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TFCP2 transcription factor CP2 [ Homo sapiens (human) ]

Gene ID: 7024, updated on 2-Nov-2024

Summary

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Official Symbol
TFCP2provided by HGNC
Official Full Name
transcription factor CP2provided by HGNC
Primary source
HGNC:HGNC:11748
See related
Ensembl:ENSG00000135457 MIM:189889; AllianceGenome:HGNC:11748
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
LSF; SEF; LBP1C; LSF1D; TFCP2C
Summary
This gene encodes a transcription factor that binds the alpha-globin promoter and activates transcription of the alpha-globin gene. The encoded protein regulates erythroid gene expression, plays a role in the transcriptional switch of globin gene promoters, and it activates many other cellular and viral gene promoters. The gene product interacts with certain inflammatory response factors, and polymorphisms of this gene may be involved in the pathogenesis of Alzheimer's disease. [provided by RefSeq, Mar 2010]
Expression
Ubiquitous expression in appendix (RPKM 10.8), lymph node (RPKM 10.8) and 25 other tissues See more
Orthologs
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Genomic context

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See TFCP2 in Genome Data Viewer
Location:
12q13.12-q13.13
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (51093656..51173135, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (51056573..51136022, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (51487439..51566918, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 1273, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6366 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6367 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:51441816-51442354 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:51442355-51442893 Neighboring gene LETM1 domain containing 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:51463214-51463714 Neighboring gene cysteine and serine rich nuclear protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4458 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:51477804-51478430 Neighboring gene ribosomal protein L35a pseudogene 29 Neighboring gene PHB1 pseudogene 19 Neighboring gene RNA, U6 small nuclear 199, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6370 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:51566351-51567098 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6371 Neighboring gene uncharacterized LOC124902933 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4459 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6372 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:51593597-51594096 Neighboring gene POU class 6 homeobox 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4460 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4461

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Analysis of the Expression of LSF Transcription Factor in the Regulation of Transcription and TSG101 during the Neoplastic Transformation of Endometrial Cells.
    Title: Analysis of the Expression of LSF Transcription Factor in the Regulation of Transcription and TSG101 during the Neoplastic Transformation of Endometrial Cells.
  2. Multi-omic and functional analysis for classification and treatment of sarcomas with FUS-TFCP2 or EWSR1-TFCP2 fusions.
    Title: Multi-omic and functional analysis for classification and treatment of sarcomas with FUS-TFCP2 or EWSR1-TFCP2 fusions.
  3. Human umbilical cord mesenchymal stem cell-derived extracellular vesicles loaded with TFCP2 activate Wnt/beta-catenin signaling to alleviate preeclampsia.
    Title: Human umbilical cord mesenchymal stem cell-derived extracellular vesicles loaded with TFCP2 activate Wnt/β-catenin signaling to alleviate preeclampsia.
  4. TFCP2 is a transcriptional regulator of heparan sulfate assembly and melanoma cell growth.
    Title: TFCP2 is a transcriptional regulator of heparan sulfate assembly and melanoma cell growth.
  5. Transcription factor cellular promoter 2 is required for upstream binding protein 1 -mediated angiogenesis.
    Title: Transcription factor cellular promoter 2 is required for upstream binding protein 1 -mediated angiogenesis.
  6. circITCH suppresses cell proliferation and metastasis through miR-660/TFCP2 pathway in melanoma.
    Title: circITCH suppresses cell proliferation and metastasis through miR-660/TFCP2 pathway in melanoma.
  7. DNA hypermethylation contributes to colorectal cancer metastasis by regulating the binding of CEBPB and TFCP2 to the CPEB1 promoter.
    Title: DNA hypermethylation contributes to colorectal cancer metastasis by regulating the binding of CEBPB and TFCP2 to the CPEB1 promoter.
  8. Transcription factors CP2 and YY1 as prognostic markers in head and neck squamous cell carcinoma: analysis of The Cancer Genome Atlas and a second independent cohort.
    Title: Transcription factors CP2 and YY1 as prognostic markers in head and neck squamous cell carcinoma: analysis of The Cancer Genome Atlas and a second independent cohort.
  9. A subset of epithelioid and spindle cell rhabdomyosarcomas is associated with TFCP2 fusions and common ALK upregulation.
    Title: A subset of epithelioid and spindle cell rhabdomyosarcomas is associated with TFCP2 fusions and common ALK upregulation.
  10. The microtubule-associated histone methyltransferase SET8, facilitated by transcription factor LSF, methylates alpha-tubulin.
    Title: The microtubule-associated histone methyltransferase SET8, facilitated by transcription factor LSF, methylates α-tubulin.
Submit: New GeneRIF Correction See all GeneRIFs (43)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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

Potential readthrough

Included gene: SMAGP

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding TAS
Traceable Author Statement
more info
 PubMed 
enables DNA-binding transcription activator activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription factor activity TAS
Traceable Author Statement
more info
 PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables cis-regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables transcription factor binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in mRNA transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in 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 IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in chromatin ISA
Inferred from Sequence Alignment
more info
  
located_in cytosol 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 
part_of protein-containing complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of protein-containing complex IMP
Inferred from Mutant Phenotype
more info
 PubMed 

General protein information

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Preferred Names
alpha-globin transcription factor CP2
Names
SAA3 enhancer factor

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_029908.1 RefSeqGene

    Range
    5009..84488
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001173452.2 → NP_001166923.1  alpha-globin transcription factor CP2 isoform 2

    See identical proteins and their annotated locations for NP_001166923.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
    Source sequence(s)
    AC087884, AK291264, BX479302
    UniProtKB/Swiss-Prot
    Q12800
    Conserved Domains (2) summary
    cd09589
    Location:329 → 395
    SAM_TFCP2; SAM domain of TFCP2 transcription factors
    pfam04516
    Location:52 → 259
    CP2; CP2 transcription factor

  2. NM_001173453.2 → NP_001166924.1  alpha-globin transcription factor CP2 isoform 3

    See identical proteins and their annotated locations for NP_001166924.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon in the central coding region, and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform 3), compared to isoform 1.
    Source sequence(s)
    AC087884, BX479302, U03495
    Consensus CDS
    CCDS55827.1
    UniProtKB/Swiss-Prot
    Q12800
    Related
    ENSP00000447991.1, ENST00000548115.5
    Conserved Domains (2) summary
    cd09589
    Location:278 → 344
    SAM_TFCP2; SAM domain of TFCP2 transcription factors
    pfam04516
    Location:52 → 208
    CP2; CP2 transcription factor

  3. NM_005653.5 → NP_005644.2  alpha-globin transcription factor CP2 isoform 1

    See identical proteins and their annotated locations for NP_005644.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC087884, AC139768, BC003634, BX479302
    Consensus CDS
    CCDS8808.1
    UniProtKB/Swiss-Prot
    A8K5E9, Q12800, Q12801, Q9UD75, Q9UD77
    Related
    ENSP00000257915.5, ENST00000257915.10
    Conserved Domains (2) summary
    cd09589
    Location:329 → 395
    SAM_TFCP2; SAM domain of TFCP2 transcription factors
    pfam04516
    Location:52 → 259
    CP2; CP2 transcription factor

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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    51093656..51173135 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    51056573..51136022 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q12800.2 GenPept UniProtKB/Swiss-Prot:Q12800

Gene LinkOut

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