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Hnf1b HNF1 homeobox B [ Mus musculus (house mouse) ]

Gene ID: 21410, updated on 8-Feb-2024

Summary

Official Symbol
Hnf1bprovided by MGI
Official Full Name
HNF1 homeobox Bprovided by MGI
Primary source
MGI:MGI:98505
See related
Ensembl:ENSMUSG00000020679 AllianceGenome:MGI:98505
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
LFB3; Tcf2; Tcf-2; vHNF1; HNF-1B; Hnf1beta; HNF-1Beta; 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. Acts upstream of or within several processes, including negative regulation of mesenchymal cell apoptotic process; regulation of transcription by RNA polymerase II; and tube morphogenesis. Located in nucleus. Part of transcription regulator complex. Is expressed in several structures, including central nervous system; early conceptus; genitourinary system; gut; and sensory organ. 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 adult (RPKM 51.9), colon adult (RPKM 15.8) and 11 other tissues See more
Orthologs
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Genomic context

See Hnf1b in Genome Data Viewer
Location:
11 C; 11 51.23 cM
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (83741035..83796743)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (83850209..83905917)

Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene COMM domain containing 9 pseudogene Neighboring gene predicted gene, 38934 Neighboring gene STARR-positive B cell enhancer ABC_E8436 Neighboring gene predicted gene 12576 Neighboring gene STARR-positive B cell enhancer ABC_E3983 Neighboring gene STARR-positive B cell enhancer ABC_E7031 Neighboring gene STARR-seq mESC enhancer starr_30206 Neighboring gene STARR-seq mESC enhancer starr_30207 Neighboring gene predicted gene, 51869 Neighboring gene STARR-positive B cell enhancer ABC_E5256 Neighboring gene DExD box helicase 52 Neighboring gene STARR-positive B cell enhancer ABC_E11769 Neighboring gene synergin, gamma Neighboring gene STARR-positive B cell enhancer mm9_chr11:83845520-83845821

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (7)  1 citation
  • Endonuclease-mediated (2) 

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

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 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 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
 
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 binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein homodimerization activity ISO
Inferred from Sequence Orthology
more info
 
enables protein-containing complex binding ISO
Inferred from Sequence Orthology
more info
 
enables sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables transcription cis-regulatory region binding IDA
Inferred from Direct Assay
more info
PubMed 
enables transcription coregulator binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
acts_upstream_of_or_within Notch signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within anterior/posterior pattern specification IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of apoptotic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within branching morphogenesis of an epithelial tube IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in circadian regulation of gene expression ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within embryonic digestive tract morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in embryonic morphogenesis ISO
Inferred from Sequence Orthology
more info
 
involved_in endocrine pancreas development ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within endoderm development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within endoderm formation ISO
Inferred from Sequence Orthology
more info
PubMed 
acts_upstream_of_or_within endodermal cell fate specification IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within epithelial cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within epithelium development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in genitalia development ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within hepatoblast differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within hindbrain development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within inner cell mass cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within insulin secretion IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within kidney development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in kidney development ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within kidney morphogenesis IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within liver development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of mesenchymal cell apoptotic process involved in metanephros development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within mesonephric duct development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within mesonephric duct formation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within mesonephric tubule development IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within negative regulation of apoptotic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within negative regulation of mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within negative regulation of mesenchymal cell apoptotic process involved in metanephros development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within nephric duct development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within nephric duct formation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in pancreas development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within positive regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within positive regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within 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 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
 
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 ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within regulation of Wnt signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within regulation of branch elongation involved in ureteric bud branching IMP
Inferred from Mutant Phenotype
more info
PubMed 
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 regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within response to glucose IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within ureteric bud elongation IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
located_in intracellular membrane-bounded organelle ISO
Inferred from Sequence Orthology
more info
 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
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
 
part_of transcription regulator complex IPI
Inferred from Physical Interaction
more info
PubMed 

General protein information

Preferred Names
hepatocyte nuclear factor 1-beta
Names
homeoprotein LFB3
transcription factor 2

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_001291268.1NP_001278197.1  hepatocyte nuclear factor 1-beta isoform 2

    See identical proteins and their annotated locations for NP_001278197.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the central coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
    Source sequence(s)
    AK004837, AK019258, AV140806
    Consensus CDS
    CCDS70271.1
    UniProtKB/Swiss-Prot
    P27889
    Related
    ENSMUSP00000103749.3, ENSMUST00000108114.9
    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:8173
    HNF-1_N; Hepatocyte nuclear factor 1 (HNF-1), N terminus
  2. NM_001291269.1NP_001278198.1  hepatocyte nuclear factor 1-beta isoform 3

    See identical proteins and their annotated locations for NP_001278198.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) contains an alternate 5'-terminal exon, lacks part of the 5' coding region, and uses a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AK004837, AK019258, AL669868, AV140806
    Consensus CDS
    CCDS70272.1
    UniProtKB/Swiss-Prot
    P27889
    Related
    ENSMUSP00000103748.2, ENSMUST00000108113.3
    Conserved Domains (3) summary
    cd00086
    Location:109182
    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:191428
    HNF-1B_C; Hepatocyte nuclear factor 1 (HNF-1), beta isoform C-terminus
    pfam04814
    Location:151
    HNF-1_N; Hepatocyte nuclear factor 1 (HNF-1), N-terminus
  3. NM_009330.3NP_033356.2  hepatocyte nuclear factor 1-beta isoform 1

    See identical proteins and their annotated locations for NP_033356.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AK004837, AK019258, AV140806
    Consensus CDS
    CCDS25179.1
    UniProtKB/Swiss-Prot
    P27889, Q5NC37, Q8R162, Q9CS26, Q9R1W1, Q9R1W2, Q9WTL5, Q9WTL6
    Related
    ENSMUSP00000021016.3, ENSMUST00000021016.10
    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:8173
    HNF-1_N; Hepatocyte nuclear factor 1 (HNF-1), N terminus

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000077.7 Reference GRCm39 C57BL/6J

    Range
    83741035..83796743
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006532794.3XP_006532857.1  hepatocyte nuclear factor 1-beta isoform X3

    Conserved Domains (3) summary
    cd00086
    Location:120193
    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:202439
    HNF-1B_C; Hepatocyte nuclear factor 1 (HNF-1), beta isoform C-terminus
    pfam04814
    Location:162
    HNF-1_N; Hepatocyte nuclear factor 1 (HNF-1), N-terminus
  2. XM_006532791.4XP_006532854.1  hepatocyte nuclear factor 1-beta isoform X1

    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
  3. XM_006532793.4XP_006532856.1  hepatocyte nuclear factor 1-beta isoform X2

    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:288524
    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
  4. XM_006532796.4XP_006532859.1  hepatocyte nuclear factor 1-beta isoform X4

    See identical proteins and their annotated locations for XP_006532859.1

    UniProtKB/Swiss-Prot
    P27889
    Conserved Domains (3) summary
    cd00086
    Location:109182
    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:191428
    HNF-1B_C; Hepatocyte nuclear factor 1 (HNF-1), beta isoform C-terminus
    pfam04814
    Location:151
    HNF-1_N; Hepatocyte nuclear factor 1 (HNF-1), N-terminus