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    TCF20 transcription factor 20 [ Homo sapiens (human) ]

    Gene ID: 6942, updated on 5-Mar-2024

    Summary

    Official Symbol
    TCF20provided by HGNC
    Official Full Name
    transcription factor 20provided by HGNC
    Primary source
    HGNC:HGNC:11631
    See related
    Ensembl:ENSG00000100207 MIM:603107; AllianceGenome:HGNC:11631
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    AR1; SPBP; DDVIBA; TCF-20
    Summary
    This gene encodes a transcription factor that recognizes the platelet-derived growth factor-responsive element in the matrix metalloproteinase 3 promoter. The encoded protein is thought to be a transcriptional coactivator, enhancing the activity of transcription factors such as JUN and SP1. Mutations in this gene are associated with autism spectrum disorders. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2015]
    Expression
    Ubiquitous expression in testis (RPKM 9.0), thyroid (RPKM 8.8) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See TCF20 in Genome Data Viewer
    Location:
    22q13.2; 22q13.3
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (42160013..42343537, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (42639511..42824582, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (42556019..42679933, complement)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377203 Neighboring gene ccytochrome P450 family 2 subfamily D member 8, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:42610989-42611488 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr22:42613759-42614347 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19154 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19155 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13820 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13823 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13822 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13821 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:42670872-42671668 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr22:42671669-42672465 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19156 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42678224-42679074 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42679075-42679924 Neighboring gene opioid growth factor receptor pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:42690639-42691452 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:42693767-42694412 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42695786-42696464 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42696465-42697143 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:42697144-42697822 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:42706428-42707134 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42709047-42709876 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42710708-42711537 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42714279-42715176 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42716129-42716966 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:42721410-42722037 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:42734449-42735057 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:42735333-42735954 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:42735955-42736576 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:42747603-42748103 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19160 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:42759143-42759796 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42761307-42762149 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42763534-42764468 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19161 Neighboring gene Sharpr-MPRA regulatory region 6115 Neighboring gene uncharacterized LOC124905126 Neighboring gene long intergenic non-protein coding RNA 1315

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Developmental delay with variable intellectual impairment and behavioral abnormalities
    MedGen: C5193092 OMIM: 618430 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2019-06-26)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2019-06-26)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    Biological insights from 108 schizophrenia-associated genetic loci.
    EBI GWAS Catalog

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of transcription factor 20 (AR1) (PDCD2L) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA0292

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables RNA binding HDA PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in positive regulation of transcription by RNA polymerase II NAS
    Non-traceable Author Statement
    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 IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    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 

    General protein information

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

    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.

    Genomic

    1. NG_028982.3 RefSeqGene

      Range
      64690..188604
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1025

    mRNA and Protein(s)

    1. NM_001378418.1NP_001365347.1  transcription factor 20 isoform 1

      Status: REVIEWED

      Source sequence(s)
      BX247885, Z83851
      Consensus CDS
      CCDS14033.1
      UniProtKB/Swiss-Prot
      A9JX12, O14528, Q13078, Q4V353, Q9H4M0, Q9UGU0
      UniProtKB/TrEMBL
      W5ZR30
      Related
      ENSP00000503828.1, ENST00000677622.1
      Conserved Domains (1) summary
      cd15699
      Location:17051932
      ePHD_TCF20; Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20)
    2. NM_005650.4NP_005641.1  transcription factor 20 isoform 1

      See identical proteins and their annotated locations for NP_005641.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AB006630, BU732753, KF851355
      Consensus CDS
      CCDS14033.1
      UniProtKB/Swiss-Prot
      A9JX12, O14528, Q13078, Q4V353, Q9H4M0, Q9UGU0
      UniProtKB/TrEMBL
      W5ZR30
      Related
      ENSP00000352463.3, ENST00000359486.8
      Conserved Domains (1) summary
      cd15699
      Location:17051932
      ePHD_TCF20; Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20)
    3. NM_181492.3NP_852469.1  transcription factor 20 isoform 2

      See identical proteins and their annotated locations for NP_852469.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an exon in the 3' coding region resulting in a frameshift, compared to variant 1. Isoform 2 has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      BX247885, Z83851
      Consensus CDS
      CCDS14032.1
      UniProtKB/Swiss-Prot
      Q9UGU0
      Conserved Domains (1) summary
      cd15699
      Location:17051932
      ePHD_TCF20; Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      42160013..42343537 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047441476.1XP_047297432.1  transcription factor 20 isoform X3

      Related
      ENSP00000335561.4, ENST00000335626.8
    2. XM_047441474.1XP_047297430.1  transcription factor 20 isoform X1

      UniProtKB/Swiss-Prot
      A9JX12, O14528, Q13078, Q4V353, Q9H4M0, Q9UGU0
      UniProtKB/TrEMBL
      W5ZR30
    3. XM_011530353.3XP_011528655.1  transcription factor 20 isoform X2

      See identical proteins and their annotated locations for XP_011528655.1

      Conserved Domains (1) summary
      cd15699
      Location:17051932
      ePHD_TCF20; Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20)
    4. XM_047441478.1XP_047297434.1  transcription factor 20 isoform X3

    5. XM_047441475.1XP_047297431.1  transcription factor 20 isoform X1

      UniProtKB/Swiss-Prot
      A9JX12, O14528, Q13078, Q4V353, Q9H4M0, Q9UGU0
      UniProtKB/TrEMBL
      W5ZR30
    6. XM_005261722.4XP_005261779.1  transcription factor 20 isoform X1

      See identical proteins and their annotated locations for XP_005261779.1

      UniProtKB/Swiss-Prot
      A9JX12, O14528, Q13078, Q4V353, Q9H4M0, Q9UGU0
      UniProtKB/TrEMBL
      W5ZR30
      Related
      ENSP00000508272.1, ENST00000683686.1
      Conserved Domains (1) summary
      cd15699
      Location:17051932
      ePHD_TCF20; Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20)
    7. XM_047441477.1XP_047297433.1  transcription factor 20 isoform X3

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_009646207.1 Reference GRCh38.p14 PATCHES

      Range
      62817..118147 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_009646208.1 Reference GRCh38.p14 PATCHES

      Range
      59299..114612 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_014040930.1 Reference GRCh38.p14 PATCHES

      Range
      62196..117515 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_014040931.1 Reference GRCh38.p14 PATCHES

      Range
      81021..136334 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_015148968.1 Reference GRCh38.p14 PATCHES

      Range
      51431..106747 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NW_003315971.2 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      70204..125539 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_3

    Genomic

    1. NT_187682.1 Reference GRCh38.p14 ALT_REF_LOCI_3

      Range
      82358..137688 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      42639511..42824582 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054325885.1XP_054181860.1  transcription factor 20 isoform X3

    2. XM_054325882.1XP_054181857.1  transcription factor 20 isoform X1

      UniProtKB/Swiss-Prot
      A9JX12, O14528, Q13078, Q4V353, Q9H4M0, Q9UGU0
      UniProtKB/TrEMBL
      W5ZR30
    3. XM_054325887.1XP_054181862.1  transcription factor 20 isoform X3

    4. XM_054325883.1XP_054181858.1  transcription factor 20 isoform X1

      UniProtKB/Swiss-Prot
      A9JX12, O14528, Q13078, Q4V353, Q9H4M0, Q9UGU0
      UniProtKB/TrEMBL
      W5ZR30
    5. XM_054325881.1XP_054181856.1  transcription factor 20 isoform X1

      UniProtKB/Swiss-Prot
      A9JX12, O14528, Q13078, Q4V353, Q9H4M0, Q9UGU0
      UniProtKB/TrEMBL
      W5ZR30
    6. XM_054325886.1XP_054181861.1  transcription factor 20 isoform X3

    7. XM_054325884.1XP_054181859.1  transcription factor 20 isoform X2