug (SLUG)  0.665  148  FAM001601 
 64 Wilms tumor protein 0.35  375  FAM001607 
 65 Integrin beta-1 subunit 0.376  789  FAM001621 
 66 Muscle regulatory factor (MRF4) 0.38  239  FAM001622c 
 67 Achaete-scute homologue 0.293  189  FAM001624 
 68 Collagenase-3 (matrix metalloproteinase-13) 1.02  378  FAM001631c 
 69 Fos-related antigen-2 (fra-2) 0.336  313  FAM001679a 
 70 Follistatin (activin antagonist)  0.354  315  FAM001730 
 71 Structure-specific recognition protein 1 (SSRP1) 0.305  529  FAM001987 
 72 Gonadotrophin-releasing hormone (GnRH) 3.093  87  FAM002205 
 73 Alpha 2,8-sialyltransferase-1 (pst-1) 0.577  353  FAM002490 
 74 Syndecan-3 (Syn-3) 2.598  317  FAM002852 
 75 Distal-less 3 (Dlx-5) homeobox  0.331  278  FAM002888a 
 76 Homeobox protein Nkx-2.5 subunit 1.097  285  FAM002890b 
 77 Corticotrophin-releasing factor type1 receptor  0.375  410  FAM003058b 
 78 T-cell leukemia (LERK-2)  0.439  326  FAM003670 
 79 Delta-1 protein 0.584  705  FAM003932a 
 80 Conductin/axin (AXIN)  0.667  818  FAM006148 
 81 Transforming growth factor beta3 0.653  389  FAM000027b
 82 Na, K-ATPase beta-2 subunit (ATP1B2)  1.61  271  FAM000134b
 83 Embryonic beta-type globin 1.364  137  FAM000214b
 84 Alpha globin 1.277  142  FAM000215b
 85 Heat shock protein 0.138  650  FAM000300b
 86 Lactate dehydrogenase-A 0.616  330  FAM000364ab
 87 Histone H2A 0.149  129  FAM000427b
 88 bcl-x regulator of cell death 0.764  200  FAM000506b
 89 c-ets-1 (p54) protein 0.202  437  FAM000514b
 90 Glutamine synthetase 0.471  368  FAM000534ab
 91 Bone morphogenetic receptor 0.28  522  FAM000306db
 92 Cyclin (D2, D3) 0.291  288  FAM000646b
 93 Furin 0.522  768  FAM000747b
 94 Hepatocyte growth factor (HGF) 1.261  686  FAM001247b
 95 Liver glyceraldehyde-3-phosphate dehydrogenase 0.243  332  FAM001297b
 96 Nucleolin  1.793  605  FAM001318b
 97 Vimentin 0.361  454  FAM001327b
 98 Lamin B1  0.675  578  FAM001331b
 99 Nucleolar phosphoprotein B23 (NPM1)  1.022  285  FAM001359b
 100 N-myc protein 0.698  398  FAM001383b
 101 CDC2 involved in cell cycle control 0.332  296  FAM001432b
 102 Protein tyrosine phosphatase (PTPase-alpha)  0.280  778  FAM001447b
 103 Phosphotyrosil protein phosphatase 0.084  591  FAM001456b
 104 M-sam fibroblast growth factor 0.314  807  FAM001479b
 

a Gene family names from Hovergen database.
b Entries 81-104 from Hovergen 1996 Release.


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