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

Gene ID: 84382, updated on 2-Nov-2024

Summary

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Official Symbol
Tcf4provided by RGD
Official Full Name
transcription factor 4provided by RGD
Primary source
RGD:69271
See related
EnsemblRapid: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; Lynch syndrome; and Pitt-Hopkins syndrome. Orthologous to human TCF4 (transcription factor 4). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Heart (RPKM 220.1), Brain (RPKM 214.5) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Tcf4 in Genome Data Viewer
Location:
18q12.1
Exon count:
29
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 18 NC_086036.1 (65216840..65563186)
RS_2023_06 previous assembly 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_086036.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC108348808 Neighboring gene uncharacterized LOC108348809 Neighboring gene uncharacterized LOC134482985 Neighboring gene coiled-coil domain containing 68

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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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Related articles in PubMed

  1. Upregulation of transcription factor 4 downregulates Na(V)1.8 expression in DRG neurons and prevents the development of rat inflammatory and neuropathic hypersensitivity. Li N, et al. Exp Neurol, 2020 May. PMID 32045596
  2. The Intellectual Disability and Schizophrenia Associated Transcription Factor TCF4 Is Regulated by Neuronal Activity and Protein Kinase A. Sepp M, et al. J Neurosci, 2017 Oct 25. PMID 28951451, Free PMC Article
  3. Role of the basic helix-loop-helix protein ITF2 in the hormonal regulation of Sertoli cell differentiation. Muir T, et al. Mol Reprod Dev, 2006 Apr. PMID 16425294
  4. 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. Liu X, et al. Cell Mol Neurobiol, 2016 Aug. PMID 27090258
  5. TCF4 Mediates the Maintenance of Neuropathic Pain Through Wnt/β-Catenin Signaling Following Peripheral Nerve Injury in Rats. Xu Z, et al. J Mol Neurosci, 2015 Jun. PMID 25963533

See all (32) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Functional consequences of TCF4 missense substitutions associated with Pitt-Hopkins syndrome, mild intellectual disability, and schizophrenia.
    Title: Functional consequences of TCF4 missense substitutions associated with Pitt-Hopkins syndrome, mild intellectual disability, and schizophrenia.
  2. Upregulation of transcription factor 4 downregulates NaV1.8 expression in DRG neurons and prevents the development of rat inflammatory and neuropathic hypersensitivity.
    Title: Upregulation of transcription factor 4 downregulates Na(V)1.8 expression in DRG neurons and prevents the development of rat inflammatory and neuropathic hypersensitivity.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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

Pathways from PubChem

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General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
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 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
  
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
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
  
enables RNA polymerase II transcription 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 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 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 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 DNA-templated transcription 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 protein-DNA complex assembly ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within regulation of DNA-templated transcription 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
  
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 ISO
Inferred from Sequence Orthology
more info
  
located_in chromatin IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in chromatin ISO
Inferred from Sequence Orthology
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
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
  
part_of transcription regulator complex ISO
Inferred from Sequence Orthology
more info
  

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.

mRNA and Protein(s)

  1. NM_053369.2 → NP_445821.2  transcription factor 4

    Status: PROVISIONAL

    Source sequence(s)
    JAXUCZ010000018
    UniProtKB/TrEMBL
    A0A0G2JWU7
    Related
    ENSRNOP00000070021.2, ENSRNOT00000081797.3
    Conserved Domains (2) summary
    COG5422
    Location:81 → 295
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:555 → 639
    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: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086036.1 Reference GRCr8

    Range
    65216840..65563186
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_063277625.1 → XP_063133695.1  transcription factor 4 isoform X13

  2. XM_063277624.1 → XP_063133694.1  transcription factor 4 isoform X12

  3. XM_039097159.2 → XP_038953087.1  transcription factor 4 isoform X1

    UniProtKB/TrEMBL
    A0A0G2JWU7, A6IXY6, F1LQ90
    Related
    ENSRNOP00000106951.1, ENSRNOT00000126184.1
    Conserved Domains (2) summary
    COG5422
    Location:135 → 296
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:560 → 644
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins

  4. XM_039097169.2 → XP_038953097.1  transcription factor 4 isoform X10

    UniProtKB/Swiss-Prot
    Q62655, Q99N33
    UniProtKB/TrEMBL
    A6IXY7
    Conserved Domains (2) summary
    COG5422
    Location:111 → 272
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:536 → 620
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins

  5. XM_063277623.1 → XP_063133693.1  transcription factor 4 isoform X11

  6. XM_063277626.1 → XP_063133696.1  transcription factor 4 isoform X14

  7. XM_039097157.2 → XP_038953085.1  transcription factor 4 isoform X1

    UniProtKB/TrEMBL
    A0A0G2JWU7, A6IXY6, F1LQ90
    Conserved Domains (2) summary
    COG5422
    Location:135 → 296
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:560 → 644
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins

  8. XM_063277622.1 → XP_063133692.1  transcription factor 4 isoform X10

    UniProtKB/TrEMBL
    A6IXY7

  9. XM_063277621.1 → XP_063133691.1  transcription factor 4 isoform X9

  10. XM_063277618.1 → XP_063133688.1  transcription factor 4 isoform X6

  11. XM_063277617.1 → XP_063133687.1  transcription factor 4 isoform X5

  12. XM_063277615.1 → XP_063133685.1  transcription factor 4 isoform X3

  13. XM_063277616.1 → XP_063133686.1  transcription factor 4 isoform X4

  14. XM_063277620.1 → XP_063133690.1  transcription factor 4 isoform X8

  15. XM_039097158.2 → XP_038953086.1  transcription factor 4 isoform X1

    UniProtKB/TrEMBL
    A0A0G2JWU7, A6IXY6, F1LQ90
    Conserved Domains (2) summary
    COG5422
    Location:135 → 296
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:560 → 644
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins

  16. XM_063277619.1 → XP_063133689.1  transcription factor 4 isoform X7

  17. XM_063277614.1 → XP_063133684.1  transcription factor 4 isoform X2

  18. XM_039097170.2 → XP_038953098.1  transcription factor 4 isoform X10

    UniProtKB/Swiss-Prot
    Q62655, Q99N33
    UniProtKB/TrEMBL
    A6IXY7
    Conserved Domains (2) summary
    COG5422
    Location:111 → 272
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:536 → 620
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins

  19. XM_039097160.2 → XP_038953088.1  transcription factor 4 isoform X1

    UniProtKB/TrEMBL
    A0A0G2JWU7, A6IXY6, F1LQ90
    Conserved Domains (2) summary
    COG5422
    Location:135 → 296
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:560 → 644
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins

  20. XM_039097177.2 → XP_038953105.2  transcription factor 4 isoform X19

    UniProtKB/TrEMBL
    A6IXY8
    Related
    ENSRNOP00000020431.9, ENSRNOT00000020431.9

  21. XM_039097173.2 → XP_038953101.1  transcription factor 4 isoform X15

    UniProtKB/Swiss-Prot
    Q62655, Q99N33
    Related
    ENSRNOP00000096285.2, ENSRNOT00000114956.2
    Conserved Domains (2) summary
    COG5422
    Location:65 → 226
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:490 → 574
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins

  22. XM_063277627.1 → XP_063133697.1  transcription factor 4 isoform X17

  23. XM_039097174.2 → XP_038953102.1  transcription factor 4 isoform X16

    UniProtKB/Swiss-Prot
    Q62655, Q99N33
    Conserved Domains (2) summary
    COG5422
    Location:64 → 225
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:489 → 573
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins

  24. XM_039097176.2 → XP_038953104.1  transcription factor 4 isoform X18

    UniProtKB/Swiss-Prot
    Q62655, Q99N33
    Conserved Domains (2) summary
    COG5422
    Location:64 → 225
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:485 → 569
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins

  25. XM_063277628.1 → XP_063133698.1  transcription factor 4 isoform X20

  26. XM_039097184.2 → XP_038953112.1  transcription factor 4 isoform X19

    UniProtKB/TrEMBL
    A0A0G2JXN5, A6IXY8
    Conserved Domains (2) summary
    COG5422
    Location:6 → 167
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:431 → 515
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins

  27. XM_039097185.2 → XP_038953113.1  transcription factor 4 isoform X19

    UniProtKB/TrEMBL
    A0A0G2JXN5, A6IXY8
    Related
    ENSRNOP00000070343.3, ENSRNOT00000080844.3
    Conserved Domains (2) summary
    COG5422
    Location:6 → 167
    ROM1; RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]
    cd18945
    Location:431 → 515
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins

  28. XM_063277629.1 → XP_063133699.1  transcription factor 4 isoform X20

  29. XM_039097186.2 → XP_038953114.1  transcription factor 4 isoform X21

    UniProtKB/TrEMBL
    A0A8I6A561, A0A8I6GLJ0, A6IXY9
    Related
    ENSRNOP00000099053.1, ENSRNOT00000144722.1
    Conserved Domains (1) summary
    cd18945
    Location:401 → 485
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins

  30. XM_039097189.2 → XP_038953117.1  transcription factor 4 isoform X24

    UniProtKB/TrEMBL
    A0A8I6A561
    Related
    ENSRNOP00000087117.1, ENSRNOT00000118039.2
    Conserved Domains (1) summary
    cd18945
    Location:397 → 481
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins

  31. XM_039097187.2 → XP_038953115.1  transcription factor 4 isoform X23

    UniProtKB/TrEMBL
    A0A8I6A561
    Conserved Domains (1) summary
    cd18945
    Location:400 → 484
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins

  32. XM_063277630.1 → XP_063133700.1  transcription factor 4 isoform X25

  33. XM_039097188.2 → XP_038953116.1  transcription factor 4 isoform X22

    UniProtKB/TrEMBL
    A0A8I6A561
    Conserved Domains (1) summary
    cd18945
    Location:400 → 484
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins

  34. XM_039097190.2 → XP_038953118.1  transcription factor 4 isoform X26

    UniProtKB/TrEMBL
    A0A8I6A561
    Conserved Domains (1) summary
    cd18945
    Location:396 → 480
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins

  35. XM_063277631.1 → XP_063133701.1  transcription factor 4 isoform X27

  36. XM_039097191.2 → XP_038953119.1  transcription factor 4 isoform X28

    UniProtKB/TrEMBL
    A0A8I6A561
    Conserved Domains (1) summary
    cd18945
    Location:345 → 429
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q62655.2 GenPept UniProtKB/Swiss-Prot:Q62655

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