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TFCP2 transcription factor CP2 [ Homo sapiens (human) ]

Gene ID: 7024, updated on 3-Mar-2019

Summary

Official Symbol
TFCP2provided by HGNC
Official Full Name
transcription factor CP2provided by HGNC
Primary source
HGNC:HGNC:11748
See related
Ensembl:ENSG00000135457 MIM:189889
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

Genomic context

See TFCP2 in Genome Data Viewer
Location:
12q13.12-q13.13
Exon count:
15
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 12 NC_000012.12 (51093756..51173143, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (51487539..51566926, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 1273, pseudogene Neighboring gene LETM1 domain containing 1 Neighboring gene cysteine and serine rich nuclear protein 2 Neighboring gene ribosomal protein L35a pseudogene 29 Neighboring gene prohibitin pseudogene 19 Neighboring gene RNA, U6 small nuclear 199, pseudogene Neighboring gene POU class 6 homeobox 1 Neighboring gene DAZ associated protein 2 Neighboring gene small cell adhesion glycoprotein

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 FunctionsWhat's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Tat tat YY1 and LSF transcription factors cooperatively recruit histone deacetylase 1 (HDAC1) to the HIV-1 LTR promoter, thereby inhibiting transcription and Tat activation of the promoter PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Potential readthrough

Included gene: SMAGP

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
mRNA transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
cytosol 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 IDA
Inferred from Direct Assay
more info
PubMed 
protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 
protein-containing complex IMP
Inferred from Mutant Phenotype
more info
PubMed 

General protein information

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

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_029908.1 RefSeqGene

    Range
    5001..84388
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001173452.1NP_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:329395
    SAM_TFCP2; SAM domain of TFCP2 transcription factors
    pfam04516
    Location:52257
    CP2; CP2 transcription factor
  2. NM_001173453.1NP_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:278344
    SAM_TFCP2; SAM domain of TFCP2 transcription factors
    pfam04516
    Location:52206
    CP2; CP2 transcription factor
  3. NM_005653.4NP_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
    Q12800
    UniProtKB/TrEMBL
    A0A024R120
    Related
    ENSP00000257915.5, ENST00000257915.9
    Conserved Domains (2) summary
    cd09589
    Location:329395
    SAM_TFCP2; SAM domain of TFCP2 transcription factors
    pfam04516
    Location:52257
    CP2; CP2 transcription factor

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p12 Primary Assembly

    Range
    51093756..51173143 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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