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

Gene ID: 25640, updated on 30-Sep-2021

Summary

Official Symbol
Hnf1bprovided by RGD
Official Full Name
HNF1 homeobox Bprovided by RGD
Primary source
RGD:3830
See related
EnsemblRapid:ENSRNOG00000002598
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
transcription factor specific to the liver; member of the homeobox-containing basic helix-turn-helix family [RGD, Feb 2006]
Expression
Biased expression in Kidney (RPKM 244.8), Lung (RPKM 21.6) and 1 other tissue See more
Orthologs
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Genomic context

See Hnf1b in Genome Data Viewer
Location:
10q26
Exon count:
9
Annotation release Status Assembly Chr Location
108 current 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_051345.1Genomic Context describing neighboring genes Neighboring gene WAP four-disulfide core domain 21 Neighboring gene HEAT repeat containing 6 Neighboring gene DExD-box helicase 52 Neighboring gene synergin, gamma

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

General gene information

Markers

Homology

Clone Names

  • MGC93549

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 
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
PubMed 
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 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
PubMed 
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 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
 
Process Evidence Code Pubs
acts_upstream_of_or_within Notch signaling pathway ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within anterior/posterior pattern specification ISO
Inferred from Sequence Orthology
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 
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
 
acts_upstream_of_or_within endodermal cell fate specification ISO
Inferred from Sequence Orthology
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 
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 
acts_upstream_of_or_within hindbrain development ISO
Inferred from Sequence Orthology
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
 
involved_in liver development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within liver development ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within mesonephric duct development ISO
Inferred from Sequence Orthology
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
 
acts_upstream_of_or_within negative regulation of mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis ISO
Inferred from Sequence Orthology
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
 
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 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 from RNA polymerase II promoter ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within positive regulation of transcription, DNA-templated ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of transcription, DNA-templated ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
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 
acts_upstream_of_or_within regulation of Wnt signaling pathway ISO
Inferred from Sequence Orthology
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 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
PubMed 
involved_in regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
involved_in response to carbohydrate IEP
Inferred from Expression Pattern
more info
PubMed 
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 
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
PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus IEA
Inferred from Electronic Annotation
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 
located_in nucleus TAS
Traceable Author Statement
more info
PubMed 
part_of transcription regulator complex ISO
Inferred from Sequence Orthology
more info
 

General protein information

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)

  1. NM_001308148.1NP_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)
    JACYVU010000220
    UniProtKB/TrEMBL
    A1EC66
    Related
    ENSRNOP00000046025.5, ENSRNOT00000047427.6
    Conserved Domains (3) summary
    cd00086
    Location:232305
    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:314551
    HNF-1B_C; Hepatocyte nuclear factor 1 (HNF-1), beta isoform C-terminus
    pfam04814
    Location:8174
    HNF-1_N; Hepatocyte nuclear factor 1 (HNF-1), N-terminus
  2. NM_001308149.1NP_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)
    JACYVU010000220
    UniProtKB/TrEMBL
    A1EC67
    Conserved Domains (3) summary
    cd00086
    Location:206279
    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:288525
    HNF-1B_C; Hepatocyte nuclear factor 1 (HNF-1), beta isoform C-terminus
    pfam04814
    Location:8174
    HNF-1_N; Hepatocyte nuclear factor 1 (HNF-1), N-terminus
  3. NM_013103.2NP_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)
    JACYVU010000220
    UniProtKB/Swiss-Prot
    P23899
    Conserved Domains (3) summary
    cd00086
    Location:232305
    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:314550
    HNF-1B_C; Hepatocyte nuclear factor 1 (HNF-1), beta isoform C-terminus
    pfam04814
    Location:8174
    HNF-1_N; Hepatocyte nuclear factor 1 (HNF-1), N-terminus

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 108 details...Open this link in a new tab

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

Reference mRatBN7.2 Primary Assembly

Genomic

  1. NC_051345.1 Reference mRatBN7.2 Primary Assembly

    Range
    68735894..68789888
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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