Table S1A. HNF4alpha Binding Motifs H4.1-71 and H4.142-217: sequence and original literature reference.  
version 1.1      
HNF4 Motif Finder, Sladek Lab Website    
    Literature Gene        
H4 No.1 Motif Sequence Position2 Symbol3 Full Gene Name Species Reference PMID  
H4.1 GGGCCAaAGGTCT -92/-104 Hmgcs2   HMG-CoA synthase rat Rodriguez et al. 1998 9464279  
H4.2 GGTTCAaAGGTCT -669/-681 Acaa1   3-ketoacyl-CoA thiolase B rat Nicolas-Frances et al. 2000 10708554  
H4.3 GGGGCTaAGTCCA -109/-121 SERPINA1   alpha-1-anti-trypsin human Hardon et al. 1988 2844524    
H4.4 AGTCAAaAGTCCA -2758/-2770 AMBP   alpha-1-microglobulin & bikunin human Rouet et al. 1995 7533900    
H4.5 CTGCCAaGGGCCA -2786/-2774 AMBP   alpha-1-microglobulin & bikunin human Rouet et al. 1998 9729465    
H4.6 GTCTAAgAGTCCA -2924/-2936 AMBP   alpha-1-microglobulin & bikunin human Rouet et al. 1998 9729465    
H4.7 AGGACAaAGGTCA -558/-570 Acox   acyl-CoA oxidase rat Tugwood et al. 1992 1537328    
H4.8 AGGTCAgGGTCCC -357/-345 ALDH2   aldehyde dehydrogenase 2 human Pinaire et al. 1999 10352676    
H4.9 GGGTCAaAGGCAC -321/-309 ALDH2   aldehyde dehydrogenase 2 human Stewart et al. 1998 9765594    
H4.10 AGGGCAgAGGGCA -395/-407 AGT   angiotensinogen human Yanai et al. 1999 10574924    
H4.11 GGGGCCaAGGTTC -260/-272 AGT   angiotensinogen human Yanai et al. 1999 10574924    
H4.12 AGGTCAaAGGCTG -73/-85 SERPINC1   antithrombin III human Tremp et al. 1995 7758957    
H4.13 AGTGTAgAGCCCA -111/-123 SERPINC1   antithrombin III human Fernandez-Rachubinski et al. 1996 8910619    
H4.14 AGTTCAaGGATCA -120/-132 APOA1   apolipoprotein A1 human Chan et al. 1993 8464705    
H4.15 GGGGTCaAGGGTT -198/-210 APOA1   apolipoprotein A1 human Hardon et al. 1988 2844524    
H4.16 AGGGTAaAGGTTG -721/-733 APOA2   apolipoprotein A2 human Ladias et al. 1992 1639815    
H4.17 GTCACAaAAGTCC -140/-128 APOA4   apolipoprotein A4 human Ktistaki et al. 1994 7984419    
H4.18 GGTCCAaAGGGCG -66/-78 APOB   apolipoprotein B human Metzger et al. 1993 8344962    
H4.19 AGAACAaAGAGCA >55kb APOB   apolipoprotein B human Antes et al. 2000 10859308    
H4.20 AGGCCAaAGTCCT -81/-93 APOC2   apolipoprotein C2 human Kardassis et al. 1998 9651383    
H4.21 TGGGCAaAGGTCA -70/-82 APOC3   apolipoprotein C3 human Sladek et al. 1990 2279702    
H4.22 AGTCCAgAGGTCA -2987/-2975 APOC3   apolipoprotein C3 human Vergnes et al. 1997 9366246    
H4.23 GGTCCAgAGGGCA -731/-719 APOC3   apolipoprotein C3 human Kardassis et al. 1997 9012660    
H4.24 TGATCAgACAAAG -144/-132 CEACAM1   biliary glycoprotein human Hauck et al. 1994 8055923    
H4.25 GAGTCAaAGGTCA -62/-74 RBP2   cellular retinol binding protein 2 rat Nakshatri and Chambon 1994 8288643    
H4.26 AGACCAaAGTCCG -61/-49 Cyp2a4   cytochrome 2A4 mouse Yokomori et al. 1997 9408084    
H4.27 GGACCAaAGTCCA -117/-105 Cyp2c1   cytochrome 2C1 rabbit Chen et al. 1994a 7772258    
H4.28 GGTCCAaAGTCCA -112/-100 Cyp2c2   cytochrome 2C2 rabbit Chen et al. 1994b 8106524    
H4.29 AGACCAaAGTGCA -96/-84 Cyp2c3   cytochrome 2C3 rabbit Chen et al. 1994a 7772258    
H4.30 GGGTCAaAGTCCT -150/-138 CYP2C9   cytochrome 2C9 human Ibeanu and Goldstein 1995 7794915    
H4.31 AGGGCAaAGGCCA -55/-43 CYP2D6   cytochrome 2D6 human Cairns et al. 1996 8810289    
H4.32 GTACCAaAGTCCA -103/-91 Cyp3A1   cytochrome 3A1 rat Ogino et al. 1999 9917326    
H4.33 TGGACTtAGTTCA -146/-134 CYP7A1   cytochrome 7A1 human Crestani et al. 1998 9799805    
H4.34 AGGTCCaAGGGCA -60/-48 Cyp8b1   sterol 12alpha-hydroxylase rat del Castillo-Olivares and Gil 2001 11574686    
H4.35 TGTCCAaAGTCCA -700/-688 AKR1C4   dihydrodiol dehydrogenase 4 human  zeki et al. 2001 11284743    
H4.36 AGGTCGaGAGGTC 3496/3484 EPO   erythropoietin human Blanchard et al. 1992 1448072    
H4.37 CTAGCAaAGGTTA 18/30 F9   coagulation factor IX human Naka and Brownlee 1996 8562402    
H4.38 GTACCAaAGTACA -15/-27 F9   coagulation factor IX human Reijnen et al. 1992 1631121    
H4.39 AGTGGTaAGGTCG 6/-6 F9   coagulation factor IX human Naka and Brownlee 1996 8562402    
H4.40 CGGGCAaAGTTCT -4/-16 F7   coagulation factor VII human  Arbini et al. 1997 8978290    
H4.41 AGGGCAaAGGTCA -35/-47 F7   coagulation factor VII mouse  Stauffer et al. 1998 9442072    
H4.42 GGGGCAtAAGTCT -123/-111 F8   coagulation factor VIII human  Figueiredo and Brownlee 1995 7744832    
H4.43 GGAGCAaAGTCCA -47/-59 F10   coagulation factor X human  Miao et al. 1992 1313796    
H4.44 AAACCAaAGTTCA -32/-44 GUCY2C   guanylyl cyclase C human  Swenson et al. 1999 10070050    
H4.45 GGGGTAaAGGTTC 1151/1139 N/A   hepatitis B virus enhancer I human HBV  Garcia et al. 1993 8389913    
H4.46 AGTCCAaGAGTCC 1674/1662 N/A   hepatitis B virus enhancer II human HBV  Guo et al. 1993 8417343    
H4.47 AGGTTAaAGGTCT 1757/1769 N/A   hepatitis B virus nucleocapsid human HBV  Raney et al. 1997 8995626    
H4.48 AGGTCAgGGTCCA -124/-112 MST1   hepatocyte growth factor-like protein human  Waltz et al. 1996 8621550    
H4.49 GGTCCAaAGTTCA -267/-255 Hnf1a   hepatocyte nuclear factor 1alpha Xenopus  Zapp et al. 1993 8413240    
H4.50 AGTCCAaAGTTCA -63/-51 TCF1   hepatocyte nuclear factor 1alpha human  Gragnoli et al. 1997 9313764    
H4.51 GGGCTGaAGTCCA -70/-58 TCF1   hepatocyte nuclear factor 1alpha human Sladek, unpublished      
H4.52 CGGGCAaAGGCCA -652/-640 Onecut1   hepatocyte nuclear factor 6 rat  Lahuna et al. 2000 10674400    
H4.53 GGGCCAaGGGTCA -355/-343 HIV LTR   HIV  long terminal repeat hHIV  Ladias 1994 8119938    
H4.54 AGTTCAaAGTTCA -84/-72 Fabp2   intestinal fatty acid binding protein rat  Rottman and Gordon 1993 8505324    
H4.55 GGGCCAgAGTCCA -130/-142 Pklr   liver-type pyruvate kinase rat  Diaz Guerra et al. 1993 8246989    
H4.56 AGGTCTcAGGTCA -83/-71 MST1   macrophage stimulating protein human  Ueda et al. 1998 9668124    
H4.57 GGGTCAcAGTGCA 21/33 MST1   macrophage stimulating protein human  Ueda et al. 1998 9668124    
H4.58 CGGGTAaAGGTGA -323/-311 ACADM   medium-chain acylCoA dehydrogenase human  Carter et al. 1993 8314750    
H4.59 GGTTTAaAGTTCA 95/83 Otc   ornithine transcarbamylase rat  Nishiyori et al. 1994 8288597    
H4.60 GGATCAaAGGTCC -18/-30 Otc   ornithine transcarbamylase rat  Kimura et al. 1993 8496174    
H4.61 AGTTCAgAGGTTA 180/168 Otc   ornithine transcarbamylase rat  Nishiyori et al. 1994 8288597    
H4.62 GGCTTAaAGTTCA -112/-100 Otc   ornithine transcarbamylase rat  Kimura et al. 1993 8496174    
H4.63 CGGCCAaAGGTCA -439/-451 Pck1   phosphoenol pyruvate carboxykinase (PEPCK) rat  Hall et al. 1992 1333043    
H4.64 GGGGCAaAGTCAA 22/10 Prlr   prolactin receptor rat  Moldrup et al. 1996 8776726    
H4.65 GGGTTAaAGGTTG -23/-35 SHBG   sex hormone-binding globulin human  Janne and Hammond 1998 9852068    
H4.66 GGGTCAaGGGTCA -82/-70 SHBG   sex hormone-binding globulin human  Janne and Hammond 1998 9852068    
H4.67 AGGTCAaAGATTG -68/-56 Trf   transferrin mouse  Schaeffer et al. 1993 8226864    
H4.68 GGCAAGgTTCATA -151/-139 Ttr   transthyretin mouse  Sladek et al. 1990 2279702    
H4.69 AGATCAaAGAGCA -3586/-3598 Tat   tyrosine  aminotransferase rat  Nitsch et al. 1993 8100067    
H4.70 AGTCCAaAGGTCC 1818/1806 WhvEnII   woodchuck hepatitis virus enhancer II woodchuck  Ueda et al. 1996 8676498    
H4.71 GGAGTAaAGTTCA 2150/2162 Aldob   aldolase B rat  Gregori et al. 1998 9737987    
H4.142 TGGGCAaAGGTCG -193/-181 Ghr   growth hormone receptor 1A bovine  Jiang and Lucy 2001 11376119    
H4.143 TGGGCAaAGAGCA -164/-152 Ghr   growth hormone receptor 1A bovine  Jiang and Lucy 2001 11376119    
H4.144 CTGAAGgGCTCAC -85/-97 MTTP   microsomal triglyceride transfer protein human  Hagan et al. 1994 7961826    
H4.145 TGGGAGgGCTGAC -79/-91 Mtp   microsomal triglyceride transfer protein hamster  Hagan et al. 1994 7961826    
H4.146 AGGTCAgAGACCT >15 kb APOE   apolipoprotein E human  Dang et al. 1995 7673250    
H4.147 ATACCAaAGTTCA -4040/-4028 AFP   alpha fetal protein human  Nakabayashi et al. 2004 15144905    
H4.148 AGGACAaAGGCCA -739/-727 Cyp4a6   cytochrome P450 4A6 rabbit  Muerhoff et al. 1992 1605646    
H4.149 TGGGCAaGGGTCA -21/-9 Cyp4a6   cytochrome P450 4A6 rabbit  Muerhoff et al. 1992 1605646    
H4.150 TAGGCAaGAGGCA -21/-9 CYP4A1   cytochrome P450 4A1 rat  Muerhoff et al. 1992 1605646    
H4.151 GGGACAaAGTTCA -237/-225 Hnf1   hepatocyte nuclear factor 1 salmon  McNair et al. 2000 11085951    
H4.152 TGAGCAaAGTCTT -6478/-6466 Hnf4a   hepatocyte nuclear factor 4alpha mouse  Bailly et al. 2001 11522818    
H4.153 AGACCTtTGAGTT -1954/-1942 PAX4   paired homeodomain transcription factor human  Smith et al. 2000 10967107    
H4.154 AGGGCAaGGTCCA 208/220 CYP8B1   sterol 12alpha hydroxylase human  Zhang and Chiang 2001 11535594    
H4.155 TGGGCAaAGTCCT -554/-566 NR0B2   small heterodimer partner human  Shih et al. 2001 11679424    
H4.156 TGATTAaAGTCCA -65/-53 Hp-25   hibernation-specific protein chipmunk  Kojima et al. 2000 10903495    
H4.157 CGACCAaAGTCCA -132/-120 Cyp3a16   cytochrome P450 3A16 mouse  Nakayama et al. 2001 11573935    
H4.158 AGGTCAaGCTCCT -463/-451 Fmo1   flavin-containing monooxygenases rabbit  Luo and Hines 2001 11723251    
H4.159  AGGCTAaAGTACA   -194/-182 Fmo1   flavin-containing monooxygenases rabbit  Luo and Hines 2001 11723251    
H4.160 AGATCAgACTCCT -485/-473 FMO1   flavin-containing monooxygenases human  Luo and Hines 2001 11723251    
H4.161 GGGGCAaAGTTCA -1493/-1481 PPARA   peroxisome proliferator-activated receptor alpha human  Pineda Torra et al. 2002 11981036    
H4.162 GGGACAaAGAGCA -903/-915 F2   prothrombin human  Ceelie et al. 2003 12911579    
H4.163 ACGGCAaAGTCCA -69/-57 Ins1   insulin I rat  Bartoov-Shifman et al. 2002 11994285    
H4.164 GGAACCaGGGCCA  5/17 G6pc   glucose-6-phosphatase rat  Rajas et al. 2002 11864989    
H4.165 TGACCCcAGGTCC -665/-653 G6pc   glucose-6-phosphatase mouse  Rajas et al. 2002 11864989    
H4.166 AGGTCAgGGGACA -1455/-1443 Inos   inducible nitric oxide synthetase rat  Guo et al. 2002 11741883    
H4.167 CAATTAaAGGTCA -7784/-7772 CYP3A4   cytochrome P450 3A4 human  Tirona et al. 2003 12514743    
H4.168 AGTCCAaAGGTCA -258/-246 Tcf2   hepatocyte  nuclear  factor 1beta mouse  Power and Cereghini 1996 8622679    
H4.169 AGGTCAaAGGTCA   synthetic      Jiang et al. 1997 9126270    
H4.170 AGGTCAaAGGTTA -6969 Aldob aldolase B, fructose-bisphosphate mouse Garrison et al. 2006 16618389    
H4.171 AGAGCAaAGGTGT 1105 Apoc2 apolipoprotein CII mouse Garrison et al. 2006 16618389    
H4.172 AGGCCAgAGGTCA -5505 Crb3 crumbs homolog 3  Drosophila mouse Garrison et al. 2006 16618389    
H4.173 AGGTCAgAGGACA -2867 Apoc2 apolipoprotein CII mouse Garrison et al. 2006 16618389    
H4.174 AGAGCAaAGGTCT -7325 Aqp4 aquaporin 4 mouse Garrison et al. 2006 16618389    
H4.175 AGGTCAgAGGCCT -1996 Cldn2 claudin 2 mouse Garrison et al. 2006 16618389    
H4.176 AGGGCAaGGAGCA -6333 Gatm glycine amidinotransferase  mouse Garrison et al. 2006 16618389    
H4.177 GGTTCAaAGGGCA -1439 Mucdhl mucin and cadherin-like mouse Garrison et al. 2006 16618389    
H4.178 CTAGCAaAGTCCA -241 Neu3 sialidase 3  membrane sialidase mouse Garrison et al. 2006 16618389    
H4.179 GTACCAaAGGTCC -2349 Saa1 serum amyloid A1 mouse Garrison et al. 2006 16618389    
H4.180 GGTCCAcAGTTCA -8995 Slc39a4 solute carrier family 39 (zinc transporter), member 4 mouse Garrison et al. 2006 16618389    
H4.181 AGGGCTaGGGTCA -948 Slc39a4 solute carrier family 39 (zinc transporter), member 4 mouse Garrison et al. 2006 16618389    
H4.182 AGTCCAaAGGCCG -6134 Cdh1 cadherin 1 mouse Battle et al. 2006 16714383    
H4.183 AGATCAaAGTGCA -6919 Cxadr coxsackie virus and adenovirus receptor mouse Battle et al. 2006 16714383    
H4.184 AGATCAaTGTCCA -2346 Cxadr coxsackie virus and adenovirus receptor mouse Battle et al. 2006 16714383    
H4.185 AGTCCAaAGGTTC -6501 Gjb1 gap junction protein, beta 1 mouse Battle et al. 2006 16714383    
H4.186 GGGTCAgAGGTCA -2056 Gpld1 glycosylphosphatidylinositol specific phospholipase D1 mouse Battle et al. 2006 16714383    
H4.187 TGGGCAaAGGTCT -4626 Lgals9 lectin, galactose binding, soluble 9 mouse Battle et al. 2006 16714383    
H4.188 GGCTCAaAGTTCA -7251 Npnt nephronectin mouse Battle et al. 2006 16714383    
H4.189 AGGTCAgAGGGCA -8995 Npnt nephronectin mouse Battle et al. 2006 16714383    
H4.190 GGGTTAgAGTCCA -7328 Pkp2 plakophilin 2 mouse Battle et al. 2006 16714383    
H4.191 GGTCCAgAGTTCA -672 Rhpn2 rhophilin, Rho GTPase binding protein 2 mouse Battle et al. 2006 16714383    
H4.192 AGGGCAaAGGTTT -6793 Vtn vitronectin mouse Battle et al. 2006 16714383    
H4.193 AGTCCAaAGTCAA -4419 Vtn vitronectin mouse Battle et al. 2006 16714383    
H4.194 AGGTTAaAGGTCA  -271/-259 apoa5 apolipoprotein A-V human Prieur et al. 2003 16051671    
H4.195 GGGACAaATTCCA  -372/-360 UGT1A9 UDP glucuronosyltransferase 1 human Barbier et al. 2005 15470081    
H4.196 AGACCAaAGGACA  -150/-138 CYP2C9 cytochrome P450, family 2, subfamily C, polypeptide 9 human Kawashima et al. 2006 16540586    
H4.197 AGACCAaAGGGCA -2300  Kcnj11 potassium inwardly-rectifying channel, subfamily J, member 11 mouse Gupta et al. 2005 15761495    
H4.198 GTGGTAaAGGTCT  -451/-439 Pck1 phosphoenolpyruvate carboxykinase mouse Scribner et al. 2007 16713227    
H4.199 AGGTCAAAAGTAC  -224/-243 Acms A-amino-B- carboxymuconate-e-semialdehyde mouse Shin et al. 2006 16807375    
H4.200 AGGTCAaAGGCCT  -7093/-7106 Fasn Fatty Acid Synthase rat Adamson et al. 2006 16800817    
H4.201 AGTTTGgAGTCTG  -61/-49 MTTP Microsomal triglyceride transfer protein human Hirokane et al. 2004 15337761    
H4.202 TGGAACtGGGTCA   G6pc glucose 6 phosphate rat Rajas et al. 2002 11864989    
H4.203 AGGGCAaAGACCT  -6/-18 Nr1i3 constitutive androstane receptor mouse Ding et al. 2006 16825189    
H4.204 TGTGCAaGGTTCA   Ces2 carboxylesterase 2 mouse Furihata et al. 2006 16527247    
H4.205 TGTCACAAGGTCA   -39/-52 Gck Glucose kinase rat Roth et al. 2002 11950391    
H4.206 AGGACAGAGTCCA  -162/-150 Vlacsr solute carrier family 27  fatty acid transporter , member 5 mouse Inoue et al. 2004 14583614    
H4.207 AGTTCCAAGGTCT  -18/-6 Baat bile acid-Coenzyme A mouse Inoue et al. 2004 14583614    
H4.208 TGGGCAaGGGGCA  -49/-37 Prodh2   proline oxidase mouse Kamiya et al. 2004 15581617    
H4.209 GGGACAgAGGTCA  -137/-149 Prodh2  proline oxidase mouse Kamiya et al. 2004 15581617    
H4.210 AGTGCAAGGGTCT  -240/-252 G6PC glucose 6 phosphatase human Rhee et al. 2003 12651943    
H4.211 AGGACAgAGTCTA  -291/-303 G6PC glucose 6 phosphatase human Hirota et al. 2005 15702243    
H4.212 TGAACTtAGGTCC  -83/-71 MTTP Microsomal triglyceride transfer protein human Sheena et al. 2005 15547294    
H4.213 TGGGGAaAGGTCA  -38/-50 MTTP Microsomal triglyceride transfer protein human Sheena et al 2005 15547294    
H4.214 TGATTAaAGTTCA -1766 PAK7 p21-activated kinase 7 (previously PAK5) human Niehof and Borlak 2005 15615695    
H4.215 GGGTACaATGTTC   PAK7 p21-activated kinase 7 (previously PAK5) human Niehof and Borlak 2005 15615695    
H4.216 CTGACTaAGGTAC   PAK7 p21-activated kinase 7 (previously PAK5) human Niehof and Borlak 2005 15615695    
H4.217 AGGGCAtAGGTCA -1430/-1422 RPS6KA6 ribosomal protein S6 kinase (previously RSK4) human Niehof and Borlak 2005 15615695    
DR2 (Direct Repeat with a spacing of 2)              
DR2.1 CGCTCAaaAGGTTG -2053 RPS6KA6 ribosomal protein S6 kinase (previously RSK4) human Niehof and Borlak 2005 15615695    
DR2.2 AGCCCTatTGACCC -1479/-1466 SLC22A1 solute carrier family 22 (organic cation transporter), member 1 (previously OCT1) human Saborowski et al 2006 16436500    
DR2.3 TGATCTctTGTCCT -1454/1441 SLC22A1 solute carrier family 22 (organic cation transporter), member 1 (previously OCT1) human Saborowski et al 2006 16436500    
 
Legend:  
 
1See Table S1B for motifs H4.72 through H4.141  
2Postion given in reference. See Table S2A for current position in human genes UCSC Genome Browser (vers. 18)  
3Current gene symbol is given, may be different from that in reference. See HGNC (HUGO: http://www.genenames.org/index.html)  
 
 
Prepared 11/07 by:  
Eugene Bolotin, Jake Scnabl, Frances M Sladek