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Tcf4 transcription factor 4 [ Rattus norvegicus (Norway rat) ]

Gene ID: 84382, updated on 18-Nov-2018

Summary

Official Symbol
Tcf4provided by RGD
Official Full Name
transcription factor 4provided by RGD
Primary source
RGD:69271
See related
Ensembl:ENSRNOG00000012405
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
Summary
transcription factor that acts as an enhancer of the rat tyrosine hydroxylase gene [RGD, Feb 2006]
Annotation information
Annotation category: partial on reference assembly
Expression
Biased expression in Heart (RPKM 220.1), Brain (RPKM 214.5) and 9 other tissues See more
Orthologs

Genomic context

See Tcf4 in Genome Data Viewer
Location:
18q12.1
Exon count:
17
Annotation release Status Assembly Chr Location
106 current Rnor_6.0 (GCF_000001895.5) 18 NC_005117.4 (65285320..65507983)
104 previous assembly Rnor_5.0 (GCF_000001895.4) 18 NC_005117.3 (64471373..64694036)

Chromosome 18 - NC_005117.4Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC108348809 Neighboring gene uncharacterized LOC102548128 Neighboring gene uncharacterized LOC103694237 Neighboring gene DNA polymerase iota

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 FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Wnt Signaling Pathway NetPath, organism-specific biosystem (from WikiPathways)
    Wnt Signaling Pathway NetPath, organism-specific biosystemWnt family of proteins are a large family of cysteine-rich secreted glycoproteins that regulate cell-cell interactions. They bind to members of the Frizzled family of 7 transmembrane receptors. Bindi...

General gene information

Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
DNA binding ISO
Inferred from Sequence Orthology
more info
 
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
 
DNA-binding transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA-binding transcription factor activity ISO
Inferred from Sequence Orthology
more info
 
DNA-binding transcription factor activity NAS
Non-traceable Author Statement
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISO
Inferred from Sequence Orthology
more info
 
E-box binding IEA
Inferred from Electronic Annotation
more info
 
E-box binding ISO
Inferred from Sequence Orthology
more info
 
E-box binding ISS
Inferred from Sequence or Structural Similarity
more info
 
RNA polymerase II proximal promoter sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA polymerase II proximal promoter sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
TFIIB-class transcription factor binding IEA
Inferred from Electronic Annotation
more info
 
TFIIB-class transcription factor binding ISO
Inferred from Sequence Orthology
more info
 
bHLH transcription factor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
bHLH transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
chromatin binding IEA
Inferred from Electronic Annotation
more info
 
chromatin binding ISO
Inferred from Sequence Orthology
more info
 
double-stranded DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
identical protein binding ISO
Inferred from Sequence Orthology
more info
 
protein C-terminus binding ISO
Inferred from Sequence Orthology
more info
 
protein dimerization activity IEA
Inferred from Electronic Annotation
more info
 
protein heterodimerization activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein heterodimerization activity IEA
Inferred from Electronic Annotation
more info
 
protein heterodimerization activity ISO
Inferred from Sequence Orthology
more info
 
protein heterodimerization activity ISS
Inferred from Sequence or Structural Similarity
more info
 
protein homodimerization activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein self-association IEA
Inferred from Electronic Annotation
more info
 
protein self-association ISO
Inferred from Sequence Orthology
more info
 
transcription corepressor activity IEA
Inferred from Electronic Annotation
more info
 
transcription corepressor activity ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
DNA-templated transcription, initiation ISO
Inferred from Sequence Orthology
more info
 
endothelial cell activation IEA
Inferred from Electronic Annotation
more info
 
endothelial cell activation ISO
Inferred from Sequence Orthology
more info
 
negative regulation of angiogenesis IEA
Inferred from Electronic Annotation
more info
 
negative regulation of angiogenesis ISO
Inferred from Sequence Orthology
more info
 
negative regulation of gene expression ISO
Inferred from Sequence Orthology
more info
 
negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
positive regulation of neuron differentiation IBA
Inferred from Biological aspect of Ancestor
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
 
positive regulation of neuron differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
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
 
positive regulation of transcription, DNA-templated ISO
Inferred from Sequence Orthology
more info
 
protein-DNA complex assembly IEA
Inferred from Electronic Annotation
more info
 
protein-DNA complex assembly ISO
Inferred from Sequence Orthology
more info
 
regulation of transcription, DNA-templated ISO
Inferred from Sequence Orthology
more info
 
regulation of vascular endothelial growth factor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
regulation of vascular endothelial growth factor signaling pathway ISO
Inferred from Sequence Orthology
more info
 
transcription initiation from RNA polymerase II promoter IEA
Inferred from Electronic Annotation
more info
 
transcription initiation from RNA polymerase II promoter ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
beta-catenin-TCF complex ISO
Inferred from Sequence Orthology
more info
 
beta-catenin-TCF7L2 complex ISO
Inferred from Sequence Orthology
more info
 
nuclear chromatin ISO
Inferred from Sequence Orthology
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IEA
Inferred from Electronic Annotation
more info
 
nucleus ISO
Inferred from Sequence Orthology
more info
 
transcription factor complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription factor complex IEA
Inferred from Electronic Annotation
more info
 
transcription factor complex ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
transcription factor 4
Names
ITF-2
R8f DNA-binding protein
RITF-2
SEF-2
SL3-3 enhancer factor 2
TCF-4
immunoglobulin transcription factor 2

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_053369.1NP_445821.1  transcription factor 4

    See identical proteins and their annotated locations for NP_445821.1

    Status: PROVISIONAL

    Source sequence(s)
    AF149284
    UniProtKB/Swiss-Prot
    Q62655
    Related
    ENSRNOP00000020431.7, ENSRNOT00000020431.7
    Conserved Domains (1) summary
    smart00353
    Location:488541
    HLH; helix loop helix 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_005117.4 Reference Rnor_6.0 Primary Assembly

    Range
    65285320..65507983
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate Rn_Celera

Genomic

  1. AC_000086.1 Alternate Rn_Celera

    Range
    61145273..61368542
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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