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TCF20 transcription factor 20 [ Homo sapiens (human) ]

Gene ID: 6942, updated on 24-Sep-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
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (42160013..42343537, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (42639511..42824582, complement)
RS_2024_09 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 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)

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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.

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_2024_08

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