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

    Gene ID: 21423, updated on 4-Jan-2025

    Summary

    Official Symbol
    Tcf3provided by MGI
    Official Full Name
    transcription factor 3provided by MGI
    Primary source
    MGI:MGI:98510
    See related
    Ensembl:ENSMUSG00000020167 AllianceGenome:MGI:98510
    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
    Summary
    Enables several functions, including DNA-binding transcription factor binding activity; E-box binding activity; and protein heterodimerization activity. Contributes to DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in gastrulation; positive regulation of neuron differentiation; and positive regulation of transcription by RNA polymerase II. Acts upstream of with a positive effect on transcription by RNA polymerase II. Acts upstream of or within several processes, including immune system development; lymphocyte differentiation; and regulation of gene expression. Located in cytosol and nucleus. Part of RNA polymerase II transcription regulator complex and nucleosome. Is expressed in several structures, including brain; branchial arch; genitourinary system; integument; and retina. Used to study acute lymphoblastic leukemia. Human ortholog(s) of this gene implicated in agammaglobulinemia 8A; agammaglobulinemia 8B; and colorectal cancer. Orthologous to human TCF3 (transcription factor 3). [provided by Alliance of Genome Resources, Jan 2025]
    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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    Genomic context

    See Tcf3 in Genome Data Viewer
    Location:
    10 C1; 10 39.72 cM
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_02 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)

    Chromosome 10 - NC_000076.7Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 3300002P09 gene Neighboring gene methyl-CpG binding domain protein 3 Neighboring gene STARR-positive B cell enhancer ABC_E5156 Neighboring gene ubiquinol-cytochrome c reductase, complex III subunit XI Neighboring gene STARR-positive B cell enhancer ABC_E9795 Neighboring gene STARR-positive B cell enhancer ABC_E6881 Neighboring gene STARR-positive B cell enhancer ABC_E367 Neighboring gene STARR-positive B cell enhancer ABC_E11445 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)
    • Endonuclease-mediated (3) 
    • Targeted (22)  1 citation

    Pathways from PubChem

    Interactions

    General gene information

    Gene Ontology Provided by MGI

    Items 1 - 25 of 45
    Function Evidence Code Pubs
    contributes_to DNA binding  
    enables DNA binding  
    contributes_to DNA binding  
    enables DNA binding  
    contributes_to DNA-binding transcription activator activity, RNA polymerase II-specific PubMed 
    enables DNA-binding transcription activator activity, RNA polymerase II-specific PubMed 
    enables DNA-binding transcription activator activity, RNA polymerase II-specific PubMed 
    enables DNA-binding transcription activator activity, RNA polymerase II-specific  
    enables DNA-binding transcription activator activity, RNA polymerase II-specific  
    enables DNA-binding transcription factor activity PubMed 
    enables DNA-binding transcription factor activity  
    enables DNA-binding transcription factor activity  
    enables DNA-binding transcription factor activity PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific PubMed 
    enables DNA-binding transcription factor binding  
    enables DNA-binding transcription factor binding  
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific  
    contributes_to E-box binding PubMed 
    enables E-box binding PubMed 
    enables E-box binding PubMed 
    contributes_to E-box binding  
    enables E-box binding  
    enables PDZ domain binding  
    contributes_to RNA polymerase II cis-regulatory region sequence-specific DNA binding PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding  
    enables RNA polymerase II-specific DNA-binding transcription factor binding PubMed 
    enables RNA polymerase II-specific DNA-binding transcription factor binding  
    enables bHLH transcription factor binding PubMed 
    enables bHLH transcription factor binding  
    enables chromatin binding PubMed 
    enables cis-regulatory region sequence-specific DNA binding PubMed 
    enables identical protein binding PubMed 
    enables mitogen-activated protein kinase kinase kinase binding  
    enables protein binding PubMed 
    enables protein heterodimerization activity PubMed 
    enables protein heterodimerization activity  
    enables protein homodimerization activity  
    enables protein homodimerization activity  
    enables sequence-specific DNA binding PubMed 
    enables sequence-specific DNA binding PubMed 
    contributes_to transcription cis-regulatory region binding  
    enables vitamin D response element binding  
    Items 1 - 25 of 45
    Items 1 - 25 of 45
    Process Evidence Code Pubs
    involved_in B cell lineage commitment  
    involved_in B cell lineage commitment  
    acts_upstream_of_or_within Peyer's patch development PubMed 
    acts_upstream_of_or_within T cell differentiation in thymus PubMed 
    acts_upstream_of_or_within cell development PubMed 
    acts_upstream_of_or_within chromatin remodeling PubMed 
    acts_upstream_of_negative_effect erythrocyte differentiation PubMed 
    involved_in gastrulation PubMed 
    acts_upstream_of gene expression PubMed 
    involved_in immunoglobulin V(D)J recombination  
    acts_upstream_of_or_within immunoglobulin V(D)J recombination PubMed 
    acts_upstream_of_or_within immunoglobulin V(D)J recombination PubMed 
    acts_upstream_of_or_within lymphocyte differentiation PubMed 
    acts_upstream_of_or_within natural killer cell differentiation PubMed 
    involved_in negative regulation of transcription by RNA polymerase II  
    involved_in nervous system development  
    involved_in positive regulation of B cell proliferation  
    involved_in positive regulation of B cell proliferation  
    involved_in positive regulation of DNA-binding transcription factor activity  
    involved_in positive regulation of DNA-binding transcription factor activity  
    acts_upstream_of_or_within positive regulation of DNA-templated transcription PubMed 
    involved_in positive regulation of DNA-templated transcription  
    involved_in positive regulation of DNA-templated transcription  
    involved_in positive regulation of cell cycle  
    involved_in positive regulation of cell cycle  
    acts_upstream_of_or_within positive regulation of gene expression PubMed 
    involved_in positive regulation of gene expression  
    involved_in positive regulation of neuron differentiation PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II PubMed 
    involved_in positive regulation of transcription by RNA polymerase II PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II PubMed 
    involved_in positive regulation of transcription by RNA polymerase II PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II PubMed 
    involved_in positive regulation of transcription by RNA polymerase II  
    acts_upstream_of_or_within protein stabilization PubMed 
    acts_upstream_of_or_within regulation of DNA-templated transcription PubMed 
    acts_upstream_of_or_within regulation of DNA-templated transcription PubMed 
    involved_in regulation of G1/S transition of mitotic cell cycle  
    involved_in regulation of G1/S transition of mitotic cell cycle  
    involved_in regulation of transcription by RNA polymerase II  
    acts_upstream_of_or_within regulation of transcription by RNA polymerase II PubMed 
    acts_upstream_of_or_within response to lipopolysaccharide PubMed 
    acts_upstream_of_or_within response to xenobiotic stimulus PubMed 
    acts_upstream_of transcription by RNA polymerase II PubMed 
    acts_upstream_of_positive_effect transcription by RNA polymerase II PubMed 
    Items 1 - 25 of 45
    Items 1 - 20 of 21
    Component Evidence Code Pubs
    part_of RNA polymerase II transcription regulator complex PubMed 
    part_of RNA polymerase II transcription regulator complex PubMed 
    part_of RNA polymerase II transcription regulator complex  
    located_in chromatin  
    located_in chromatin  
    located_in cytoplasm  
    located_in cytoplasm  
    located_in cytosol PubMed 
    located_in euchromatin  
    located_in nucleoplasm  
    located_in nucleoplasm  
    part_of nucleosome PubMed 
    located_in nucleus PubMed 
    located_in nucleus  
    located_in nucleus  
    part_of protein-containing complex  
    part_of protein-containing complex  
    part_of transcription regulator complex  
    part_of transcription regulator complex PubMed 
    part_of transcription regulator complex PubMed 
    part_of transcription regulator complex  
    Items 1 - 20 of 21

    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, E9PWE5
      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

      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/TrEMBL
      A0A0R4J014, E9PWE5
      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

      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, Q3U153, Q8CAH9, Q8VCY4, Q922S2, Q99MB8, Q9CYJ4
      UniProtKB/TrEMBL
      E9PWE5
      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, E9PWE3
      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

      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/TrEMBL
      A0A0R4J011, E9PWE3
      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, E9PWE3
      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
      E9PWE3, 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
      UniProtKB/TrEMBL
      E9PWE5
      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
      UniProtKB/TrEMBL
      E9PWE5
      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
      UniProtKB/TrEMBL
      E9PWE5
      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
      UniProtKB/TrEMBL
      E9PWE5
      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
      UniProtKB/TrEMBL
      E9PWE5
      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
      UniProtKB/TrEMBL
      E9PWE3
      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
      UniProtKB/TrEMBL
      E9PWE3
    15. NM_001378914.1NP_001365843.1  transcription factor E2-alpha isoform 16

      Status: VALIDATED

      Source sequence(s)
      AC152062
      UniProtKB/TrEMBL
      E9PWE3
    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/TrEMBL
      E9PWE3
      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: GCF_000001635.27-RS_2024_02

    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

      UniProtKB/TrEMBL
      E9PWE3
      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

      UniProtKB/TrEMBL
      E9PWE5
      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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