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TCF20 transcription factor 20 [ Homo sapiens (human) ]

Gene ID: 6942, updated on 2-Oct-2018

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; Vega:OTTHUMG00000150920
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; 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

Genomic context

See TCF20 in Genome Data Viewer
Location:
22q13.2; 22q13.3
Exon count:
8
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 22 NC_000022.11 (42160013..42283927, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (42556019..42664768, 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 opioid growth factor receptor pseudogene 1 Neighboring gene long intergenic non-protein coding RNA 1315 Neighboring gene NFAT activating protein with ITAM motif 1 Neighboring gene uncharacterized LOC101927344

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2018-07-25)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2018-07-25)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci.
NHGRI GWA 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 BioSystems

  • Matrix Metalloproteinases, organism-specific biosystem (from WikiPathways)
    Matrix Metalloproteinases, organism-specific biosystemMatrix metalloproteinases (MMPs) are zinc-dependent endopeptidases; other family members are adamalysins, serralysins, and astacins. The MMPs belong to a larger family of proteases known as the metzi...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0292

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding NAS
Non-traceable Author Statement
more info
PubMed 
DNA-binding transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA binding HDA PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription coactivator activity NAS
Non-traceable Author Statement
more info
PubMed 
transcription regulatory region DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of transcription, DNA-templated NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
nuclear body IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus NAS
Non-traceable Author Statement
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)

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)

mRNA and Protein(s)

  1. NM_005650.3NP_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
    Q9UGU0
    UniProtKB/TrEMBL
    W5ZR30
    Related
    ENSP00000352463.3, OTTHUMP00000198708, ENST00000359486.7, OTTHUMT00000320531
    Conserved Domains (1) summary
    cd15699
    Location:17051932
    ePHD_TCF20; Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20)
  2. NM_181492.2NP_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)
    BU732753, BX247885, U19345
    Consensus CDS
    CCDS14032.1
    UniProtKB/Swiss-Prot
    Q9UGU0
    Related
    ENSP00000335561.4, OTTHUMP00000198709, ENST00000335626.8, OTTHUMT00000320532
    Conserved Domains (1) summary
    cd15699
    Location:17051932
    ePHD_TCF20; Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20)

RefSeqs of Annotated Genomes: Homo sapiens 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 GRCh38.p12 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p12 Primary Assembly

    Range
    42160013..42283927 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011530354.2XP_011528656.1  transcription factor 20 isoform X3

    See identical proteins and their annotated locations for XP_011528656.1

    UniProtKB/Swiss-Prot
    Q9UGU0
    Conserved Domains (1) summary
    cd15699
    Location:17051932
    ePHD_TCF20; Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20)
  2. XM_006724313.3XP_006724376.1  transcription factor 20 isoform X1

    See identical proteins and their annotated locations for XP_006724376.1

    UniProtKB/Swiss-Prot
    Q9UGU0
    UniProtKB/TrEMBL
    W5ZR30
    Conserved Domains (1) summary
    cd15699
    Location:17051932
    ePHD_TCF20; Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20)
  3. XM_005261722.3XP_005261779.1  transcription factor 20 isoform X1

    See identical proteins and their annotated locations for XP_005261779.1

    UniProtKB/Swiss-Prot
    Q9UGU0
    UniProtKB/TrEMBL
    W5ZR30
    Conserved Domains (1) summary
    cd15699
    Location:17051932
    ePHD_TCF20; Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20)
  4. XM_011530353.2XP_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)

Reference GRCh38.p12 PATCHES

Genomic

  1. NW_009646207.1 Reference GRCh38.p12 PATCHES

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

Reference GRCh38.p12 PATCHES

Genomic

  1. NW_009646208.1 Reference GRCh38.p12 PATCHES

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

Reference GRCh38.p12 PATCHES

Genomic

  1. NW_014040930.1 Reference GRCh38.p12 PATCHES

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

Reference GRCh38.p12 PATCHES

Genomic

  1. NW_014040931.1 Reference GRCh38.p12 PATCHES

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

Reference GRCh38.p12 PATCHES

Genomic

  1. NW_015148968.1 Reference GRCh38.p12 PATCHES

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

Reference GRCh38.p12 ALT_REF_LOCI_1

Genomic

  1. NW_003315971.2 Reference GRCh38.p12 ALT_REF_LOCI_1

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

Reference GRCh38.p12 ALT_REF_LOCI_3

Genomic

  1. NT_187682.1 Reference GRCh38.p12 ALT_REF_LOCI_3

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