Format

Send to:

Choose Destination

Foxa1 forkhead box A1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 25098, updated on 18-Apr-2019

Summary

Official Symbol
Foxa1provided by RGD
Official Full Name
forkhead box A1provided by RGD
Primary source
RGD:2807
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
Hnf3a
Summary
may act as a transcription factor for hepatocyte specific gene expression [RGD, Feb 2006]
Annotation information
Annotation category: partial on reference assembly
Expression
Biased expression in Liver (RPKM 36.6), Lung (RPKM 18.7) and 1 other tissue See more
Orthologs

Genomic context

See Foxa1 in Genome Data Viewer
Location:
6q23
Exon count:
4
Annotation release Status Assembly Chr Location
106 current Rnor_6.0 (GCF_000001895.5) 6 NC_005105.4 (78516579..78549669, complement)
104 previous assembly Rnor_5.0 (GCF_000001895.4) 6 NC_005105.3 (88041150..88074240, complement)

Chromosome 6 - NC_005105.4Genomic Context describing neighboring genes Neighboring gene solute carrier family 25 member 21 Neighboring gene uncharacterized LOC102552151 Neighboring gene ribose-phosphate pyrophosphokinase I -like Neighboring gene mirror-image polydactyly 1 Neighboring gene uncharacterized LOC102553136 Neighboring gene transcription elongation factor B (SIII), polypeptide 1 Neighboring gene similar to C14orf25 protein Neighboring gene similar to 40S ribosomal protein S6

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

General gene information

Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
DNA binding ISO
Inferred from Sequence Orthology
more info
PubMed 
DNA-binding transcription activator activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription activator activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
 
DNA-binding transcription activator activity, RNA polymerase II-specific ISO
Inferred from Sequence Orthology
more info
PubMed 
DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription factor activity ISO
Inferred from Sequence Orthology
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
double-stranded DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
protein domain specific binding IDA
Inferred from Direct Assay
more info
PubMed 
protein domain specific binding IEA
Inferred from Electronic Annotation
more info
 
sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
PubMed 
transcription factor binding IEA
Inferred from Electronic Annotation
more info
 
transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription regulatory region DNA binding IEA
Inferred from Electronic Annotation
more info
 
transcription regulatory region DNA binding ISO
Inferred from Sequence Orthology
more info
PubMed 
Process Evidence Code Pubs
Notch signaling pathway IEA
Inferred from Electronic Annotation
more info
 
Notch signaling pathway ISO
Inferred from Sequence Orthology
more info
PubMed 
alveolar secondary septum development IEA
Inferred from Electronic Annotation
more info
 
alveolar secondary septum development ISO
Inferred from Sequence Orthology
more info
PubMed 
anatomical structure formation involved in morphogenesis IEA
Inferred from Electronic Annotation
more info
 
anatomical structure formation involved in morphogenesis ISO
Inferred from Sequence Orthology
more info
PubMed 
anatomical structure morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chromatin organization IEA
Inferred from Electronic Annotation
more info
 
chromatin remodeling IEA
Inferred from Electronic Annotation
more info
 
chromatin remodeling ISO
Inferred from Sequence Orthology
more info
PubMed 
connective tissue development ISO
Inferred from Sequence Orthology
more info
PubMed 
dorsal/ventral neural tube patterning IEA
Inferred from Electronic Annotation
more info
 
dorsal/ventral neural tube patterning ISO
Inferred from Sequence Orthology
more info
PubMed 
epithelial cell maturation involved in prostate gland development IEA
Inferred from Electronic Annotation
more info
 
epithelial cell maturation involved in prostate gland development ISO
Inferred from Sequence Orthology
more info
PubMed 
epithelial tube branching involved in lung morphogenesis IEA
Inferred from Electronic Annotation
more info
 
epithelial tube branching involved in lung morphogenesis ISO
Inferred from Sequence Orthology
more info
PubMed 
epithelial-mesenchymal signaling involved in prostate gland development IEA
Inferred from Electronic Annotation
more info
 
epithelial-mesenchymal signaling involved in prostate gland development ISO
Inferred from Sequence Orthology
more info
PubMed 
glucose homeostasis IEA
Inferred from Electronic Annotation
more info
 
glucose homeostasis ISO
Inferred from Sequence Orthology
more info
PubMed 
hormone metabolic process IEA
Inferred from Electronic Annotation
more info
 
hormone metabolic process ISO
Inferred from Sequence Orthology
more info
PubMed 
lung development ISO
Inferred from Sequence Orthology
more info
PubMed 
lung epithelial cell differentiation IEA
Inferred from Electronic Annotation
more info
 
lung epithelial cell differentiation ISO
Inferred from Sequence Orthology
more info
PubMed 
lung morphogenesis ISO
Inferred from Sequence Orthology
more info
PubMed 
multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of epithelial to mesenchymal transition IEA
Inferred from Electronic Annotation
more info
 
negative regulation of epithelial to mesenchymal transition ISO
Inferred from Sequence Orthology
more info
PubMed 
negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
PubMed 
negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
PubMed 
neuron fate specification IEA
Inferred from Electronic Annotation
more info
 
neuron fate specification ISO
Inferred from Sequence Orthology
more info
PubMed 
positive regulation of DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
more info
 
positive regulation of DNA-binding transcription factor activity ISO
Inferred from Sequence Orthology
more info
PubMed 
positive regulation of apoptotic process IEA
Inferred from Electronic Annotation
more info
 
positive regulation of apoptotic process ISO
Inferred from Sequence Orthology
more info
PubMed 
positive regulation of intracellular estrogen receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
positive regulation of intracellular estrogen receptor signaling pathway ISO
Inferred from Sequence Orthology
more info
PubMed 
positive regulation of mitotic cell cycle IEA
Inferred from Electronic Annotation
more info
 
positive regulation of mitotic cell cycle ISO
Inferred from Sequence Orthology
more info
PubMed 
positive regulation of neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of neuron differentiation ISO
Inferred from Sequence Orthology
more info
PubMed 
positive regulation of smoothened signaling pathway IEA
Inferred from Electronic Annotation
more info
 
positive regulation of smoothened signaling pathway ISO
Inferred from Sequence Orthology
more info
PubMed 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
PubMed 
prostate gland epithelium morphogenesis IEA
Inferred from Electronic Annotation
more info
 
prostate gland epithelium morphogenesis ISO
Inferred from Sequence Orthology
more info
PubMed 
prostate gland stromal morphogenesis IEA
Inferred from Electronic Annotation
more info
 
prostate gland stromal morphogenesis ISO
Inferred from Sequence Orthology
more info
PubMed 
regulation of cell cycle ISO
Inferred from Sequence Orthology
more info
PubMed 
regulation of gene expression ISO
Inferred from Sequence Orthology
more info
PubMed 
regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
PubMed 
respiratory basal cell differentiation IEA
Inferred from Electronic Annotation
more info
 
respiratory basal cell differentiation ISO
Inferred from Sequence Orthology
more info
PubMed 
response to estradiol IEA
Inferred from Electronic Annotation
more info
 
response to estradiol ISO
Inferred from Sequence Orthology
more info
PubMed 
secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development IEA
Inferred from Electronic Annotation
more info
 
secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development ISO
Inferred from Sequence Orthology
more info
PubMed 
tube morphogenesis ISO
Inferred from Sequence Orthology
more info
PubMed 
Component Evidence Code Pubs
fibrillar center IEA
Inferred from Electronic Annotation
more info
 
fibrillar center ISO
Inferred from Sequence Orthology
more info
 
microvillus IEA
Inferred from Electronic Annotation
more info
 
microvillus ISO
Inferred from Sequence Orthology
more info
PubMed 
nucleoplasm IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus ISO
Inferred from Sequence Orthology
more info
PubMed 

General protein information

Preferred Names
hepatocyte nuclear factor 3-alpha
Names
HNF-3-alpha
HNF-3A
forkhead box protein A1

NCBI Reference Sequences (RefSeq)

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_012742.1NP_036874.1  hepatocyte nuclear factor 3-alpha

    See identical proteins and their annotated locations for NP_036874.1

    Status: PROVISIONAL

    Source sequence(s)
    X55955
    UniProtKB/Swiss-Prot
    P23512
    Conserved Domains (3) summary
    smart00339
    Location:170258
    FH; FORKHEAD
    pfam08430
    Location:17169
    Forkhead_N; Forkhead N-terminal region
    pfam09354
    Location:392455
    HNF_C; HNF3 C-terminal domain

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

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

Reference Rnor_6.0 Primary Assembly

Genomic

  1. NC_005105.4 Reference Rnor_6.0 Primary Assembly

    Range
    78516579..78549669 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate Rn_Celera

Genomic

  1. AC_000074.1 Alternate Rn_Celera

    Range
    73899792..73932602 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Support Center