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

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: human mouse all

Genomic context

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)
106	current	Rn_Celera (GCF_000002265.2)	18	AC_000086.1 (61145273..61368542)
104	previous assembly	Rnor_5.0 (GCF_000001895.4)	18	NC_005117.3 (64471373..64694036)

Chromosome 18 - NC_005117.4 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

TCF4-controlled transcription in primary cortical neurons is induced by neuronal activity and protein kinase A.
Title: The Intellectual Disability and Schizophrenia Associated Transcription Factor TCF4 Is Regulated by Neuronal Activity and Protein Kinase A.
TCF4 might promote neuronal apoptosis and microglial proliferation after traumatic brain injury
Title: T-cell factor (TCF/LEF1) binding elements (TBEs) of FasL (Fas ligand or CD95 ligand) bind and cluster Fas (CD95) and form complexes with the TCF-4 and b-catenin transcription factors in vitro and in vivo which result in triggering cell death and/or cell activation.
expression of Prx1 and Tcf4 is decreased in the developing diaphragm in the nitrofen-induced congenital diaphragmatic hernia in Sprague- Dawley rats animal model.
Title: Expression of Prx1 and Tcf4 is decreased in the diaphragmatic muscle connective tissue of nitrofen-induced congenital diaphragmatic hernia.
TCF4 is a regulator of neuronal intrinsic excitability in part by repression of Kcnq1 and Scn10a.
Title: Psychiatric Risk Gene Transcription Factor 4 Regulates Intrinsic Excitability of Prefrontal Neurons via Repression of SCN10a and KCNQ1.
Chronic constriction injury induced persistent TCF4 upregulation in the dorsal root ganglion and spinal cord.
Title: TCF4 Mediates the Maintenance of Neuropathic Pain Through Wnt/β-Catenin Signaling Following Peripheral Nerve Injury in Rats.
ITF2/Tcf4 enhances follicle-stimulating hormone activity by suppressing the actions of the inhibitors of differentiation (ID)transcription factor proteins and increasing the actions of stimulatory basic helix-loop-helix proteins in Sertoli cells.
Title: Role of the basic helix-loop-helix protein ITF2 in the hormonal regulation of Sertoli cell differentiation.

Submit: New GeneRIF Correction

Variation

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General gene information

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Markers

BE120385 (e-PCR)
- UniSTS:247319

AW534410 (e-PCR)
- UniSTS:246576

D18Rat87 (e-PCR), detects polymorphism
- UniSTS:226955

BE108561 (e-PCR)
- UniSTS:261777

d18arb7 (e-PCR)
- UniSTS:121272

BE116587 (e-PCR)
- UniSTS:248508

RH142887 (e-PCR)
- UniSTS:232134

STS-Z40794 (e-PCR)
- UniSTS:30957

Homology

Homologs of the Tcf4 gene: The Tcf4 gene is conserved in human, Rhesus monkey, dog, cow, mouse, and frog.
Orthologs from Annotation Pipeline: 265 organisms have orthologs with human gene Tcf4
Orthologs

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	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	IBA Inferred from Biological aspect of Ancestor more info	PubMed
DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info	PubMed
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	PubMed
E-box binding	IEA Inferred from Electronic Annotation more info
E-box binding	ISO Inferred from Sequence Orthology more info	PubMed
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	PubMed
TFIIB-class transcription factor binding	IEA Inferred from Electronic Annotation more info
TFIIB-class transcription factor binding	ISO Inferred from Sequence Orthology more info	PubMed
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	PubMed
double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
identical protein binding	ISO Inferred from Sequence Orthology more info	PubMed
protein C-terminus binding	ISO Inferred from Sequence Orthology more info	PubMed
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	PubMed
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	PubMed
transcription corepressor activity	IEA Inferred from Electronic Annotation more info
transcription corepressor activity	ISO Inferred from Sequence Orthology more info	PubMed

Process	Evidence Code	Pubs
DNA-templated transcription, initiation	ISO Inferred from Sequence Orthology more info	PubMed
endothelial cell activation	IEA Inferred from Electronic Annotation more info
endothelial cell activation	ISO Inferred from Sequence Orthology more info	PubMed
negative regulation of angiogenesis	IEA Inferred from Electronic Annotation more info
negative regulation of angiogenesis	ISO Inferred from Sequence Orthology more info	PubMed
negative regulation of gene expression	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	ISO Inferred from Sequence Orthology more info	PubMed
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	PubMed
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	PubMed
positive regulation of transcription, DNA-templated	ISO Inferred from Sequence Orthology more info	PubMed
protein-DNA complex assembly	IEA Inferred from Electronic Annotation more info
protein-DNA complex assembly	ISO Inferred from Sequence Orthology more info	PubMed
regulation of transcription, DNA-templated	ISO Inferred from Sequence Orthology more info	PubMed
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	PubMed
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	PubMed

Component	Evidence Code	Pubs
beta-catenin-TCF complex	ISO Inferred from Sequence Orthology more info	PubMed
beta-catenin-TCF7L2 complex	ISO Inferred from Sequence Orthology more info	PubMed
nuclear chromatin	ISO Inferred from Sequence Orthology more info	PubMed
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	PubMed
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	PubMed

General protein information

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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)

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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.