Hnf1b HNF1 homeobox B [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Hnf1bprovided by RGD
Official Full Name: HNF1 homeobox Bprovided by RGD
Primary source: RGD:3830
See related: Ensembl:ENSRNOG00000002598 AllianceGenome:RGD:3830
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Tcf2; LF-B3; VHNF1; HNF-1B; HNF-1-beta
Summary: Enables DNA-binding transcription factor activity, RNA polymerase II-specific; cis-regulatory region sequence-specific DNA binding activity; and identical protein binding activity. Involved in several processes, including hepatocyte differentiation; protein-DNA complex assembly; and regulation of gene expression. Located in nucleus. Human ortholog(s) of this gene implicated in kidney disease; maturity-onset diabetes of the young type 5; pancreas disease; renal cell carcinoma; and type 2 diabetes mellitus. Orthologous to human HNF1B (HNF1 homeobox B). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Kidney (RPKM 244.8), Lung (RPKM 21.6) and 1 other tissue See more
Orthologs: human mouse all
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Genomic context

Location:: 10q26

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	10	NC_086028.1 (69233377..69287360)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	10	NC_051345.1 (68735894..68789888)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	10	NC_005109.4 (71159863..71218902)

Chromosome 10 - NC_086028.1 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
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?

HNF-1beta is upregulated after ischemia/reperfusion renal tubule injury in proximal tubular cells in vivo. HNF-1beta controls cellular proliferation and tubule formation by regulating SOCS-3 expression and STAT3 activation
Title: Upregulation of HNF-1β during experimental acute kidney injury plays a crucial role in renal tubule regeneration.
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.
the up-regulation of TCF11/MafG binding could be suppressed by overexpression of the TGF-beta inhibitor Smad7, and a small interfering RNA to TCF11 blocked the suppression of iNOS by TGF-beta.
Title: Negative regulation of inducible nitric-oxide synthase expression mediated through transforming growth factor-beta-dependent modulation of transcription factor TCF11.

Submit: New GeneRIF Correction

General gene information

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Markers

UniSTS:465411 (e-PCR)
- UniSTS:465411

Tcf2 (e-PCR), detects polymorphism
- UniSTS:465411

AI987804 (e-PCR)
- UniSTS:180282

Hnf1b (e-PCR), detects polymorphism
- UniSTS:506980

D11Pas33 (e-PCR), detects polymorphism
- UniSTS:259429

RH71331 (e-PCR)
- UniSTS:13202

Tcf2 (e-PCR), detects polymorphism
- UniSTS:464796

Hnf1b (e-PCR), detects polymorphism
- UniSTS:545949

Tcf2 (e-PCR), detects polymorphism
- UniSTS:463525

D10Chm186 (e-PCR)
- UniSTS:518345

RH141230 (e-PCR)
- UniSTS:223226

Tcf2 (e-PCR), detects polymorphism
- UniSTS:233982

Tcf2 (e-PCR), detects polymorphism
- UniSTS:233983

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA binding	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables DNA binding	TAS Traceable Author Statement more info	PubMed
enables DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables DNA-binding transcription factor activity	TAS Traceable Author Statement more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables protein-containing complex binding	IDA Inferred from Direct Assay more info	PubMed
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 coregulator binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in Notch signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within Notch signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in anterior/posterior pattern specification	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within anterior/posterior pattern specification	ISO Inferred from Sequence Orthology more info
acts_upstream_of apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in branching morphogenesis of an epithelial tube	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within branching morphogenesis of an epithelial tube	ISO Inferred from Sequence Orthology more info
involved_in circadian regulation of gene expression	IDA Inferred from Direct Assay more info	PubMed
involved_in embryonic digestive tract morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within embryonic digestive tract morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in embryonic morphogenesis	IDA Inferred from Direct Assay more info	PubMed
involved_in endocrine pancreas development	ISO Inferred from Sequence Orthology more info
involved_in endocrine pancreas development	ISS Inferred from Sequence or Structural Similarity more info	PubMed
acts_upstream_of_or_within endoderm development	ISO Inferred from Sequence Orthology more info
involved_in endodermal cell fate specification	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within endodermal cell fate specification	ISO Inferred from Sequence Orthology more info
involved_in epithelial cell proliferation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within epithelial cell proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within epithelium development	ISO Inferred from Sequence Orthology more info
involved_in genitalia development	ISO Inferred from Sequence Orthology more info
involved_in genitalia development	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in hepatoblast differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within hepatoblast differentiation	ISO Inferred from Sequence Orthology more info
involved_in hepatocyte differentiation	IEP Inferred from Expression Pattern more info	PubMed
involved_in hindbrain development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within hindbrain development	ISO Inferred from Sequence Orthology more info
involved_in inner cell mass cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within inner cell mass cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in insulin secretion	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within insulin secretion	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within kidney development	ISO Inferred from Sequence Orthology more info
involved_in kidney development	ISO Inferred from Sequence Orthology more info
involved_in kidney development	ISS Inferred from Sequence or Structural Similarity more info	PubMed
acts_upstream_of_or_within kidney morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within liver development	ISO Inferred from Sequence Orthology more info
involved_in mesenchymal cell apoptotic process involved in metanephros development	IEA Inferred from Electronic Annotation more info
acts_upstream_of mesenchymal cell apoptotic process involved in metanephros development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within mesonephric duct development	ISO Inferred from Sequence Orthology more info
involved_in mesonephric duct formation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within mesonephric duct formation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within mesonephric tubule development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of mesenchymal cell apoptotic process involved in metanephros development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of mesenchymal cell apoptotic process involved in metanephros development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within nephric duct development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within nephric duct formation	ISO Inferred from Sequence Orthology more info
involved_in pancreas development	IEA Inferred from Electronic Annotation more info
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	PubMed
involved_in positive regulation of gene expression	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of gene expression	ISO Inferred from Sequence Orthology more info
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	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription initiation by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in pronephric nephron tubule development	IEA Inferred from Electronic Annotation more info
involved_in pronephric nephron tubule development	ISO Inferred from Sequence Orthology more info
involved_in pronephros development	ISO Inferred from Sequence Orthology more info
involved_in protein-DNA complex assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of Wnt signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in regulation of branch elongation involved in ureteric bud branching	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of branch elongation involved in ureteric bud branching	ISO Inferred from Sequence Orthology more info
involved_in regulation of pronephros size	IEA Inferred from Electronic Annotation more info
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
involved_in response to carbohydrate	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to glucose	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within response to glucose	ISO Inferred from Sequence Orthology more info
involved_in response to organic cyclic compound	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to xenobiotic stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in ureteric bud elongation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within ureteric bud elongation	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info	PubMed
part_of transcription regulator complex	IEA Inferred from Electronic Annotation 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-beta

Names: Transcription factor 2, hepatic; variant hepatic nuclear factor 1

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_001308148.1 → NP_001295077.1 hepatocyte nuclear factor 1-beta isoform 1

See identical proteins and their annotated locations for NP_001295077.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

JAXUCZ010000010

UniProtKB/TrEMBL

A1EC66

Related

ENSRNOP00000046025.5, ENSRNOT00000047427.6

Conserved Domains (3) summary

cd00086
Location:232 → 305

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:314 → 551

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

pfam04814
Location:8 → 174

HNF-1_N; Hepatocyte nuclear factor 1 (HNF-1), N-terminus
NM_001308149.1 → NP_001295078.1 hepatocyte nuclear factor 1-beta isoform 3

See identical proteins and their annotated locations for NP_001295078.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) uses an alternate in-frame splice junction in the 5' end compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

JAXUCZ010000010

UniProtKB/TrEMBL

A1EC67

Conserved Domains (3) summary

cd00086
Location:206 → 279

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:288 → 525

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

pfam04814
Location:8 → 174

HNF-1_N; Hepatocyte nuclear factor 1 (HNF-1), N-terminus
NM_013103.2 → NP_037235.1 hepatocyte nuclear factor 1-beta isoform 2

See identical proteins and their annotated locations for NP_037235.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice junction in the 3' end compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is one aa shorter compared to isoform 1.

Source sequence(s)

JAXUCZ010000010

UniProtKB/Swiss-Prot

P23899

Conserved Domains (3) summary

cd00086
Location:232 → 305

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:314 → 550

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

pfam04814
Location:8 → 174

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