Hnf1a (HNF1 homeobox A) - Rat Genome Database

Send us a Message

Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Hnf1a (HNF1 homeobox A) Mus musculus
Symbol: Hnf1a
Name: HNF1 homeobox A
RGD ID: 11397
Description: Enables several functions, including RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; identical protein binding activity; and protein dimerization activity. Involved in several processes, including glucose homeostasis; glucose transmembrane transport; and positive regulation of DNA-templated transcription. Acts upstream of or within several processes, including embryonic morphogenesis; lipid transport; and monocarboxylic acid biosynthetic process. Located in cytoplasm; photoreceptor outer segment; and pronucleus. Part of transcription regulator complex. Is expressed in several structures, including extraembryonic component; genitourinary system; gut; septum transversum hepatic component; and spleen. Used to study maturity-onset diabetes of the young type 3; phenylketonuria; and type 2 diabetes mellitus. 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).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: AI323641; hepatocyte nuclear factor 1; hepatocyte nuclear factor 1-alpha; HNF; Hnf-; Hnf-1; HNF-1-alpha; HNF-1A; HNF1; HNF1-; HNF1-alpha; HNF1[; HNF1[a]; Hnf1alpha; LFB; LFB1; liver-specific transcription factor LF-B1; Tcf-1; Tcf1; transcription factor 1
RGD Orthologs
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
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
JBrowse: View Region in Genome Browser (JBrowse)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-isolariciresinol  (ISO)
1,2-dimethylhydrazine  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (EXP)
2,2',5,5'-tetrachlorobiphenyl  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (ISO)
2,6-di-tert-butyl-4-methylphenol  (EXP)
5-aza-2'-deoxycytidine  (ISO)
5-azacytidine  (ISO)
5-fluorouracil  (ISO)
acetylsalicylic acid  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (ISO)
ammonium chloride  (ISO)
amphetamine  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
Aroclor 1254  (ISO)
baicalin  (EXP,ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
butanal  (ISO)
Butylbenzyl phthalate  (ISO)
butyric acid  (ISO)
caffeine  (ISO)
cannabidiol  (ISO)
carbamazepine  (ISO)
carmustine  (ISO)
cisplatin  (ISO)
D-glucose  (ISO)
dexamethasone  (ISO)
dextran sulfate  (EXP)
dibutyl phthalate  (ISO)
diclofenac  (ISO)
diethylstilbestrol  (ISO)
dioxygen  (EXP,ISO)
dipentyl phthalate  (ISO)
epoxiconazole  (EXP)
ethanol  (EXP,ISO)
folic acid  (EXP)
genistein  (EXP)
gentamycin  (ISO)
glucose  (ISO)
lipopolysaccharide  (EXP,ISO)
lithocholic acid  (ISO)
LY294002  (ISO)
mercury atom  (ISO)
mercury(0)  (ISO)
methapyrilene  (ISO)
methidathion  (EXP)
N-acetylsphingosine  (ISO)
N-nitrosodiethylamine  (ISO)
Nonylphenol  (ISO)
ochratoxin A  (ISO)
oleanolic acid  (EXP)
oltipraz  (ISO)
ozone  (ISO)
paracetamol  (ISO)
PCB138  (EXP)
perfluorooctanoic acid  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
propanal  (ISO)
prothioconazole  (ISO)
Ptaquiloside  (EXP)
resveratrol  (ISO)
salvianolic acid B  (ISO)
senecionine  (EXP)
silicon dioxide  (ISO)
simvastatin  (EXP)
sodium arsenite  (EXP,ISO)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (ISO)
thymoquinone  (ISO)
titanium dioxide  (EXP)
trichloroethene  (ISO)
trimellitic anhydride  (EXP)
triptonide  (EXP)
urethane  (ISO)
ursodeoxycholic acid  (ISO)
valproic acid  (EXP,ISO)
zinc atom  (EXP)
zinc(0)  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

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

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
abnormal circulating amino acid level  (IAGP)
abnormal energy homeostasis  (IAGP)
abnormal hepatocyte morphology  (IAGP)
abnormal liver morphology  (IAGP)
abnormal pancreatic islet morphology  (IAGP)
abnormal renal glucose reabsorption  (IAGP)
abnormal reproductive system morphology  (IAGP)
abnormal sexual interaction  (IAGP)
abnormal spermatogenesis  (IAGP)
abnormal stomach glandular epithelium morphology  (IAGP)
abnormal urine calcium level  (IAGP)
abnormal urine homeostasis  (IAGP)
absent subcutaneous adipose tissue  (IAGP)
aminoaciduria  (IAGP)
argininuria  (IAGP)
cachexia  (IAGP)
decreased body size  (IAGP)
decreased body weight  (IAGP)
decreased bone mineral density  (IAGP)
decreased circulating insulin level  (IAGP)
decreased circulating insulin-like growth factor I level  (IAGP)
decreased creatinine clearance  (IAGP)
decreased insulin secretion  (IAGP)
decreased liver function  (IAGP)
decreased pancreas weight  (IAGP)
decreased pancreatic beta cell mass  (IAGP)
decreased pancreatic beta cell number  (IAGP)
decreased renal glomerular filtration rate  (IAGP)
enlarged liver  (IAGP)
hepatic steatosis  (IAGP)
hyperglycemia  (IAGP)
increased cholesterol level  (IAGP)
increased circulating alanine transaminase level  (IAGP)
increased circulating ammonia level  (IAGP)
increased circulating aspartate transaminase level  (IAGP)
increased circulating bilirubin level  (IAGP)
increased circulating cholesterol level  (IAGP)
increased circulating glucose level  (IAGP)
increased circulating growth hormone level  (IAGP)
increased hepatocyte proliferation  (IAGP)
increased liver weight  (IAGP)
increased urine glucose level  (IAGP)
increased urine phosphate level  (IAGP)
increased urine uric acid level  (IAGP)
infertility  (IAGP)
jaundice  (IAGP)
muscular atrophy  (IAGP)
oroticaciduria  (IAGP)
polyphagia  (IAGP)
polyuria  (IAGP)
postnatal growth retardation  (IAGP)
premature death  (IAGP)
prenatal lethality, incomplete penetrance  (IAGP)
small pancreatic islets  (IAGP)

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. 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.
10. Hepatocyte nuclear factor 1 and hypertensive nephropathy. Dmitrieva RI, etal., Hypertension. 2008 Jun;51(6):1583-9. Epub 2008 Apr 28.
11. 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.
12. Cytokine-independent repression of rodent Ntcp in obstructive cholestasis. Geier A, etal., Hepatology. 2005 Mar;41(3):470-7. doi: 10.1002/hep.20594.
13. 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.
14. 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.
15. 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.
16. Wnt signalling and its impact on development and cancer. Klaus A and Birchmeier W, Nat Rev Cancer. 2008 May;8(5):387-98.
17. 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.
18. 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.
19. 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.
20. 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.
21. Characterization of a cofactor that regulates dimerization of a mammalian homeodomain protein. Mendel DB, etal., Science 1991 Dec 20;254(5039):1762-7.
22. Electronic Transfer of Homolog Data MGD and Homologene mouse data transfer
23. MGDs mouse GO annotations MGD data from the GO Consortium
25. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
26. 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.
27. 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.
28. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
29. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
30. 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.
31. Mouse MP Annotation Import Pipeline RGD automated import pipeline
32. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
33. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
34. 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.
35. 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.
36. 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.
37. 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.
38. Evidence of impaired adipogenesis in insulin resistance. Yang X, etal., Biochem Biophys Res Commun. 2004 May 14;317(4):1045-51.
39. The epimorphin gene is highly conserved among humans, mice, and rats and maps to human chromosome 7, mouse chromosome 5, and rat chromosome 12. Zha H, etal., Genomics 1996 Nov 1;37(3):386-9.
40. 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:1284028   PMID:1354855   PMID:1363228   PMID:1387105   PMID:1535333   PMID:1617216   PMID:1685890   PMID:1685988   PMID:1707031   PMID:2044952   PMID:2263635   PMID:2264930  
PMID:7692743   PMID:7914432   PMID:8052626   PMID:8325367   PMID:8330635   PMID:8598044   PMID:8639776   PMID:9077551   PMID:9119393   PMID:9168903   PMID:9313764   PMID:9321462  
PMID:9420335   PMID:9502734   PMID:9551868   PMID:9566924   PMID:9593777   PMID:9609100   PMID:9689059   PMID:9733737   PMID:10049364   PMID:10205167   PMID:10349636   PMID:10352021  
PMID:10559638   PMID:10617683   PMID:10772805   PMID:10852923   PMID:10866673   PMID:11002334   PMID:11027604   PMID:11042159   PMID:11076861   PMID:11106484   PMID:11121425   PMID:11217851  
PMID:11269503   PMID:11279518   PMID:11287626   PMID:11679424   PMID:11733582   PMID:11756330   PMID:11904435   PMID:11934848   PMID:12011081   PMID:12060663   PMID:12189445   PMID:12367519  
PMID:12466851   PMID:12475773   PMID:12477932   PMID:12529398   PMID:12606287   PMID:12837760   PMID:12860991   PMID:14570708   PMID:14599559   PMID:14610273   PMID:14656222   PMID:14993241  
PMID:15005571   PMID:15014077   PMID:15067314   PMID:15142986   PMID:15159395   PMID:15182178   PMID:15355796   PMID:15561929   PMID:15581617   PMID:15618518   PMID:15647252   PMID:15793583  
PMID:15866165   PMID:16103155   PMID:16141072   PMID:16141073   PMID:16223943   PMID:16274963   PMID:16330323   PMID:16330324   PMID:16380477   PMID:16469839   PMID:16498401   PMID:16873682  
PMID:16912278   PMID:17033837   PMID:17183527   PMID:17272516   PMID:17448459   PMID:17724432   PMID:17785413   PMID:17805472   PMID:17855651   PMID:17923767   PMID:17996499   PMID:18028902  
PMID:18029548   PMID:18038450   PMID:18287559   PMID:18356246   PMID:18492944   PMID:18497863   PMID:18505824   PMID:18583462   PMID:18722179   PMID:18778483   PMID:18799693   PMID:18803630  
PMID:19048126   PMID:19174539   PMID:19181415   PMID:19188435   PMID:19246514   PMID:19289501   PMID:19303461   PMID:19304666   PMID:19376774   PMID:19487809   PMID:19737917   PMID:19924231  
PMID:20059953   PMID:20211142   PMID:20235219   PMID:20388655   PMID:20412781   PMID:20523905   PMID:20555317   PMID:20808783   PMID:20810608   PMID:20842632   PMID:20943816   PMID:20979532  
PMID:21176092   PMID:21193557   PMID:21267068   PMID:21628466   PMID:21731673   PMID:21784843   PMID:21873635   PMID:21887698   PMID:21948943   PMID:22166339   PMID:22383952   PMID:22554936  
PMID:22589549   PMID:22780989   PMID:22877752   PMID:22988430   PMID:23362349   PMID:23500137   PMID:23761103   PMID:24038112   PMID:24389307   PMID:24427299   PMID:24449835   PMID:24952961  
PMID:25652089   PMID:25979074   PMID:26015543   PMID:26332085   PMID:26779601   PMID:26800876   PMID:26856890   PMID:26901059   PMID:27083284   PMID:27591083   PMID:27820600   PMID:28465351  
PMID:28547778   PMID:28838957   PMID:29109103   PMID:29463648   PMID:29712641   PMID:30555544   PMID:30575739   PMID:31223625   PMID:31300510   PMID:31868807   PMID:31970666   PMID:32154941  
PMID:32561878   PMID:32711050   PMID:33372138   PMID:33527355   PMID:33737325   PMID:34599818   PMID:35273595   PMID:35460694   PMID:36202974   PMID:36614058   PMID:37219942   PMID:37440709  
PMID:37524711   PMID:37730861  


Comparative Map Data
(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
(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
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
GRCr81247,299,171 - 47,333,457 (+)NCBIGRCr8
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
(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_mPanPan1-v210129,049,056 - 129,071,348 (+)NCBINHGRI_mPanPan1-v2
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 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
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
664 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1455
Count of miRNA genes:602
Interacting mature miRNAs:736
Transcripts:ENSMUST00000031535, ENSMUST00000176550, ENSMUST00000176911, ENSMUST00000184027
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
11341716Rvfs3_mRift Valley fever susceptibility 3 (mouse)526441234138455402Mouse
4142064Tmc1m4_mTmc1 modifier 4 (mouse)Not determined554500177127001072Mouse
26884395Humsd2_mhumerus midshaft diameter 2, 10 week (mouse)570057343132528839Mouse
27226719Tibw6_mtibia width 6, proximal, 16 week (mouse)572857343139985755Mouse
25314315Mlh1fc4_mMLH1 foci count 4 (mouse)574460661132528839Mouse
13506928Recrq8_mrecombination rate in male meiosis QTL 8 (mouse)574460661132528839Mouse
1357431Cia27_mcollagen induced arthritis 27 (mouse)Not determined575315348120018629Mouse
10401245Bglu18_mblood glucose level 18 (mouse)Not determined582838468116838597Mouse
13464242Ahl17_mage related hearing loss, early onset 17 (mouse)582838468116838597Mouse
10043958Chldq12_mcholesterol and HDL QTL 12 (mouse)Not determined587386871121387065Mouse
1301126Bwem1_mbody weight day 30 males 1 (mouse)Not determined587386871121387065Mouse
13464241Ahl18_mage related hearing loss, early onset 18 (mouse)587386871121387065Mouse
1300801Drb2_mdopamine receptor binding 2 (mouse)Not determined587386871121387065Mouse
1301399Cpfd3_mcerebellum pattern fissures (mouse)Not determined587386871121387065Mouse
1357725Eae39_mexperimental allergic encephalomyelitis 39 (mouse)Not determined589418876118864028Mouse
1300968Skts4_mskin tumor susceptibility 4 (mouse)Not determined589418876124238239Mouse
1301362Prnr1_mprion resistance 1 (mouse)Not determined589418876146787935Mouse
11049562Lmr24f_mleishmaniasis resistance 24f (mouse)590320962124321041Mouse
1301457Cfsw2_mcystic fibrosis survival to weaning 2 (mouse)Not determined590561006124561151Mouse
1300993Hycdc_mhypercapnic duty cycle (mouse)Not determined590561006124561151Mouse
9587780Afw16_mabdominal fat weight QTL 16 (mouse)Not determined592830166126830285Mouse
1301974Chab7_mcholesterol absorption 7 (mouse)Not determined595233214129233330Mouse
1357644Egrd1_mearly growth rate, direct effect 1 (mouse)Not determined595434580129434786Mouse
10402486Dipa1_mdrug induced psychomotor activation 1 (mouse)Not determined595465549129465722Mouse
13464244Ahl19_mage related hearing loss, early onset 19 (mouse)595465549129465722Mouse
1558774Lith17_mlithogenic gene 17 (mouse)Not determined595465549129465722Mouse
1300940Actd3_mactivity-distance traveled 3 (mouse)Not determined596320385130320533Mouse
1300659Pcd8ts1_mp-glycoprotein positive CD8 T cell subset 1 (mouse)Not determined597021753131021986Mouse
1301858Smdq1_msegregation of mitochondrial DNA QTL 1 (mouse)Not determined597021753131021986Mouse
1301042Elmaz1_melevated maze behavior 1 (mouse)Not determined598019649116876624Mouse
4141519Hmtb5_mhemostasis and thrombosis bleeding time 5 (mouse)Not determined99949422126882944Mouse
12904945Tammq2_mtibialis anterior muscle mass QTL 2 (mouse)5100665965134665965Mouse
12904959Smmq1_msoleus muscle mass QTL 1 (mouse)5100665965134665965Mouse
12859290Criq2_mCitrobacter rodentium infection QTL 2 (mouse)5101332579135332579Mouse
1301624Aevm2_mautoimmune extremity vasculitis in MRL mice 2 (mouse)Not determined5101863832135864028Mouse
14746986Manh58_mmandible shape 58 (mouse)5102446283136446283Mouse
11532736Sluc33b_msusceptibility to lung cancer 33b (mouse)5102945037136945196Mouse
25314310Syncl4_msynaptonemal complex length 4 (mouse)5103047866115538059Mouse
11528550Sluc33_msusceptibility to lung cancer 33 (mouse)5104386871120711986Mouse
1357886Diht_mdopamine-induced hypothermia (mouse)Not determined5104498738115101540Mouse
10412202Bbaa26_mB.burgdorferi-associated arthritis 26 (mouse)Not determined5104583688138555455Mouse
10412239Alpq7_malcohol preference QTL 7 (mouse)Not determined5104705939138705939Mouse
10043890Trigq4_mtriglyceride QTL 4 (mouse)Not determined5107906299141906412Mouse
4142473Chlq11_mcirculating hormone level QTL 11 (mouse)Not determined5107906299141906412Mouse
13464243Ahl20_mage related hearing loss, early onset 20 (mouse)5107906299141906412Mouse
4141139Hmtb4_mhemostasis and thrombosis rebleeding time 4 (mouse)Not determined108762509126882944Mouse
10412197Bbaa25_mB.burgdorferi-associated arthritis 25 (mouse)Not determined5109167240143167381Mouse
13464251Ahl21_mage related hearing loss, early onset 21 (mouse)5109167240143167381Mouse
1301543Hypch_mhypercholesterolemia (mouse)Not determined5109238624139118905Mouse
1300913Bwefm_mbody weight females and males day 10 (mouse)Not determined5109439348143439459Mouse
4141652Mrdq2_mmodifier of retinal degeneration QTL 2 (mouse)Not determined110253106118093673Mouse
1301102Cia14_mcollagen induced arthritis 14 (mouse)Not determined5113320385138555455Mouse
1357662Lprq4_mlipoprotein QTL 4 (mouse)Not determined5114021753129632606Mouse

Markers in Region
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm385114,949,250 - 114,949,372UniSTSGRCm38
MGSCv375115,399,259 - 115,399,381UniSTSGRCm37
Celera5112,044,095 - 112,044,217UniSTS
Cytogenetic Map5FUniSTS
cM Map565.0UniSTS
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm385114,970,871 - 114,970,986UniSTSGRCm38
MGSCv375115,420,880 - 115,420,995UniSTSGRCm37
Celera5112,067,137 - 112,067,252UniSTS
Cytogenetic Map5FUniSTS
cM Map565.0UniSTS
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm385114,949,251 - 114,949,413UniSTSGRCm38
MGSCv375115,399,260 - 115,399,422UniSTSGRCm37
Celera5112,044,096 - 112,044,258UniSTS
Cytogenetic Map5FUniSTS
cM Map565.0UniSTS
Whitehead_YAC5 UniSTS
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm385114,963,169 - 114,963,481UniSTSGRCm38
MGSCv375115,413,178 - 115,413,490UniSTSGRCm37
Celera5112,059,434 - 112,059,750UniSTS
Cytogenetic Map5FUniSTS
cM Map562.0UniSTS
Whitehead Genetic548.1UniSTS
Whitehead_YAC5 UniSTS
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm385114,970,719 - 114,970,995UniSTSGRCm38
MGSCv375115,420,728 - 115,421,004UniSTSGRCm37
Celera5112,066,985 - 112,067,261UniSTS
Cytogenetic Map5FUniSTS
cM Map565.0UniSTS
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm385114,970,432 - 114,971,033UniSTSGRCm38
MGSCv375115,420,441 - 115,421,042UniSTSGRCm37
Celera5112,066,698 - 112,067,299UniSTS
Cytogenetic Map5FUniSTS
cM Map565.0UniSTS
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm385114,970,432 - 114,970,626UniSTSGRCm38
MGSCv375115,420,441 - 115,420,635UniSTSGRCm37
Celera5112,066,698 - 112,066,892UniSTS
Cytogenetic Map5FUniSTS
cM Map565.0UniSTS
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map5FUniSTS
cM Map565.0UniSTS
Mouse AssemblyChrPosition (strand)SourceJBrowse
MGSCv375115,398,874 - 115,399,076UniSTSGRCm37
MGSCv375115,405,431 - 115,405,909UniSTSGRCm37
Celera5112,043,710 - 112,043,912UniSTS
Celera5112,050,287 - 112,050,765UniSTS
Cytogenetic Map5FUniSTS
cM Map565.0UniSTS
cM Map565.0UniSTS
cM Map565.0UniSTS
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm385114,948,865 - 114,949,067UniSTSGRCm38
MGSCv375115,398,874 - 115,399,076UniSTSGRCm37
Celera5112,043,710 - 112,043,912UniSTS
Cytogenetic Map5FUniSTS
cM Map565.0UniSTS
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm385114,955,422 - 114,955,900UniSTSGRCm38
MGSCv375115,405,431 - 115,405,909UniSTSGRCm37
Celera5112,050,287 - 112,050,765UniSTS
Cytogenetic Map5FUniSTS
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map5FUniSTS



RefSeq Acc Id: ENSMUST00000031535   ⟹   ENSMUSP00000031535
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl5115,087,039 - 115,109,126 (-)Ensembl
GRCm38.p6 Ensembl5114,948,980 - 114,971,067 (-)Ensembl
RefSeq Acc Id: ENSMUST00000176550   ⟹   ENSMUSP00000135678
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl5115,090,638 - 115,108,903 (-)Ensembl
GRCm38.p6 Ensembl5114,952,579 - 114,970,844 (-)Ensembl
RefSeq Acc Id: ENSMUST00000176911   ⟹   ENSMUSP00000135539
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl5115,088,120 - 115,108,903 (-)Ensembl
GRCm38.p6 Ensembl5114,950,061 - 114,970,844 (-)Ensembl
RefSeq Acc Id: ENSMUST00000184027
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl5115,106,764 - 115,109,153 (-)Ensembl
GRCm38.p6 Ensembl5114,968,705 - 114,971,094 (-)Ensembl
RefSeq Acc Id: NM_009327   ⟹   NP_033353
RefSeq Status: VALIDATED
Mouse AssemblyChrPosition (strand)Source
GRCm395115,087,039 - 115,109,121 (-)NCBI
GRCm385114,948,980 - 114,971,062 (-)ENTREZGENE
MGSCv375115,398,989 - 115,421,071 (-)RGD
Celera5112,043,825 - 112,067,328 (-)RGD
RefSeq Acc Id: XM_011248192   ⟹   XP_011246494
Mouse AssemblyChrPosition (strand)Source
GRCm395115,087,039 - 115,102,779 (-)NCBI
GRCm385114,948,980 - 114,964,720 (-)NCBI
RefSeq Acc Id: NP_033353   ⟸   NM_009327
- UniProtKB: E9QP86 (UniProtKB/Swiss-Prot),   P22361 (UniProtKB/Swiss-Prot),   Q66JY7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_011246494   ⟸   XM_011248192
- Peptide Label: isoform X1
- UniProtKB: Q66JY7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000031535   ⟸   ENSMUST00000031535
RefSeq Acc Id: ENSMUSP00000135539   ⟸   ENSMUST00000176911
RefSeq Acc Id: ENSMUSP00000135678   ⟸   ENSMUST00000176550
Protein Domains
HNF-p1   Homeobox   POU-specific atypical

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P22361-F1-model_v2 AlphaFold P22361 1-628 view protein structure

RGD ID:6887714
Promoter ID:EPDNEW_M7308
Type:initiation region
Description:Mus musculus HNF1 homeobox A , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database,
Experiment Methods:Single-end sequencing.
Mouse AssemblyChrPosition (strand)Source
GRCm385114,971,073 - 114,971,133EPDNEW
RGD ID:6837708
Promoter ID:MM_KWN:43616
SO ACC ID:SO:0000170
Tissues & Cell Lines:BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   Kidney,   Liver,   Lung
Mouse AssemblyChrPosition (strand)Source
MGSCv365115,399,341 - 115,400,697 (-)MPROMDB
RGD ID:6837705
Promoter ID:MM_KWN:43619
SO ACC ID:SO:0000170
Tissues & Cell Lines:ES_Cell,   Kidney,   Liver
Mouse AssemblyChrPosition (strand)Source
MGSCv365115,420,714 - 115,421,214 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:98504 AgrOrtholog
Ensembl Genes ENSMUSG00000029556 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000031535 ENTREZGENE
  ENSMUST00000031535.12 UniProtKB/Swiss-Prot
  ENSMUST00000176550.2 UniProtKB/TrEMBL
  ENSMUST00000176911.8 UniProtKB/TrEMBL
Gene3D-CATH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/Swiss-Prot, 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 mmu:21405 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR11568 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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 SSF100957 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF46689 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF47413 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt Secondary E9QP86 UniProtKB/Swiss-Prot