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Tcf3 transcription factor 3 [ Mus musculus (house mouse) ]

Gene ID: 21423, updated on 25-Nov-2021

Summary

Official Symbol
Tcf3provided by MGI
Official Full Name
transcription factor 3provided by MGI
Primary source
MGI:MGI:98510
See related
Ensembl:ENSMUSG00000020167
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
A1; E12; E2A; E47; KA1; ME2; ALF2; Pan1; Pan2; VDIR; TCF-3; Tcfe2a; E12/E47; bHLHb21; AA408400; AW209082
Expression
Ubiquitous expression in thymus adult (RPKM 71.9), spleen adult (RPKM 58.4) and 28 other tissues See more
Orthologs
NEW
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Try the new Transcript table

Genomic context

See Tcf3 in Genome Data Viewer
Location:
10 C1; 10 39.72 cM
Exon count:
21
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 10 NC_000076.7 (80245375..80269814, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (80409541..80433976, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 10 NC_000076.5 (79871910..79896398, complement)

Chromosome 10 - NC_000076.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 30823 Neighboring gene methyl-CpG binding domain protein 3 Neighboring gene ubiquinol-cytochrome c reductase, complex III subunit XI Neighboring gene predicted gene, 40716 Neighboring gene one cut domain, family member 3

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
contributes_to DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables DNA binding ISO
Inferred from Sequence Orthology
more info
 
contributes_to DNA-binding transcription activator activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
PubMed 
enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
PubMed 
enables DNA-binding transcription activator activity, RNA polymerase II-specific IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables DNA-binding transcription activator activity, RNA polymerase II-specific ISO
Inferred from Sequence Orthology
more info
 
enables DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
enables DNA-binding transcription factor activity ISO
Inferred from Sequence Orthology
more info
 
enables DNA-binding transcription factor activity TAS
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 IDA
Inferred from Direct Assay
more info
PubMed 
enables DNA-binding transcription factor binding ISO
Inferred from Sequence Orthology
more info
 
enables DNA-binding transcription repressor activity, RNA polymerase II-specific ISO
Inferred from Sequence Orthology
more info
 
contributes_to E-box binding IDA
Inferred from Direct Assay
more info
PubMed 
enables E-box binding IDA
Inferred from Direct Assay
more info
PubMed 
enables E-box binding IPI
Inferred from Physical Interaction
more info
PubMed 
contributes_to E-box binding ISO
Inferred from Sequence Orthology
more info
 
enables E-box binding ISO
Inferred from Sequence Orthology
more info
 
enables PDZ domain binding ISO
Inferred from Sequence Orthology
more info
 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
contributes_to RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables RNA polymerase II-specific DNA-binding transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables RNA polymerase II-specific DNA-binding transcription factor binding ISO
Inferred from Sequence Orthology
more info
 
enables bHLH transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables bHLH transcription factor binding ISO
Inferred from Sequence Orthology
more info
 
enables chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
enables cis-regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables mitogen-activated protein kinase kinase kinase binding ISO
Inferred from Sequence Orthology
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein dimerization activity IEA
Inferred from Electronic Annotation
more info
 
enables protein heterodimerization activity IDA
Inferred from Direct Assay
more info
PubMed 
enables protein heterodimerization activity ISO
Inferred from Sequence Orthology
more info
 
enables protein homodimerization activity ISO
Inferred from Sequence Orthology
more info
 
enables sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables sequence-specific DNA binding IGI
Inferred from Genetic Interaction
more info
PubMed 
contributes_to transcription cis-regulatory region binding ISO
Inferred from Sequence Orthology
more info
 
enables transmembrane receptor protein tyrosine kinase activator activity IDA
Inferred from Direct Assay
more info
PubMed 
enables vitamin D response element binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
involved_in B cell lineage commitment ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within Peyer's patch development IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within T cell differentiation in thymus IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within cell development IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within cell differentiation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_negative_effect erythrocyte differentiation TAS
Traceable Author Statement
more info
PubMed 
involved_in gastrulation IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within histone H3 acetylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within histone H4 acetylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in immunoglobulin V(D)J recombination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within immunoglobulin V(D)J recombination IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within immunoglobulin V(D)J recombination ISO
Inferred from Sequence Orthology
more info
PubMed 
acts_upstream_of_or_within lymphocyte differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within natural killer cell differentiation IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within nervous system development IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of B cell proliferation ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of DNA-binding transcription factor activity ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of cell cycle ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within positive regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of gene expression ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of neuron differentiation IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within 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 IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
PubMed 
involved_in positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within positive regulation of transcription, DNA-templated IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in positive regulation of transcription, DNA-templated ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within protein stabilization IDA
Inferred from Direct Assay
more info
PubMed 
involved_in regulation of G1/S transition of mitotic cell cycle 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 by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within regulation of transcription, DNA-templated IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within response to lipopolysaccharide IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within response to xenobiotic stimulus IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
part_of RNA polymerase II transcription regulator complex IDA
Inferred from Direct Assay
more info
PubMed 
part_of RNA polymerase II transcription regulator complex ISO
Inferred from Sequence Orthology
more info
 
located_in chromatin ISO
Inferred from Sequence Orthology
more info
 
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in cytosol IDA
Inferred from Direct Assay
more info
PubMed 
located_in euchromatin ISO
Inferred from Sequence Orthology
more info
 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
part_of nucleosome IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 
part_of protein-containing complex 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 IDA
Inferred from Direct Assay
more info
PubMed 
part_of transcription regulator complex IPI
Inferred from Physical Interaction
more info
PubMed 
part_of transcription regulator complex ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
transcription factor E2-alpha
Names
immunoglobulin enhancer-binding factor E12/E47
transcription factor A1
transcription factor E2a

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_001164147.2NP_001157619.1  transcription factor E2-alpha isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC152062
    Consensus CDS
    CCDS48636.1
    UniProtKB/TrEMBL
    E9PWE2
    Related
    ENSMUSP00000100979.2, ENSMUST00000105342.8
    Conserved Domains (2) summary
    smart00353
    Location:554607
    HLH; helix loop helix domain
    cl23750
    Location:487562
    vATP-synt_E; ATP synthase (E/31 kDa) subunit
  2. NM_001164148.2NP_001157620.1  transcription factor E2-alpha isoform 2

    See identical proteins and their annotated locations for NP_001157620.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) has an alternate splice site in the coding region, compared to variant 1. The resulting isoform (2) lacks an internal aa, compared to isoform 1.
    Source sequence(s)
    AC152062
    Consensus CDS
    CCDS48634.1
    UniProtKB/Swiss-Prot
    P15806
    UniProtKB/TrEMBL
    A0A0R4J014
    Related
    ENSMUSP00000020377.7, ENSMUST00000020377.13
    Conserved Domains (2) summary
    smart00353
    Location:553606
    HLH; helix loop helix domain
    cl23750
    Location:486561
    vATP-synt_E; ATP synthase (E/31 kDa) subunit
  3. NM_001164149.2NP_001157621.1  transcription factor E2-alpha isoform 3

    See identical proteins and their annotated locations for NP_001157621.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) has two alternate splice sites in the coding region, compared to variant 1. The resulting isoform (3) lacks two internal aa, compared to isoform 1.
    Source sequence(s)
    AC152062
    Consensus CDS
    CCDS48630.1
    UniProtKB/Swiss-Prot
    P15806
    Related
    ENSMUSP00000100983.4, ENSMUST00000105346.10
    Conserved Domains (2) summary
    smart00353
    Location:552605
    HLH; helix loop helix domain
    cl23750
    Location:485560
    vATP-synt_E; ATP synthase (E/31 kDa) subunit
  4. NM_001164150.2NP_001157622.1  transcription factor E2-alpha isoform 4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) has an alternate penultimate coding exon, compared to variant 1. The resulting isoform (4) has a distinct segment in the C-terminal region, compared to isoform 1.
    Source sequence(s)
    AC152062
    Consensus CDS
    CCDS48635.1
    UniProtKB/TrEMBL
    E9PVV1
    Related
    ENSMUSP00000100981.2, ENSMUST00000105344.8
    Conserved Domains (2) summary
    smart00353
    Location:551604
    HLH; helix loop helix domain
    pfam08614
    Location:455573
    ATG16; Autophagy protein 16 (ATG16)
  5. NM_001164151.2NP_001157623.1  transcription factor E2-alpha isoform 5

    See identical proteins and their annotated locations for NP_001157623.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) has an alternate splice site and an alternate penultimate coding exon, compared to variant 1. The resulting isoform (5) lacks an internal aa and has a distinct segment in the C-terminal region, compared to isoform 1.
    Source sequence(s)
    AC152062
    Consensus CDS
    CCDS48632.1
    UniProtKB/Swiss-Prot
    P15806
    UniProtKB/TrEMBL
    A0A0R4J011
    Related
    ENSMUSP00000020379.7, ENSMUST00000020379.13
    Conserved Domains (2) summary
    smart00353
    Location:550603
    HLH; helix loop helix domain
    pfam08614
    Location:454572
    ATG16; Autophagy protein 16 (ATG16)
  6. NM_001164152.2NP_001157624.1  transcription factor E2-alpha isoform 6

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) has an alternate splice site and an alternate penultimate coding exon, compared to variant 1. The resulting isoform (6) lacks an internal aa and has a distinct segment in the C-terminal region, compared to isoform 1.
    Source sequence(s)
    AC152062
    Consensus CDS
    CCDS48633.1
    UniProtKB/TrEMBL
    E9PVV2
    Related
    ENSMUSP00000100980.2, ENSMUST00000105343.8
    Conserved Domains (2) summary
    smart00353
    Location:550603
    HLH; helix loop helix domain
    pfam08614
    Location:454572
    ATG16; Autophagy protein 16 (ATG16)
  7. NM_001164153.2NP_001157625.1  transcription factor E2-alpha isoform 7

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) has an alternate splice site and an alternate penultimate coding exon, compared to variant 1. The resulting isoform (7) lacks an internal aa and has a distinct segment in the C-terminal region, compared to isoform 1.
    Source sequence(s)
    AC152062
    Consensus CDS
    CCDS48631.1
    UniProtKB/TrEMBL
    E9PWE4
    Related
    ENSMUSP00000100977.2, ENSMUST00000105340.8
    Conserved Domains (1) summary
    smart00353
    Location:549602
    HLH; helix loop helix domain
  8. NM_001378903.1NP_001365832.1  transcription factor E2-alpha isoform 9

    Status: VALIDATED

    Source sequence(s)
    AC152062
    Conserved Domains (2) summary
    PHA03247
    Location:128380
    PHA03247; large tegument protein UL36; Provisional
    cd18945
    Location:541625
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins
  9. NM_001378904.1NP_001365833.1  transcription factor E2-alpha isoform 10

    Status: VALIDATED

    Source sequence(s)
    AC152062
    Conserved Domains (2) summary
    PHA03247
    Location:128381
    PHA03247; large tegument protein UL36; Provisional
    cl00081
    Location:548604
    bHLH_SF; basic Helix Loop Helix (bHLH) domain superfamily
  10. NM_001378905.1NP_001365834.1  transcription factor E2-alpha isoform 11

    Status: VALIDATED

    Source sequence(s)
    AC152062
    Conserved Domains (2) summary
    PHA03247
    Location:128380
    PHA03247; large tegument protein UL36; Provisional
    cl00081
    Location:547603
    bHLH_SF; basic Helix Loop Helix (bHLH) domain superfamily
  11. NM_001378908.1NP_001365837.1  transcription factor E2-alpha isoform 12

    Status: VALIDATED

    Source sequence(s)
    AC152062
    Conserved Domains (2) summary
    PHA03247
    Location:128381
    PHA03247; large tegument protein UL36; Provisional
    cl00081
    Location:547603
    bHLH_SF; basic Helix Loop Helix (bHLH) domain superfamily
  12. NM_001378910.1NP_001365839.1  transcription factor E2-alpha isoform 13

    Status: VALIDATED

    Source sequence(s)
    AC152062
    Conserved Domains (2) summary
    PHA03247
    Location:128380
    PHA03247; large tegument protein UL36; Provisional
    cl00081
    Location:546602
    bHLH_SF; basic Helix Loop Helix (bHLH) domain superfamily
  13. NM_001378912.1NP_001365841.1  transcription factor E2-alpha isoform 14

    Status: VALIDATED

    Source sequence(s)
    AC152062
    Conserved Domains (1) summary
    PHA03247
    Location:128379
    PHA03247; large tegument protein UL36; Provisional
  14. NM_001378913.1NP_001365842.1  transcription factor E2-alpha isoform 15

    Status: VALIDATED

    Source sequence(s)
    AC152062
  15. NM_001378914.1NP_001365843.1  transcription factor E2-alpha isoform 16

    Status: VALIDATED

    Source sequence(s)
    AC152062
  16. NM_011548.5NP_035678.3  transcription factor E2-alpha isoform 8

    Status: VALIDATED

    Description
    Transcript Variant: This variant (8) has two alternate splice sites and an alternate penultimate coding exon, compared to variant 1. The resulting isoform (8) lacks two internal aa and has a distinct segment in the C-terminal region, compared to isoform 1.
    Source sequence(s)
    AC152062
    Consensus CDS
    CCDS24022.1
    UniProtKB/Swiss-Prot
    P15806
    Related
    ENSMUSP00000100982.4, ENSMUST00000105345.10
    Conserved Domains (2) summary
    smart00353
    Location:549602
    HLH; helix loop helix domain
    pfam08614
    Location:453571
    ATG16; Autophagy protein 16 (ATG16)

RNA

  1. NR_166173.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC152062

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000076.7 Reference GRCm39 C57BL/6J

    Range
    80245375..80269814 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030244995.2XP_030100855.1  transcription factor E2-alpha isoform X2

    Conserved Domains (1) summary
    PHA03247
    Location:128379
    PHA03247; large tegument protein UL36; Provisional
  2. XM_017313872.3XP_017169361.1  transcription factor E2-alpha isoform X1

    Conserved Domains (2) summary
    PHA03247
    Location:92345
    PHA03247; large tegument protein UL36; Provisional
    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

RNA

  1. XR_001779500.3 RNA Sequence

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