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    TFCP2 transcription factor CP2 [ Homo sapiens (human) ]

    Gene ID: 7024, updated on 27-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
    mouse all
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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
    • 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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    Related articles in PubMed

    1. GeneChip, geNorm, and gastrointestinal tumors: novel reference genes for real-time PCR. Kidd M, et al. Physiol Genomics, 2007 Aug 20. PMID 17456737
    2. A Feedback Loop Comprising EGF/TGFα Sustains TFCP2-Mediated Breast Cancer Progression. Zhao Y, et al. Cancer Res, 2020 Jun 1. PMID 32193292
    3. Transcription factor LSF (TFCP2) inhibits melanoma growth. Goto Y, et al. Oncotarget, 2016 Jan 19. PMID 26506241, Free PMC Article
    4. LSF expression and its prognostic implication in colorectal cancer. Jiang H, et al. Int J Clin Exp Pathol, 2014. PMID 25337247, Free PMC Article
    5. Transcription factor Late SV40 Factor (LSF) functions as an oncogene in hepatocellular carcinoma. Yoo BK, et al. Proc Natl Acad Sci U S A, 2010 May 4. PMID 20404171, Free PMC Article

    See all (130) citations in PubMed

    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)

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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