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

    Gene ID: 25640, updated on 25-Nov-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
    NEW
    Try the new Gene table
    Try the new Transcript table

    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
     
    enables transcription coregulator 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)

    NEW Try the new Transcript table

    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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