Hnf1a (HNF1 homeobox A) - Rat Genome Database

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Gene: Hnf1a (HNF1 homeobox A) Rattus norvegicus
Symbol: Hnf1a
Name: HNF1 homeobox A
RGD ID: 3828
Description: Enables DNA binding activity; DNA-binding transcription activator activity, RNA polymerase II-specific; and transcription coactivator binding activity. Involved in several processes, including cellular response to organonitrogen compound; regulation of nucleobase-containing compound metabolic process; and regulation of protein phosphorylation. Located in nucleus. Part of chromatin. Used to study hepatocellular adenoma and hepatocellular carcinoma. Biomarker of extrahepatic cholestasis and kidney disease. Human ortholog(s) of this gene implicated in several diseases, including artery disease (multiple); cerebral infarction; 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
Previously 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
RGD Orthologs
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Rat AssemblyChrPosition (strand)SourceGenome Browsers
mRatBN7.21241,638,536 - 41,672,806 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1241,645,587 - 41,672,104 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1242,813,476 - 42,840,991 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01243,427,059 - 43,454,573 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01242,487,542 - 42,515,057 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-isolariciresinol  (ISO)
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)
5-fluorouracil  (ISO)
acetylsalicylic acid  (EXP)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
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)
caffeine  (ISO)
cannabidiol  (EXP)
carbamazepine  (ISO)
carmustine  (ISO)
cisplatin  (EXP,ISO)
D-glucose  (ISO)
dexamethasone  (EXP,ISO)
dextran sulfate  (ISO)
dibutyl phthalate  (EXP)
diclofenac  (ISO)
diethylstilbestrol  (EXP)
dioxygen  (ISO)
dipentyl phthalate  (EXP)
epoxiconazole  (ISO)
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)
methidathion  (ISO)
N-acetylsphingosine  (EXP,ISO)
N-nitrosodiethylamine  (EXP)
Nonylphenol  (EXP)
ochratoxin A  (EXP)
oleanolic acid  (ISO)
oltipraz  (ISO)
ozone  (EXP)
paracetamol  (EXP,ISO)
PCB138  (ISO)
perfluorooctanoic acid  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
propanal  (ISO)
prothioconazole  (ISO)
Ptaquiloside  (ISO)
resveratrol  (ISO)
salvianolic acid B  (ISO)
senecionine  (ISO)
silicon dioxide  (ISO)
simvastatin  (ISO)
sodium arsenite  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
thymoquinone  (ISO)
titanium dioxide  (ISO)
trichloroethene  (EXP)
trimellitic anhydride  (ISO)
triptonide  (ISO)
urethane  (ISO)
ursodeoxycholic acid  (ISO)
valproic acid  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of protein kinase activity  (IMP)
apoptotic nuclear changes  (IMP)
bile acid and bile salt transport  (ISO)
bile acid biosynthetic process  (ISO)
blastocyst development  (ISO)
bone resorption  (ISO)
cellular response to glucose stimulus  (IMP)
cellular response to leucine  (IMP)
cellular response to rapamycin  (IMP)
cholesterol metabolic process  (ISO)
chromatin remodeling  (ISO)
embryonic limb morphogenesis  (ISO)
fatty acid biosynthetic process  (ISO)
fatty acid transport  (ISO)
glucose homeostasis  (ISO)
glucose import  (ISO)
heme biosynthetic process  (ISO)
insulin secretion  (ISO)
liver development  (ISO)
negative regulation of apoptotic process  (IMP)
negative regulation of cysteine-type endopeptidase activity involved in apoptotic process  (IMP)
negative regulation of miRNA processing  (IMP)
negative regulation of peptidyl-threonine phosphorylation  (IMP)
negative regulation of transcription by RNA polymerase II  (IDA)
pancreas development  (IEA)
paraxial mesoderm formation  (ISO)
placenta development  (ISO)
positive regulation of ATP biosynthetic process  (IMP)
positive regulation of DNA-templated transcription  (ISO,ISS)
positive regulation of gene expression  (IMP)
positive regulation of insulin secretion  (IEP)
positive regulation of mitochondrial membrane potential  (IMP)
positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction  (IMP)
positive regulation of protein phosphorylation  (IMP)
positive regulation of transcription by RNA polymerase II  (IDA,IMP,ISO)
positive regulation of transcription initiation by RNA polymerase II  (ISO)
protein localization  (ISO)
regulation of DNA-templated transcription  (ISO)
regulation of hormone secretion  (ISO)
regulation of NADP metabolic process  (IMP)
regulation of pronephros size  (ISO)
regulation of transcription by RNA polymerase II  (IBA,ISO)
regulation of Wnt signaling pathway  (ISO)
renal glucose absorption  (ISO)
reproductive structure development  (ISO)
response to glucose  (ISO)
response to oxidative stress  (ISO)
reverse cholesterol transport  (ISO)
SMAD protein signal transduction  (ISO)
transcription by RNA polymerase II  (IDA)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View

References - curated
# Reference Title Reference Citation
1. Association of I27L polymorphism of hepatocyte nuclear factor-1 alpha gene with high-density lipoprotein cholesterol level. Babaya N, etal., J Clin Endocrinol Metab. 2003 Jun;88(6):2548-51. doi: 10.1210/jc.2002-021891.
2. Familial liver adenomatosis associated with hepatocyte nuclear factor 1alpha inactivation. Bacq Y, etal., Gastroenterology. 2003 Nov;125(5):1470-5. doi: 10.1016/j.gastro.2003.07.012.
3. The type and the position of HNF1A mutation modulate age at diagnosis of diabetes in patients with maturity-onset diabetes of the young (MODY)-3. Bellanne-Chantelot C, etal., Diabetes. 2008 Feb;57(2):503-8. Epub 2007 Nov 14.
4. HNF1A gene p.I27L is associated with co-existing preeclampsia in gestational diabetes mellitus. Beysel S, etal., Gynecol Endocrinol. 2020 Jun;36(6):530-534. doi: 10.1080/09513590.2019.1698023. Epub 2019 Dec 11.
5. Hepatocellular adenoma subtype classification using molecular markers and immunohistochemistry. Bioulac-Sage P, etal., Hepatology. 2007 Sep;46(3):740-8. doi: 10.1002/hep.21743.
6. Bi-allelic inactivation of TCF1 in hepatic adenomas. Bluteau O, etal., Nat Genet. 2002 Oct;32(2):312-5. doi: 10.1038/ng1001. Epub 2002 Sep 23.
7. Identification of circulating microRNAs in HNF1A-MODY carriers. Bonner C, etal., Diabetologia. 2013 Aug;56(8):1743-51. doi: 10.1007/s00125-013-2939-4. Epub 2013 May 15.
8. The Metabolic Phenotype of Youth Onset Type 2 Diabetes: The Role of Pregestational Diabetes Exposure and the Hepatic Nuclear Factor 1Alpha G319S Polymorphism. Charison J, etal., Can J Diabetes. 2016 Jun;40(3):210-5. doi: 10.1016/j.jcjd.2015.10.003. Epub 2016 Mar 3.
9. A distal dimerization domain is essential for DNA-binding by the atypical HNF1 homeodomain. Chouard T, etal., Nucleic Acids Res 1990 Oct 11;18(19):5853-63.
10. The HNF1α-regulated lncRNA HNF1A-AS1 reverses the malignancy of hepatocellular carcinoma by enhancing the phosphatase activity of SHP-1. Ding CH, etal., Mol Cancer. 2018 Feb 21;17(1):63. doi: 10.1186/s12943-018-0813-1.
11. Hepatocyte nuclear factor 1 and hypertensive nephropathy. Dmitrieva RI, etal., Hypertension. 2008 Jun;51(6):1583-9. Epub 2008 Apr 28.
12. Transcriptional coactivators CBP and p300 cooperatively enhance HNF-1alpha-mediated expression of the albumin gene in hepatocytes. Dohda T, etal., J Biochem (Tokyo). 2004 Sep;136(3):313-9.
13. Transcriptional coactivators CBP and p300 cooperatively enhance HNF-1alpha-mediated expression of the albumin gene in hepatocytes. Dohda T, etal., J Biochem. 2004 Sep;136(3):313-9.
14. Partial and whole gene deletion mutations of the GCK and HNF1A genes in maturity-onset diabetes of the young. Ellard S, etal., Diabetologia. 2007 Nov;50(11):2313-7. Epub 2007 Sep 8.
15. Rapamycin protects against dominant negative-HNF1A-induced apoptosis in INS-1 cells. Farrelly AM, etal., Apoptosis. 2011 Nov;16(11):1128-37. doi: 10.1007/s10495-011-0641-x.
16. The liver-specific transcription factor LF-B1 contains a highly diverged homeobox DNA binding domain. Frain M, etal., Cell 1989 Oct 6;59(1):145-57.
17. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
18. Cytokine-independent repression of rodent Ntcp in obstructive cholestasis. Geier A, etal., Hepatology. 2005 Mar;41(3):470-7. doi: 10.1002/hep.20594.
19. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
20. Differential expression of LEF1/TCFs family members in colonic carcinogenesis. Han W, etal., Mol Carcinog. 2017 Nov;56(11):2372-2381. doi: 10.1002/mc.22530. Epub 2017 May 22.
21. Common variants in maturity-onset diabetes of the young genes and future risk of type 2 diabetes. Holmkvist J, etal., Diabetes. 2008 Jun;57(6):1738-44. Epub 2008 Mar 10.
22. Alterations in the DNA binding activity of transcriptional factors activator protein-1, Sp1, and hepatocyte nuclear factor-1 in rat jejunum during starvation and refeeding. Ihara T, etal., J Gastroenterol Hepatol. 2003 Jun;18(6):705-11.
23. Polymorphic variations in the neurogenic differentiation-1, neurogenin-3, and hepatocyte nuclear factor-1alpha genes contribute to glucose intolerance in a South Indian population. Jackson AE, etal., Diabetes. 2004 Aug;53(8):2122-5.
24. AMP-activated protein kinase mediates apoptosis in response to bioenergetic stress through activation of the pro-apoptotic Bcl-2 homology domain-3-only protein BMF. Kilbride SM, etal., J Biol Chem. 2010 Nov 12;285(46):36199-206. doi: 10.1074/jbc.M110.138107. Epub 2010 Sep 14.
25. Wnt signalling and its impact on development and cancer. Klaus A and Birchmeier W, Nat Rev Cancer. 2008 May;8(5):387-98.
26. Improved Progression-Free Survival in Irinotecan-Treated Metastatic Colorectal Cancer Patients Carrying the HNF1A Coding Variant p.I27L. Labriet A, etal., Front Pharmacol. 2017 Oct 10;8:712. doi: 10.3389/fphar.2017.00712. eCollection 2017.
27. HNF1A G319S variant, active cigarette smoking and incident type 2 diabetes in Aboriginal Canadians: a population-based epidemiological study. Ley SH, etal., BMC Med Genet. 2011 Jan 5;12:1. doi: 10.1186/1471-2350-12-1.
28. Assessing the association of the HNF1A G319S variant with C-reactive protein in Aboriginal Canadians: a population-based epidemiological study. Ley SH, etal., Cardiovasc Diabetol. 2010 Aug 18;9:39. doi: 10.1186/1475-2840-9-39.
29. A Polymorphism in Hepatocyte Nuclear Factor 1 Alpha, rs7310409, Is Associated with Left Main Coronary Artery Disease. Liu R, etal., Biochem Res Int. 2014;2014:924105. doi: 10.1155/2014/924105. Epub 2014 Aug 18.
30. Characterization of a cofactor that regulates dimerization of a mammalian homeodomain protein. Mendel DB, etal., Science 1991 Dec 20;254(5039):1762-7.
31. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
32. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
33. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
34. A study of associations between CUBN, HNF1A, and LIPC gene polymorphisms and coronary artery disease. Park HS, etal., Sci Rep. 2020 Oct 1;10(1):16294. doi: 10.1038/s41598-020-73048-6.
35. Hepatocyte nuclear factor 1α suppresses steatosis-associated liver cancer by inhibiting PPARγ transcription. Patitucci C, etal., J Clin Invest. 2017 May 1;127(5):1873-1888. doi: 10.1172/JCI90327. Epub 2017 Apr 10.
36. LFB1/HNF1 acts as a repressor of its own transcription. Piaggio G, etal., Nucleic Acids Res 1994 Oct 11;22(20):4284-90.
37. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
38. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
39. Germline hepatocyte nuclear factor 1alpha and 1beta mutations in renal cell carcinomas. Rebouissou S, etal., Hum Mol Genet. 2005 Mar 1;14(5):603-14. doi: 10.1093/hmg/ddi057. Epub 2005 Jan 13.
40. GOA pipeline RGD automated data pipeline
41. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
42. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
43. Synergy between tumor suppressor APC and the beta-catenin-Tcf4 target Tcf1. Roose J, etal., Science. 1999 Sep 17;285(5435):1923-6. doi: 10.1126/science.285.5435.1923.
44. Common variants in MODY genes increase the risk of gestational diabetes mellitus. Shaat N, etal., Diabetologia. 2006 Jul;49(7):1545-51. Epub 2006 Apr 26.
45. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
46. Molecular targets of a human HNF1 alpha mutation responsible for pancreatic beta-cell dysfunction. Wang H, etal., EMBO J. 2000 Aug 15;19(16):4257-64. doi: 10.1093/emboj/19.16.4257.
47. Hepatocyte nuclear factor-4alpha interacts with other hepatocyte nuclear factors in regulating transthyretin gene expression. 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.
48. Decreased expression levels of rat liver glutathione S-transferase A2 and albumin during the acute phase response are mediated by HNF1 (hepatic nuclear factor 1) and IL6DEX-NP. Whalen R, etal., Biochem J. 2004 Feb 1;377(Pt 3):763-8.
49. Genome-wide association study in mice identifies loci affecting liver-related phenotypes including Sel1l influencing serum bile acids. Wu W, etal., Hepatology. 2016 Jun;63(6):1943-56. doi: 10.1002/hep.28495. Epub 2016 Mar 24.
50. Mutations in the hepatocyte nuclear factor-1alpha gene in maturity-onset diabetes of the young (MODY3) Yamagata K, etal., Nature. 1996 Dec 5;384(6608):455-8.
51. Evidence of impaired adipogenesis in insulin resistance. Yang X, etal., Biochem Biophys Res Commun. 2004 May 14;317(4):1045-51.
52. Association of the HNF1A polymorphisms and serum lipid traits, the risk of coronary artery disease and ischemic stroke. Zhou YJ, etal., J Gene Med. 2017 Jan;19(1-2):e2941. doi: 10.1002/jgm.2941.
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:21628466   PMID:21718540   PMID:21784843  
PMID:22196858   PMID:22589549   PMID:22780989   PMID:24157454   PMID:26978583   PMID:29330688   PMID:30555544   PMID:32398139   PMID:32833553  


Comparative Map Data
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
mRatBN7.21241,638,536 - 41,672,806 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1241,645,587 - 41,672,104 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1242,813,476 - 42,840,991 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01243,427,059 - 43,454,573 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01242,487,542 - 42,515,057 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11242,782,961 - 42,809,058 (+)NCBI
Celera1243,263,411 - 43,289,196 (+)NCBICelera
Cytogenetic Map12q16NCBI
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
GRCh3812120,978,543 - 121,002,512 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl12120,978,543 - 121,002,512 (+)EnsemblGRCh38hg38GRCh38
GRCh3712121,416,346 - 121,440,315 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3612119,900,932 - 119,924,698 (+)NCBINCBI36Build 36hg18NCBI36
Build 3412119,879,268 - 119,903,032NCBI
Celera12121,051,978 - 121,075,735 (+)NCBICelera
Cytogenetic Map12q24.31NCBI
HuRef12118,425,936 - 118,448,929 (+)NCBIHuRef
CHM1_112121,385,383 - 121,409,144 (+)NCBICHM1_1
T2T-CHM13v2.012120,968,229 - 120,992,127 (+)NCBIT2T-CHM13v2.0
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
GRCm395115,087,039 - 115,109,121 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl5115,087,039 - 115,109,153 (-)EnsemblGRCm39 Ensembl
GRCm385114,948,980 - 114,971,062 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5114,948,980 - 114,971,094 (-)EnsemblGRCm38mm10GRCm38
MGSCv375115,398,989 - 115,421,071 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv365115,209,360 - 115,232,037 (-)NCBIMGSCv36mm8
Celera5112,043,825 - 112,067,328 (-)NCBICelera
Cytogenetic Map5FNCBI
cM Map555.99NCBI
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
ChiLan1.0 EnsemblNW_00495545510,694,102 - 10,717,613 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495545510,694,102 - 10,717,613 (-)NCBIChiLan1.0ChiLan1.0
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
NHGRI_mPanPan112129,045,507 - 129,067,722 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v012118,562,308 - 118,584,596 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.112121,932,671 - 121,955,911 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl12121,932,671 - 121,955,911 (+)Ensemblpanpan1.1panPan2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
CanFam3.12616,805,690 - 16,826,065 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2616,805,690 - 16,824,790 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2616,808,158 - 16,828,540 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02617,072,065 - 17,092,444 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2617,072,065 - 17,091,161 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12617,032,447 - 17,052,829 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02617,107,536 - 17,127,938 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02617,150,231 - 17,170,614 (+)NCBIUU_Cfam_GSD_1.0
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
HiC_Itri_2NW_024405118145,563,569 - 145,582,683 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493666867,535 - 81,505 (-)EnsemblSpeTri2.0
SpeTri2.0NW_00493666862,103 - 81,549 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
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
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
ChlSab1.111116,334,935 - 116,358,582 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl11116,335,675 - 116,357,751 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037128,737,487 - 128,761,448 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
HetGla_female_1.0 EnsemblNW_00462474712,717,707 - 12,746,724 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474712,717,713 - 12,746,040 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Variants in Hnf1a
199 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:216
Count of miRNA genes:139
Interacting mature miRNAs:167
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 (
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7411660Foco28Food consumption QTL 2810.90.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
9590086Insglur6Insulin/glucose ratio QTL 618.970.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)12142110980Rat
8694179Bw150Body weight QTL 1502.90.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
7411586Foco5Food consumption QTL 55.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411595Foco9Food consumption QTL 940.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411545Bw128Body weight QTL 1285.20.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)12142110980Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)12142450532Rat
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12144465750Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12144503507Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12144503507Rat
634350Apr4Acute phase response QTL 46orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)12117200546172005Rat
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)12556449546669029Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)6556449546669029Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
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)12556449546669029Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
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)12556449846669029Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)12610757946669029Rat
1302792Scl21Serum cholesterol level QTL 213.80.0011blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)12719673046669029Rat
1549829Scl48Serum cholesterol level QTL 485blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)12960327746669029Rat
2293699Bss49Bone structure and strength QTL 495.610.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)121047413746669029Rat
2300186Bmd59Bone mineral density QTL 597.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)121047413746669029Rat
1331761Bp218Blood pressure QTL 2182.973arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121107382545055165Rat
61404Bw120Body weight QTL 1205.1body mass (VT:0001259)body mass index (BMI) (CMO:0000105)121235161946669029Rat
1641928Alcrsp5Alcohol response QTL 5response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)121281238546669029Rat
2303569Gluco44Glucose level QTL 442blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121281238546669029Rat
1549902Bp269Blood pressure QTL 269arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121318273646669029Rat
1549912Bp268Blood pressure QTL 268arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)101318273646669029Rat
2302060Pia37Pristane induced arthritis QTL 376.10.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)121319815746669029Rat
631560Apr1Acute phase response QTL 16.1orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)121914436246669029Rat
5684888Pia42Pristane induced arthritis QTL 42joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121961087042828880Rat
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)121961087046669029Rat
7411643Foco20Food consumption QTL 200.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)122032881946669029Rat
1300175Cm5Cardiac mass QTL 53.78heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)122806443345899022Rat
1600386Calcic2Intracellular calcium level QTL 20.001platelet physiology trait (VT:0005464)platelet intracellular calcium level (CMO:0000922)122806443346669029Rat
1300162Bp188Blood pressure QTL 1883.19arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)123210317445899022Rat

Markers in Region
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21241,644,287 - 41,644,437 (+)MAPPERmRatBN7.2
Rnor_6.01247,406,516 - 47,406,665NCBIRnor6.0
Rnor_5.01249,200,686 - 49,200,835UniSTSRnor5.0
RGSC_v3.41242,918,278 - 42,918,428RGDRGSC3.4
RGSC_v3.41242,918,279 - 42,918,428UniSTSRGSC3.4
RGSC_v3.11242,781,666 - 42,781,816RGD
Cytogenetic Map12q16UniSTS
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21241,644,278 - 41,644,473 (+)MAPPERmRatBN7.2
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
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21241,663,120 - 41,663,630 (+)MAPPERmRatBN7.2
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
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21241,671,211 - 41,671,389 (+)MAPPERmRatBN7.2
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
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21241,645,603 - 41,645,710 (+)MAPPERmRatBN7.2
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
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21241,671,734 - 41,672,033 (+)MAPPERmRatBN7.2
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
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21241,671,359 - 41,671,565 (+)MAPPERmRatBN7.2
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
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21241,645,594 - 41,645,862 (+)MAPPERmRatBN7.2
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
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21241,645,741 - 41,646,015 (+)MAPPERmRatBN7.2
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


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
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


RefSeq Acc Id: ENSRNOT00000001565   ⟹   ENSRNOP00000001565
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1241,645,587 - 41,672,104 (+)Ensembl
Rnor_6.0 Ensembl1247,407,811 - 47,433,342 (+)Ensembl
RefSeq Acc Id: NM_012669   ⟹   NP_036801
Rat AssemblyChrPosition (strand)Source
mRatBN7.21241,645,587 - 41,672,104 (+)NCBI
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
RefSeq Acc Id: XM_039089095   ⟹   XP_038945023
Rat AssemblyChrPosition (strand)Source
mRatBN7.21241,638,536 - 41,672,806 (+)NCBI
RefSeq Acc Id: NP_036801   ⟸   NM_012669
- UniProtKB: P15257 (UniProtKB/Swiss-Prot),   A6J1X4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000001565   ⟸   ENSRNOT00000001565
RefSeq Acc Id: XP_038945023   ⟸   XM_039089095
- Peptide Label: isoform X1
Protein Domains
HNF-p1   Homeobox   POU-specific atypical

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P15257-F1-model_v2 AlphaFold P15257 1-628 view protein structure


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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3828 AgrOrtholog
BioCyc Gene G2FUF-18970 BioCyc
Ensembl Genes ENSRNOG00000001183 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000001565 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000001565 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH UniProtKB/Swiss-Prot
  Homeodomain-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  lambda repressor-like DNA-binding domains UniProtKB/TrEMBL
InterPro HNF-1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HNF-1_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HNF-1_POU UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HNF1_dimer_N_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HNF1a_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HNF1b_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HNF_P1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Lambda_DNA-bd_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24817 UniProtKB/Swiss-Prot
  PTHR11568 UniProtKB/Swiss-Prot
Pfam HNF-1_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HNF-1A_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HNF-1B_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Hnf1a PhenoGen
PROSITE HNF_P1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HOMEOBOX_1 UniProtKB/Swiss-Prot
  HOMEOBOX_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  POU_4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART HOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP Dimerization cofactor of HNF-1 alpha UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
  lambda repressor-like DNA-binding domains UniProtKB/TrEMBL
  SSF100957 UniProtKB/Swiss-Prot
  SSF46689 UniProtKB/Swiss-Prot
  SSF47413 UniProtKB/Swiss-Prot
TIGR TC233597

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