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

Gene ID: 84382, updated on 25-Jan-2022

Summary

Official Symbol
Tcf4provided by RGD
Official Full Name
transcription factor 4provided by RGD
Primary source
RGD:69271
See related
Ensembl:ENSRNOG00000012405 AllianceGenome:RGD:69271
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
Enables bHLH transcription factor binding activity and double-stranded DNA binding activity. Involved in positive regulation of transcription by RNA polymerase II. Predicted to be located in chromatin and nucleus. Predicted to be part of beta-catenin-TCF7L2 complex. Human ortholog(s) of this gene implicated in Fuchs' endothelial dystrophy and Pitt-Hopkins syndrome. Orthologous to human TCF4 (transcription factor 4). [provided by Alliance of Genome Resources, Nov 2021]
Expression
Biased expression in Heart (RPKM 220.1), Brain (RPKM 214.5) and 9 other tissues See more
Orthologs
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Genomic context

See Tcf4 in Genome Data Viewer
Location:
18q12.1
Exon count:
29
Annotation release Status Assembly Chr Location
108 current mRatBN7.2 (GCF_015227675.2) 18 NC_051353.1 (62941739..63288126)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 18 NC_005117.4 (65285320..65507983)

Chromosome 18 - NC_051353.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC108348808 Neighboring gene uncharacterized LOC108348809 Neighboring gene coiled-coil domain containing 68 Neighboring gene RAB27B, member RAS oncogene family

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?

Pathways from PubChem

General gene information

Markers

Homology

Gene Ontology Provided by RGD

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

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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.

mRNA and Protein(s)

  1. NM_053369.2NP_445821.2  transcription factor 4

    Status: PROVISIONAL

    Source sequence(s)
    JACYVU010000301
    Related
    ENSRNOP00000070021.2, ENSRNOT00000081797.2
    Conserved Domains (2) summary
    COG5422
    Location:81295
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:555639
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins

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_051353.1 Reference mRatBN7.2 Primary Assembly

    Range
    62941739..63288126
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039097159.1XP_038953087.1  transcription factor 4 isoform X1

    Conserved Domains (2) summary
    COG5422
    Location:135296
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:560644
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  2. XM_039097169.1XP_038953097.1  transcription factor 4 isoform X9

    Conserved Domains (2) summary
    COG5422
    Location:111272
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:536620
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  3. XM_039097181.1XP_038953109.1  transcription factor 4 isoform X18

    Conserved Domains (2) summary
    COG5422
    Location:27188
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:452536
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  4. XM_039097178.1XP_038953106.1  transcription factor 4 isoform X16

    Conserved Domains (2) summary
    COG5422
    Location:58219
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:483567
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  5. XM_039097183.1XP_038953111.1  transcription factor 4 isoform X20

    Conserved Domains (1) summary
    COG5422
    Location:135296
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
  6. XM_039097168.1XP_038953096.1  transcription factor 4 isoform X8

    Conserved Domains (2) summary
    COG5422
    Location:81296
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:555639
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  7. XM_039097165.1XP_038953093.1  transcription factor 4 isoform X5

    Conserved Domains (2) summary
    COG5422
    Location:135296
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:558642
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  8. XM_039097166.1XP_038953094.1  transcription factor 4 isoform X6

    Conserved Domains (2) summary
    COG5422
    Location:81296
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:556640
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  9. XM_039097163.1XP_038953091.1  transcription factor 4 isoform X3

    Conserved Domains (2) summary
    COG5422
    Location:135296
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:559643
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  10. XM_039097164.1XP_038953092.1  transcription factor 4 isoform X4

    Conserved Domains (2) summary
    COG5422
    Location:135296
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:559643
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  11. XM_039097162.1XP_038953090.1  transcription factor 4 isoform X2

    Conserved Domains (2) summary
    COG5422
    Location:81295
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:559643
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  12. XM_039097167.1XP_038953095.1  transcription factor 4 isoform X7

    Conserved Domains (2) summary
    COG5422
    Location:81295
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:555639
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  13. XM_039097157.1XP_038953085.1  transcription factor 4 isoform X1

    Conserved Domains (2) summary
    COG5422
    Location:135296
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:560644
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  14. XM_039097172.1XP_038953100.1  transcription factor 4 isoform X11

    Conserved Domains (2) summary
    COG5422
    Location:81242
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:506590
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  15. XM_039097171.1XP_038953099.1  transcription factor 4 isoform X10

    Conserved Domains (2) summary
    COG5422
    Location:82243
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:507591
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  16. XM_039097161.1XP_038953089.1  transcription factor 4 isoform X1

    Conserved Domains (2) summary
    COG5422
    Location:135296
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:560644
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  17. XM_039097158.1XP_038953086.1  transcription factor 4 isoform X1

    Conserved Domains (2) summary
    COG5422
    Location:135296
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:560644
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  18. XM_039097170.1XP_038953098.1  transcription factor 4 isoform X9

    Conserved Domains (2) summary
    COG5422
    Location:111272
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:536620
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  19. XM_039097179.1XP_038953107.1  transcription factor 4 isoform X16

    Conserved Domains (2) summary
    COG5422
    Location:58219
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:483567
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  20. XM_039097160.1XP_038953088.1  transcription factor 4 isoform X1

    Related
    ENSRNOP00000020431.8, ENSRNOT00000020431.8
    Conserved Domains (2) summary
    COG5422
    Location:135296
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:560644
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  21. XM_039097177.1XP_038953105.1  transcription factor 4 isoform X15

    Conserved Domains (2) summary
    COG5422
    Location:59220
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:484568
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  22. XM_039097180.1XP_038953108.1  transcription factor 4 isoform X17

    Conserved Domains (2) summary
    COG5422
    Location:58219
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:483567
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  23. XM_039097173.1XP_038953101.1  transcription factor 4 isoform X12

    Conserved Domains (2) summary
    COG5422
    Location:65226
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:490574
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  24. XM_039097174.1XP_038953102.1  transcription factor 4 isoform X13

    Conserved Domains (2) summary
    COG5422
    Location:64225
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:489573
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  25. XM_039097176.1XP_038953104.1  transcription factor 4 isoform X14

    Conserved Domains (2) summary
    COG5422
    Location:64225
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:485569
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  26. XM_039097184.1XP_038953112.1  transcription factor 4 isoform X21

    Conserved Domains (2) summary
    COG5422
    Location:6167
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:431515
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  27. XM_039097185.1XP_038953113.1  transcription factor 4 isoform X21

    Related
    ENSRNOP00000070343.2, ENSRNOT00000080844.2
    Conserved Domains (2) summary
    COG5422
    Location:6167
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:431515
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  28. XM_039097182.1XP_038953110.1  transcription factor 4 isoform X19

    Conserved Domains (2) summary
    COG5422
    Location:20181
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:445529
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  29. XM_039097190.1XP_038953118.1  transcription factor 4 isoform X26

    Conserved Domains (1) summary
    cd18945
    Location:396480
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  30. XM_039097187.1XP_038953115.1  transcription factor 4 isoform X23

    Conserved Domains (1) summary
    cd18945
    Location:400484
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  31. XM_039097188.1XP_038953116.1  transcription factor 4 isoform X24

    Conserved Domains (1) summary
    cd18945
    Location:400484
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  32. XM_039097189.1XP_038953117.1  transcription factor 4 isoform X25

    Related
    ENSRNOP00000087117.1, ENSRNOT00000118039.1
    Conserved Domains (1) summary
    cd18945
    Location:397481
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  33. XM_039097186.1XP_038953114.1  transcription factor 4 isoform X22

    Related
    ENSRNOP00000096285.1, ENSRNOT00000114956.1
    Conserved Domains (1) summary
    cd18945
    Location:401485
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  34. XM_039097191.1XP_038953119.1  transcription factor 4 isoform X27

    Conserved Domains (1) summary
    cd18945
    Location:345429
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
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