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    Tcf20 transcription factor 20 [ Mus musculus (house mouse) ]

    Gene ID: 21411, updated on 3-Apr-2024

    Summary

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    Official Symbol
    Tcf20provided by MGI
    Official Full Name
    transcription factor 20provided by MGI
    Primary source
    MGI:MGI:108399
    See related
    Ensembl:ENSMUSG00000041852 AllianceGenome:MGI:108399
    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
    SPBP; mKIAA0292; 2810438H08Rik
    Summary
    Enables DNA-binding transcription factor activity; transcription cis-regulatory region binding activity; and transcription coactivator activity. Acts upstream of or within positive regulation of transcription by RNA polymerase II. Located in nucleus. Is expressed in several structures, including branchial arch; central nervous system; early conceptus; genitourinary system; and sensory organ. Used to study Phelan-McDermid syndrome and autism spectrum disorder. Orthologous to human TCF20 (transcription factor 20). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in thymus adult (RPKM 10.0), testis adult (RPKM 9.7) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    15 E1; 15 38.73 cM
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 15 NC_000081.7 (82692648..82872304, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 15 NC_000081.6 (82808447..82988103, complement)

    Chromosome 15 - NC_000081.7Genomic Context describing neighboring genes Neighboring gene cytochrome P450, family 2, subfamily d, member 41, pseudogene Neighboring gene cytochrome P450, family 2, subfamily d, polypeptide 26 Neighboring gene STARR-positive B cell enhancer ABC_E9917 Neighboring gene STARR-seq mESC enhancer starr_39304 Neighboring gene CapStarr-seq enhancer MGSCv37_chr15:82744980-82745163 Neighboring gene transforming growth factor beta regulated gene 3 Neighboring gene predicted gene, 20324 Neighboring gene CapStarr-seq enhancer MGSCv37_chr15:82805127-82805236 Neighboring gene microRNA 3080 Neighboring gene STARR-positive B cell enhancer mm9_chr15:82818187-82818488 Neighboring gene expressed sequence AW121686 Neighboring gene Nfat activating molecule with ITAM motif 1 Neighboring gene STARR-positive B cell enhancer ABC_E7401 Neighboring gene STARR-positive B cell enhancer ABC_E3149 Neighboring gene CapStarr-seq enhancer MGSCv37_chr15:82873210-82873393 Neighboring gene STARR-seq mESC enhancer starr_39309 Neighboring gene predicted gene, 32620 Neighboring gene STARR-positive B cell enhancer ABC_E3150 Neighboring gene predicted gene, 41366

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. The nuclear factor SPBP contains different functional domains and stimulates the activity of various transcriptional activators. Rekdal C, et al. J Biol Chem, 2000 Dec 22. PMID 10995766
    2. Cross-talk between different enhancer elements during mitogenic induction of the human stromelysin-1 gene. Kirstein M, et al. J Biol Chem, 1996 Jul 26. PMID 8663478
    3. Mutations in RAI1 associated with Smith-Magenis syndrome. Slager RE, et al. Nat Genet, 2003 Apr. PMID 12652298
    4. Interaction between the transcription factor SPBP and the positive cofactor RNF4. An interplay between protein binding zinc fingers. Lyngsø C, et al. J Biol Chem, 2000 Aug 25. PMID 10849425
    5. Disruption of MeCP2-TCF20 complex underlies distinct neurodevelopmental disorders. Zhou J, et al. Proc Natl Acad Sci U S A, 2022 Jan 25. PMID 35074918, Free PMC Article

    See all (36) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Disruption of MeCP2-TCF20 complex underlies distinct neurodevelopmental disorders.
      Title: Disruption of MeCP2-TCF20 complex underlies distinct neurodevelopmental disorders.
    2. TCF20 dysfunction leads to cortical neurogenesis defects and autistic-like behaviors in mice.
      Title: TCF20 dysfunction leads to cortical neurogenesis defects and autistic-like behaviors in mice.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA-binding transcription factor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transcription cis-regulatory region binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables transcription coactivator activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in nuclear body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    transcription factor 20
    Names
    SPRE-binding protein
    TCF-20
    nuclear factor SPBP
    stromelysin PDGF responsive element binding protein transcription factor
    stromelysin-1 PDGF-responsive element-binding protein

    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_001114140.1 → NP_001107612.1  transcription factor 20 isoform a

      See identical proteins and their annotated locations for NP_001107612.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer variant and encodes the longer isoform (a).
      Source sequence(s)
      AC129563, AK122239, BC080855
      Consensus CDS
      CCDS49681.1
      UniProtKB/Swiss-Prot
      B9EHJ7, Q60792, Q9EPQ8
      UniProtKB/TrEMBL
      Q80U46
      Related
      ENSMUSP00000105136.3, ENSMUST00000109510.10
      Conserved Domains (1) summary
      cd15699
      Location:1733 → 1959
      ePHD_TCF20; Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20)

    2. NM_001402838.1 → NP_001389767.1  transcription factor 20 isoform a

      Status: VALIDATED

      Source sequence(s)
      AC087902, AC129563
      UniProtKB/Swiss-Prot
      B9EHJ7, Q60792, Q9EPQ8
      Conserved Domains (1) summary
      cd15699
      Location:1733 → 1959
      ePHD_TCF20; Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20)

    3. NM_013836.3 → NP_038864.3  transcription factor 20 isoform b

      See identical proteins and their annotated locations for NP_038864.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon in the 3' coding region, compared to variant 1. This results in a distinct C-terminus and shorter protein (isoform b), compared to isoform a.
      Source sequence(s)
      AC129563, BC080855
      Consensus CDS
      CCDS27693.1
      UniProtKB/TrEMBL
      Q80U46
      Related
      ENSMUSP00000048486.6, ENSMUST00000048966.7
      Conserved Domains (1) summary
      cd15699
      Location:1733 → 1959
      ePHD_TCF20; Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20)

    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_000081.7 Reference GRCm39 C57BL/6J

      Range
      82692648..82872304 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006520732.3 → XP_006520795.1  transcription factor 20 isoform X1

      See identical proteins and their annotated locations for XP_006520795.1

      UniProtKB/Swiss-Prot
      B9EHJ7, Q60792, Q9EPQ8
      UniProtKB/TrEMBL
      Q80U46
      Conserved Domains (1) summary
      cd15699
      Location:1733 → 1959
      ePHD_TCF20; Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20)

    2. XM_006520733.2 → XP_006520796.1  transcription factor 20 isoform X1

      See identical proteins and their annotated locations for XP_006520796.1

      UniProtKB/Swiss-Prot
      B9EHJ7, Q60792, Q9EPQ8
      UniProtKB/TrEMBL
      Q80U46
      Conserved Domains (1) summary
      cd15699
      Location:1733 → 1959
      ePHD_TCF20; Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20)

    3. XM_011245553.4 → XP_011243855.1  transcription factor 20 isoform X3

      See identical proteins and their annotated locations for XP_011243855.1

      UniProtKB/TrEMBL
      Q80U46
      Conserved Domains (1) summary
      cd15699
      Location:1733 → 1959
      ePHD_TCF20; Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20)

    4. XM_011245552.4 → XP_011243854.1  transcription factor 20 isoform X2

      UniProtKB/TrEMBL
      Q80U46
      Conserved Domains (1) summary
      cd15699
      Location:1733 → 1959
      ePHD_TCF20; Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20)

    5. XM_011245554.4 → XP_011243856.1  transcription factor 20 isoform X4

      UniProtKB/TrEMBL
      Q80U46
      Conserved Domains (1) summary
      cl22851
      Location:1733 → 1916
      PHD_SF; PHD finger superfamily
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9EPQ8.3 GenPept UniProtKB/Swiss-Prot:Q9EPQ8

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