Hnf1a HNF1 homeobox A [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Hnf1aprovided by RGD
Official Full Name: HNF1 homeobox Aprovided by RGD
Primary source: RGD:3828
See related: EnsemblRapid:ENSRNOG00000001183 AllianceGenome:RGD:3828
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: HNF1; Lfb1; Tcf1; LF-B1
Summary: Enables DNA binding activity; DNA-binding transcription activator activity, RNA polymerase II-specific; and transcription coactivator binding activity. Involved in several processes, including positive regulation of cell communication; regulation of gene expression; and regulation of phosphate metabolic process. Located in chromatin and nucleus. Part of protein-containing complex. 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). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Kidney (RPKM 154.8), Liver (RPKM 66.8) and 1 other tissue See more
Orthologs: human mouse all
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Genomic context

Location:: 12q16

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	12	NC_086030.1 (47299171..47333457)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	12	NC_051347.1 (41638536..41672806)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	12	NC_005111.4 (47407811..47433342)

Chromosome 12 - NC_086030.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Beneficial impact of epigallocatechingallate on LDL-C through PCSK9/LDLR pathway by blocking HNF1alpha and activating FoxO3a.
Title: Beneficial impact of epigallocatechingallate on LDL-C through PCSK9/LDLR pathway by blocking HNF1α and activating FoxO3a.
HMGB1 Inhibits HNF1A to Modulate Liver Fibrogenesis via p65/miR-146b Signaling.
Title: HMGB1 Inhibits HNF1A to Modulate Liver Fibrogenesis via p65/miR-146b Signaling.
coordinated upregulation of genes encoding CRP, interleukin-6 (IL-6), HNF1alpha, and HNF4alpha in the livers and white adipose tissue (WAT) of chronic renal failure rats, as compared to the pair-fed and control animals.
Title: Hepatocyte nuclear factors as possible C-reactive protein transcriptional inducer in the liver and white adipose tissue of rats with experimental chronic renal failure.
Hnf1alpha gene expression is upregulated in the liver of rats with experimentally induced chronic renal failure, showing an association between circulating PCSK9 and TAGs
Title: Up-regulation of Hnf1α gene expression in the liver of rats with experimentally induced chronic renal failure - A possible link between circulating PCSK9 and triacylglycerol concentrations.
HNF-1alpha, HNF-4alpha and FOXA2 transcriptional factors are involved in diabetes-induced overexpression of Slc2a2 gene in the liver and kidney.
Title: Hepatocyte nuclear factors 1α/4α and forkhead box A2 regulate the solute carrier 2A2 (Slc2a2) gene expression in the liver and kidney of diabetic rats.
De novo synthesis of HNF-1alpha was seen in rat brain, and an increased interaction of HNF-1alpha with p300 and albumin promoter seems to be responsible for overexpression of albumin in ischemic condition.
Title: Hepatocyte nuclear factor-1alpha mediated upregulation of albumin expression in focal ischemic rat brain.
Hepatic nuclear factor 1alpha (HNF1alpha) dysfunction down-regulates X-box-binding protein 1 (XBP1) and sensitizes beta-cells to endoplasmic reticulum stress.
Title: Hepatic nuclear factor 1alpha (HNF1alpha) dysfunction down-regulates X-box-binding protein 1 (XBP1) and sensitizes beta-cells to endoplasmic reticulum stress.
a critical link between HNF1A-MODY-induced alterations in Bmp-3 expression and insulin gene levels
Title: Bone morphogenetic protein 3 controls insulin gene expression and is down-regulated in INS-1 cells inducibly expressing a hepatocyte nuclear factor 1A-maturity-onset diabetes of the young mutation.
Studies suggest that overexpression of DN-HNF1A induces bioenergetic stress and activation of AMPK, and this in turn mediates the transcriptional activation of BMF, coupling prolonged energy stress to apoptosis activation.
Title: 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.
analysis of isoform-specific expression of the human, mouse and rat HNF1A, HNF1B and HNF4A genes
Title: Species-specific differences in the expression of the HNF1A, HNF1B and HNF4A genes.

Submit: New GeneRIF Correction See all GeneRIFs (21)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

TCF1 (e-PCR), detects polymorphism
- UniSTS:258304

Tcf1 (e-PCR), detects polymorphism
- UniSTS:465410

RH141549 (e-PCR)
- UniSTS:223543

RH94688 (e-PCR)
- UniSTS:119935

RH94689 (e-PCR)
- UniSTS:119936

D12Wox22 (e-PCR)
- UniSTS:240259

Hnf1a (e-PCR), detects polymorphism
- UniSTS:545948

D12Mgh11 (e-PCR)
- UniSTS:239828

RH94784 (e-PCR)
- UniSTS:120031

PMC115916P1 (e-PCR)
- UniSTS:270305

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables protein dimerization activity	ISO Inferred from Sequence Orthology more info
enables protein heterodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info
enables transcription cis-regulatory region binding	ISS Inferred from Sequence or Structural Similarity more info
enables transcription coactivator binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription coregulator binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in D-glucose import	ISO Inferred from Sequence Orthology more info
involved_in activation of protein kinase activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in apoptotic nuclear changes	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within bile acid and bile salt transport	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within bile acid biosynthetic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within blastocyst development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within bone resorption	ISO Inferred from Sequence Orthology more info
involved_in cellular response to L-leucine	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to glucose stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to rapamycin	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cholesterol metabolic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within chromatin remodeling	ISO Inferred from Sequence Orthology more info
involved_in chromatin remodeling	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic limb morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within fatty acid biosynthetic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within fatty acid transport	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within glucose homeostasis	ISO Inferred from Sequence Orthology more info
involved_in glucose homeostasis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within heme biosynthetic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within insulin secretion	ISO Inferred from Sequence Orthology more info
involved_in insulin secretion	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within liver development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of cysteine-type endopeptidase activity involved in apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of miRNA processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of peptidyl-threonine phosphorylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in pancreas development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within paraxial mesoderm formation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within placenta development	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of ATP biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of insulin secretion	IEP Inferred from Expression Pattern more info	PubMed
involved_in positive regulation of mitochondrial membrane potential	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein phosphorylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription initiation by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within protein localization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in regulation of NADP metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of Wnt signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of hormone secretion	ISO Inferred from Sequence Orthology more info
NOT involved_in regulation of pronephros size	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in renal D-glucose absorption	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within reproductive structure development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to glucose	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to oxidative stress	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within reverse cholesterol transport	ISO Inferred from Sequence Orthology more info
involved_in transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in chromatin	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in photoreceptor outer segment	ISO Inferred from Sequence Orthology more info
located_in pronucleus	ISO Inferred from Sequence Orthology more info
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info
part_of transcription regulator complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: hepatocyte nuclear factor 1-alpha

Names: HNF-1-alpha; HNF-1A; LF-B1, hepatic nuclear factor (HNF1): albumin proximal factor, also TCF1; TCF-1; Transcription factor 1, hepatic; albumin proximal factor; hepatic nuclear factor 1; hepatic nuclear factor-1-alpha; liver-specific transcription factor LF-B1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_012669.1 → NP_036801.1 hepatocyte nuclear factor 1-alpha

See identical proteins and their annotated locations for NP_036801.1

Status: PROVISIONAL

Source sequence(s)

J03170

UniProtKB/Swiss-Prot

P15257

UniProtKB/TrEMBL

A6J1X4

Related

ENSRNOP00000001565.2, ENSRNOT00000001565.5

Conserved Domains (4) summary

cd00086
Location:200 → 273

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

pfam04812
Location:282 → 538

HNF-1B_C; Hepatocyte nuclear factor 1 (HNF-1), beta isoform C terminus

pfam04813
Location:540 → 627

HNF-1A_C; Hepatocyte nuclear factor 1 (HNF-1), alpha isoform C terminus

pfam04814
Location:8 → 167

HNF-1_N; Hepatocyte nuclear factor 1 (HNF-1), N terminus

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086030.1 Reference GRCr8

Range

47299171..47333457

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039089095.2 → XP_038945023.1 hepatocyte nuclear factor 1-alpha isoform X1

Conserved Domains (4) summary

cd00086
Location:93 → 166

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

pfam04812
Location:175 → 431

HNF-1B_C; Hepatocyte nuclear factor 1 (HNF-1), beta isoform C-terminus

pfam04813
Location:433 → 520

HNF-1A_C; Hepatocyte nuclear factor 1 (HNF-1), alpha isoform C-terminus

pfam04814
Location:1 → 61

HNF-1_N; Hepatocyte nuclear factor 1 (HNF-1), N-terminus