Hnf1a (HNF1 homeobox A) - Rat Genome Database
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Gene: Hnf1a (HNF1 homeobox A) Rattus norvegicus
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Symbol: Hnf1a
Name: HNF1 homeobox A
RGD ID: 3828
Description: Exhibits DNA binding activity; DNA-binding transcription activator activity, RNA polymerase II-specific; and transcription cofactor binding activity. Involved in negative regulation of transcription by RNA polymerase II; positive regulation of transcription by RNA polymerase II; and transcription by RNA polymerase II. Localizes to nucleus. Used to study hepatocellular adenoma and hepatocellular carcinoma. Biomarker of extrahepatic cholestasis and kidney disease. Human ortholog(s) of this gene implicated in glucose metabolism disease (multiple); liver disease (multiple); and renal cell carcinoma. Orthologous to human HNF1A (HNF1 homeobox A); PARTICIPATES IN forkhead class A signaling pathway; maturity-onset diabetes of the young pathway; INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: albumin proximal factor; hepatic nuclear factor 1; hepatic nuclear factor-1-alpha; hepatocyte nuclear factor 1-alpha; HNF-1-alpha; HNF-1A; HNF1; LF-B1; LF-B1 hepatic nuclear factor (HNF1): albumin proximal factor also TCF1; LF-B1, hepatic nuclear factor (HNF1): albumin proximal factor, also TCF1; Lfb1; liver-specific transcription factor LF-B1; TCF-1; Tcf1; transcription factor 1; Transcription factor 1 hepatic; Transcription factor 1, hepatic
Orthologs:
Homo sapiens (human) : HNF1A (HNF1 homeobox A)  HGNC  Alliance
Mus musculus (house mouse) : Hnf1a (HNF1 homeobox A)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Hnf1a (HNF1 homeobox A)
Pan paniscus (bonobo/pygmy chimpanzee) : HNF1A (HNF1 homeobox A)
Canis lupus familiaris (dog) : HNF1A (HNF1 homeobox A)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Hnf1a (HNF1 homeobox A)
Sus scrofa (pig) : HNF1A (HNF1 homeobox A)
Chlorocebus sabaeus (African green monkey) : HNF1A (HNF1 homeobox A)
Heterocephalus glaber (naked mole-rat) : Hnf1a (HNF1 homeobox A)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01247,407,811 - 47,433,342 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1247,407,811 - 47,433,342 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01249,195,096 - 49,226,754 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41242,919,574 - 42,945,670 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11242,782,961 - 42,809,058 (+)NCBI
Celera1243,263,411 - 43,289,196 (+)NCBICelera
Cytogenetic Map12q16NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-dinitrotoluene  (EXP)
2,6-di-tert-butyl-4-methylphenol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-azacytidine  (ISO)
acetylsalicylic acid  (EXP)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
Aroclor 1254  (EXP)
baicalin  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
butanal  (ISO)
Butylbenzyl phthalate  (EXP)
butyric acid  (EXP)
cannabidiol  (EXP)
carbamazepine  (ISO)
carmustine  (ISO)
cisplatin  (EXP,ISO)
D-glucose  (ISO)
DDT  (EXP)
dexamethasone  (EXP,ISO)
dextran sulfate  (ISO)
dibutyl phthalate  (EXP)
diclofenac  (ISO)
diethylstilbestrol  (EXP)
dioxygen  (ISO)
dipentyl phthalate  (EXP)
ethanol  (ISO)
folic acid  (ISO)
genistein  (ISO)
gentamycin  (EXP)
glucose  (ISO)
lipopolysaccharide  (EXP,ISO)
lithocholic acid  (EXP)
LY294002  (EXP)
mercury atom  (ISO)
mercury(0)  (ISO)
methapyrilene  (EXP)
N-acetylsphingosine  (EXP)
N-nitrosodiethylamine  (EXP)
Nonylphenol  (EXP)
ochratoxin A  (EXP)
paracetamol  (EXP,ISO)
perfluorooctanoic acid  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
propanal  (ISO)
Ptaquiloside  (ISO)
resveratrol  (ISO)
salvianolic acid B  (ISO)
silicon dioxide  (ISO)
simvastatin  (ISO)
sodium arsenite  (ISO)
tetrachloromethane  (EXP,ISO)
thymoquinone  (ISO)
titanium dioxide  (ISO)
trimellitic anhydride  (ISO)
urethane  (ISO)
ursodeoxycholic acid  (ISO)
valproic acid  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Bacq Y, etal., Gastroenterology. 2003 Nov;125(5):1470-5. doi: 10.1016/j.gastro.2003.07.012.
2. Bellanne-Chantelot C, etal., Diabetes. 2008 Feb;57(2):503-8. Epub 2007 Nov 14.
3. Bluteau O, etal., Nat Genet. 2002 Oct;32(2):312-5. doi: 10.1038/ng1001. Epub 2002 Sep 23.
4. Chouard T, etal., Nucleic Acids Res 1990 Oct 11;18(19):5853-63.
5. Ding CH, etal., Mol Cancer. 2018 Feb 21;17(1):63. doi: 10.1186/s12943-018-0813-1.
6. Dmitrieva RI, etal., Hypertension. 2008 Jun;51(6):1583-9. Epub 2008 Apr 28.
7. Dohda T, etal., J Biochem (Tokyo). 2004 Sep;136(3):313-9.
8. Dohda T, etal., J Biochem. 2004 Sep;136(3):313-9.
9. Ellard S, etal., Diabetologia. 2007 Nov;50(11):2313-7. Epub 2007 Sep 8.
10. Frain M, etal., Cell 1989 Oct 6;59(1):145-57.
11. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
12. Geier A, etal., Hepatology. 2005 Mar;41(3):470-7. doi: 10.1002/hep.20594.
13. GOA data from the GO Consortium
14. Holmkvist J, etal., Diabetes. 2008 Jun;57(6):1738-44. Epub 2008 Mar 10.
15. Ihara T, etal., J Gastroenterol Hepatol. 2003 Jun;18(6):705-11.
16. Jackson AE, etal., Diabetes. 2004 Aug;53(8):2122-5.
17. Klaus A and Birchmeier W, Nat Rev Cancer. 2008 May;8(5):387-98.
18. Mendel DB, etal., Science 1991 Dec 20;254(5039):1762-7.
19. MGD data from the GO Consortium
20. NCBI rat LocusLink and RefSeq merged data July 26, 2002
21. OMIM Disease Annotation Pipeline
22. Patitucci C, etal., J Clin Invest. 2017 May 1;127(5):1873-1888. doi: 10.1172/JCI90327. Epub 2017 Apr 10.
23. Piaggio G, etal., Nucleic Acids Res 1994 Oct 11;22(20):4284-90.
24. Pipeline to import KEGG annotations from KEGG into RGD
25. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
26. RGD automated data pipeline
27. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
28. RGD automated import pipeline for gene-chemical interactions
29. Shaat N, etal., Diabetologia. 2006 Jul;49(7):1545-51. Epub 2006 Apr 26.
30. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
31. Wang Z and Burke PA, FEBS J. 2010 Oct;277(19):4066-75. doi: 10.1111/j.1742-4658.2010.07802.x. Epub 2010 Aug 23.
32. Whalen R, etal., Biochem J. 2004 Feb 1;377(Pt 3):763-8.
33. Wu W, etal., Hepatology. 2016 Jun;63(6):1943-56. doi: 10.1002/hep.28495. Epub 2016 Mar 24.
34. Yamagata K, etal., Nature. 1996 Dec 5;384(6608):455-8.
35. Yang X, etal., Biochem Biophys Res Commun. 2004 May 14;317(4):1045-51.
Additional References at PubMed
PMID:1354855   PMID:1363228   PMID:1673925   PMID:1677179   PMID:1685988   PMID:1967225   PMID:1970973   PMID:1988016   PMID:1989880   PMID:2044952   PMID:2263635   PMID:7914432  
PMID:8325367   PMID:8330635   PMID:8491172   PMID:8491173   PMID:8598044   PMID:9126845   PMID:9420335   PMID:9566924   PMID:9593777   PMID:9609100   PMID:9689059   PMID:9733737  
PMID:10090727   PMID:10330009   PMID:10333057   PMID:10617683   PMID:10631168   PMID:10852923   PMID:11106484   PMID:11121425   PMID:11269503   PMID:11279518   PMID:11287626   PMID:11301190  
PMID:11733582   PMID:11980910   PMID:12189445   PMID:12367519   PMID:12453420   PMID:12530534   PMID:14570708   PMID:14656222   PMID:15014077   PMID:15067314   PMID:15142986   PMID:15182178  
PMID:15355349   PMID:15581617   PMID:15647252   PMID:15793583   PMID:15866165   PMID:15961790   PMID:16204235   PMID:16223943   PMID:16873682   PMID:16880268   PMID:16893891   PMID:16912278  
PMID:17272516   PMID:17337496   PMID:17962340   PMID:18656965   PMID:18949455   PMID:19376774   PMID:19433262   PMID:19924231   PMID:19933277   PMID:20841353   PMID:21628466   PMID:21718540  
PMID:21784843   PMID:22196858   PMID:22589549   PMID:22780989   PMID:24157454   PMID:26978583   PMID:29330688   PMID:30555544   PMID:32833553  


Genomics

Comparative Map Data
Hnf1a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01247,407,811 - 47,433,342 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1247,407,811 - 47,433,342 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01249,195,096 - 49,226,754 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41242,919,574 - 42,945,670 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11242,782,961 - 42,809,058 (+)NCBI
Celera1243,263,411 - 43,289,196 (+)NCBICelera
Cytogenetic Map12q16NCBI
HNF1A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl12120,978,543 - 121,002,512 (+)EnsemblGRCh38hg38GRCh38
GRCh3812120,977,683 - 121,002,512 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3712121,415,861 - 121,440,315 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3612119,900,932 - 119,924,698 (+)NCBINCBI36hg18NCBI36
Build 3412119,879,268 - 119,903,032NCBI
Celera12121,051,978 - 121,075,735 (+)NCBI
Cytogenetic Map12q24.31NCBI
HuRef12118,425,936 - 118,448,929 (+)NCBIHuRef
CHM1_112121,385,205 - 121,409,144 (+)NCBICHM1_1
Hnf1a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395115,087,039 - 115,109,121 (-)NCBI
GRCm385114,948,980 - 114,971,062 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5114,948,980 - 114,971,094 (-)EnsemblGRCm38mm10GRCm38
MGSCv375115,398,989 - 115,421,071 (-)NCBIGRCm37mm9NCBIm37
MGSCv365115,209,360 - 115,232,037 (-)NCBImm8
Celera5112,043,825 - 112,067,328 (-)NCBICelera
Cytogenetic Map5FNCBI
cM Map555.99NCBI
Hnf1a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545510,694,102 - 10,717,613 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495545510,694,102 - 10,717,613 (-)NCBIChiLan1.0ChiLan1.0
HNF1A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.112121,932,671 - 121,955,911 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl12121,932,671 - 121,955,911 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v012118,562,308 - 118,584,596 (+)NCBIMhudiblu_PPA_v0panPan3
HNF1A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2616,805,690 - 16,824,790 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12616,805,690 - 16,826,065 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Hnf1a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493666862,103 - 81,549 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HNF1A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1440,868,676 - 40,888,328 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11440,868,819 - 40,888,322 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21443,383,209 - 43,402,712 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HNF1A
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl11116,335,675 - 116,357,751 (+)Ensembl
ChlSab1.111116,334,935 - 116,358,582 (+)NCBI
Hnf1a
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474712,717,713 - 12,746,040 (-)NCBI

Position Markers
D12Mgh11  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01247,406,516 - 47,406,665NCBIRnor6.0
Rnor_5.01249,200,686 - 49,200,835UniSTSRnor5.0
RGSC_v3.41242,918,279 - 42,918,428UniSTSRGSC3.4
RGSC_v3.41242,918,278 - 42,918,428RGDRGSC3.4
RGSC_v3.11242,781,666 - 42,781,816RGD
Cytogenetic Map12q16UniSTS
D12Wox22  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01247,406,507 - 47,406,701NCBIRnor6.0
Rnor_5.01249,200,677 - 49,200,871UniSTSRnor5.0
RGSC_v3.41242,918,270 - 42,918,464UniSTSRGSC3.4
Cytogenetic Map12q16UniSTS
TCF1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01247,424,364 - 47,424,873NCBIRnor6.0
Rnor_5.01249,217,643 - 49,218,152UniSTSRnor5.0
RGSC_v3.41242,936,693 - 42,937,202UniSTSRGSC3.4
Celera1243,280,225 - 43,280,734UniSTS
Cytogenetic Map12q16UniSTS
RH94688  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01247,432,450 - 47,432,627NCBIRnor6.0
Rnor_5.01249,225,854 - 49,226,031UniSTSRnor5.0
RGSC_v3.41242,944,778 - 42,944,955UniSTSRGSC3.4
Celera1243,288,304 - 43,288,481UniSTS
Cytogenetic Map12q16UniSTS
RH94689  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01247,407,828 - 47,407,934NCBIRnor6.0
Rnor_5.01249,201,996 - 49,202,102UniSTSRnor5.0
RGSC_v3.41242,919,591 - 42,919,697UniSTSRGSC3.4
Celera1243,263,428 - 43,263,534UniSTS
Cytogenetic Map12q16UniSTS
RH94784  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01247,432,973 - 47,433,271NCBIRnor6.0
Rnor_5.01249,226,377 - 49,226,675UniSTSRnor5.0
RGSC_v3.41242,945,301 - 42,945,599UniSTSRGSC3.4
Celera1243,288,827 - 43,289,125UniSTS
Cytogenetic Map12q16UniSTS
RH141549  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01247,432,598 - 47,432,803NCBIRnor6.0
Rnor_5.01249,226,002 - 49,226,207UniSTSRnor5.0
RGSC_v3.41242,944,926 - 42,945,131UniSTSRGSC3.4
Celera1243,288,452 - 43,288,657UniSTS
Cytogenetic Map12q16UniSTS
PMC115916P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01247,407,819 - 47,408,086NCBIRnor6.0
Rnor_5.01249,201,987 - 49,202,254UniSTSRnor5.0
RGSC_v3.41242,919,582 - 42,919,849UniSTSRGSC3.4
Celera1243,263,419 - 43,263,686UniSTS
Cytogenetic Map12q16UniSTS
Hnf1a  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01247,407,966 - 47,408,239NCBIRnor6.0
Rnor_5.01249,202,134 - 49,202,407UniSTSRnor5.0
Celera1243,263,566 - 43,263,839UniSTS
Cytogenetic Map12q16UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12247568747475687Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12251344247513442Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12251344247513442Rat
634350Apr4Acute phase response QTL 46orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)12421005149210051Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)6922362652716770Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
8552918Pigfal7Plasma insulin-like growth factor 1 level QTL 7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922362652716770Rat
8552964Pigfal17Plasma insulin-like growth factor 1 level QTL 173.5blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922362652716770Rat
8552912Pigfal6Plasma insulin-like growth factor 1 level QTL 65blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922363052716770Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)12978983452716770Rat
1331761Bp218Blood pressure QTL 2182.973arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121312721150320041Rat
61404Bw120Body weight QTL 1205.1body mass (VT:0001259)body mass index (BMI) (CMO:0000105)121441977552716770Rat
1549829Scl48Serum cholesterol level QTL 485blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)121502198652716770Rat
2300186Bmd59Bone mineral density QTL 597.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)121590890052716770Rat
2293699Bss49Bone structure and strength QTL 495.610.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)121590890052716770Rat
1641928Alcrsp5Alcohol response QTL 5response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)121834247752716770Rat
2303569Gluco44Glucose level QTL 442blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121834247752716770Rat
2302060Pia37Pristane induced arthritis QTL 376.10.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)121872904352716770Rat
1549902Bp269Blood pressure QTL 269arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121875259352716770Rat
1549912Bp268Blood pressure QTL 268arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)101875259352716770Rat
5684888Pia42Pristane induced arthritis QTL 42joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)122265070248598906Rat
61324Eae5Experimental allergic encephalomyelitis QTL 514nervous system integrity trait (VT:0010566)percentage of study population developing relapsing-remitting experimental autoimmune encephalomyelitis during a period of time (CMO:0001402)122265070252716770Rat
631560Apr1Acute phase response QTL 16.1orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)122490659052716770Rat
7411643Foco20Food consumption QTL 200.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)122609884552716770Rat
8693658Alc33Alcohol consumption QTL 332.10.68drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)122911360949560679Rat
8693635Alc28Alcohol consumption QTL 282.70.439drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)122911360950757185Rat
1556747Calcic1Intracellular calcium level QTL 13.6platelet calcium amount (VT:0010500)platelet intracellular calcium level (CMO:0000922)123172356547433663Rat
1300175Cm5Cardiac mass QTL 53.78heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)123172356551955754Rat
1600386Calcic2Intracellular calcium level QTL 20.001platelet physiology trait (VT:0005464)platelet intracellular calcium level (CMO:0000922)123172356552716770Rat
1300162Bp188Blood pressure QTL 1883.19arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)123752188451955754Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:216
Count of miRNA genes:139
Interacting mature miRNAs:167
Transcripts:ENSRNOT00000001565
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 19 19 19 23
Low 30 22 17 22 4 8 25 4
Below cutoff 8 8 2 8 10 20 4 16 7 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000001565   ⟹   ENSRNOP00000001565
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1247,407,811 - 47,433,342 (+)Ensembl
RefSeq Acc Id: NM_012669   ⟹   NP_036801
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01247,407,811 - 47,433,342 (+)NCBI
Rnor_5.01249,195,096 - 49,226,754 (+)NCBI
RGSC_v3.41242,919,574 - 42,945,670 (+)RGD
Celera1243,263,411 - 43,289,196 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_036801   ⟸   NM_012669
- UniProtKB: P15257 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000001565   ⟸   ENSRNOT00000001565

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13698703
Promoter ID:EPDNEW_R9227
Type:multiple initiation site
Name:Hnf1a_1
Description:HNF1 homeobox A
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01247,407,741 - 47,407,801EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
12 49219910 49219911 G A snv IS-Tlk/Kyo (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3828 AgrOrtholog
Ensembl Genes ENSRNOG00000001183 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000001565 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000001565 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.260.40 UniProtKB/Swiss-Prot
InterPro HNF-1 UniProtKB/Swiss-Prot
  HNF-1_N UniProtKB/Swiss-Prot
  HNF1_dimer_N_dom_sf UniProtKB/Swiss-Prot
  HNF1a_C UniProtKB/Swiss-Prot
  HNF1b_C UniProtKB/Swiss-Prot
  Homeobox-like_sf UniProtKB/Swiss-Prot
  Homeobox_dom UniProtKB/Swiss-Prot
  Lambda_DNA-bd_dom_sf UniProtKB/Swiss-Prot
KEGG Report rno:24817 UniProtKB/Swiss-Prot
NCBI Gene 24817 ENTREZGENE
PANTHER PTHR11568 UniProtKB/Swiss-Prot
Pfam HNF-1_N UniProtKB/Swiss-Prot
  HNF-1A_C UniProtKB/Swiss-Prot
  HNF-1B_C UniProtKB/Swiss-Prot
PharmGKB HNF1A RGD
PhenoGen Hnf1a PhenoGen
PROSITE HOMEOBOX_1 UniProtKB/Swiss-Prot
  HOMEOBOX_2 UniProtKB/Swiss-Prot
SMART HOX UniProtKB/Swiss-Prot
Superfamily-SCOP SSF100957 UniProtKB/Swiss-Prot
  SSF46689 UniProtKB/Swiss-Prot
  SSF47413 UniProtKB/Swiss-Prot
TIGR TC233597
UniGene Rn.9660 ENTREZGENE
UniProt HNF1A_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-15 Hnf1a  HNF1 homeobox A  Tcf1  transcription factor 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2003-04-09 Tcf1  transcription factor 1    Transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1): albumin proximal factor, also TCF1  Name updated 629478 APPROVED
2002-06-10 Tcf1  Transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1): albumin proximal factor, also TCF1      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_regulation acts as its own transcriptional repressor 730004