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CTDP1 CTD phosphatase subunit 1 [ Homo sapiens (human) ]

Gene ID: 9150, updated on 8-Dec-2018

Summary

Official Symbol
CTDP1provided by HGNC
Official Full Name
CTD phosphatase subunit 1provided by HGNC
Primary source
HGNC:HGNC:2498
See related
Ensembl:ENSG00000060069 MIM:604927
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
FCP1; CCFDN
Summary
This gene encodes a protein which interacts with the carboxy-terminus of the RAP74 subunit of transcription initiation factor TFIIF, and functions as a phosphatase that processively dephosphorylates the C-terminus of POLR2A (a subunit of RNA polymerase II), making it available for initiation of gene expression. Mutations in this gene are associated with congenital cataracts, facial dysmorphism and neuropathy syndrome (CCFDN). Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Feb 2011]
Expression
Ubiquitous expression in testis (RPKM 8.7), colon (RPKM 6.0) and 25 other tissues See more
Orthologs

Genomic context

See CTDP1 in Genome Data Viewer
Location:
18q23
Exon count:
15
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 18 NC_000018.10 (79679801..79754510)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (77439801..77514510)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372228 Neighboring gene uncharacterized LOC284241 Neighboring gene uncharacterized LOC105376875 Neighboring gene potassium voltage-gated channel modifier subfamily G member 2 Neighboring gene PQ loop repeat containing 1 Neighboring gene heat shock factor binding protein 1 like 1

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?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association study of clinical dimensions of schizophrenia: polygenic effect on disorganized symptoms.
NHGRI GWA Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1 (CTDP1) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed
Knockdown of CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1 (CTDP1) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Protein interactions

Protein Gene Interaction Pubs
Tat tat FCP1 is required for Tat-mediated transactivation in vitro and amino acids 562-685 of FCP1 are necessary for binding to Tat in yeast two-hybrid studies PubMed
tat HIV-1 Tat binds to and strongly inhibits the activity of the CTD phosphatase (FCP1), indicating that Tat-dependent suppression of CTD phosphatase is part of the transactivation function of Tat 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

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA polymerase II CTD heptapeptide repeat phosphatase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA polymerase II CTD heptapeptide repeat phosphatase activity IDA
Inferred from Direct Assay
more info
PubMed 
TFIIF-class transcription factor complex binding IPI
Inferred from Physical Interaction
more info
PubMed 
Tat protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
phosphoprotein phosphatase activity TAS
Traceable Author Statement
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
cell division IEA
Inferred from Electronic Annotation
more info
 
dephosphorylation of RNA polymerase II C-terminal domain IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
exit from mitosis IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of cell growth involved in cardiac muscle cell development IEA
Inferred from Electronic Annotation
more info
 
positive regulation by host of viral transcription IDA
Inferred from Direct Assay
more info
PubMed 
protein dephosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 
transcription elongation from RNA polymerase II promoter TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
centrosome IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
midbody IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
protein-containing complex IMP
Inferred from Mutant Phenotype
more info
PubMed 
spindle IDA
Inferred from Direct Assay
more info
PubMed 
spindle midzone IDA
Inferred from Direct Assay
more info
PubMed 
spindle pole IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
RNA polymerase II subunit A C-terminal domain phosphatase
Names
CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1
CTD of POLR2A, phosphatase of, subunit 1
TFIIF-associating CTD phosphatase 1
serine phosphatase FCP1a
transcription factor IIF-associating CTD phosphatase 1
NP_001189433.1
NP_001305440.1
NP_004706.3
NP_430255.2
XP_011524563.1
XP_016881567.1

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_007988.1 RefSeqGene

    Range
    5001..79710
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_236

mRNA and Protein(s)

  1. NM_001202504.1NP_001189433.1  RNA polymerase II subunit A C-terminal domain phosphatase isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate 5' terminal exon compared to variant 1, resulting in translation initiation from an in-frame downstream AUG, and a shorter isoform (3, also known as FCP1a) compared to isoform 1.
    Source sequence(s)
    AA282312, AF081287, BC047999, BC052576, BM512113, DB451780, DB517021
    Consensus CDS
    CCDS74239.1
    UniProtKB/Swiss-Prot
    Q9Y5B0
    UniProtKB/TrEMBL
    A0A0A0MR03
    Related
    ENSP00000299543.8, ENST00000299543.8
    Conserved Domains (3) summary
    TIGR02250
    Location:58204
    FCP1_euk; FCP1-like phosphatase, phosphatase domain
    cd00027
    Location:517597
    BRCT; Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo ...
    pfam09309
    Location:597842
    FCP1_C; FCP1, C-terminal
  2. NM_001318511.1NP_001305440.1  RNA polymerase II subunit A C-terminal domain phosphatase isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an exon in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (4) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AA282312, AC021594, BC032515, BC047999, DR001939
    Related
    ENSP00000465119.1, ENST00000591598.5
    Conserved Domains (4) summary
    TIGR02250
    Location:177323
    FCP1_euk; FCP1-like phosphatase, phosphatase domain
    cd00027
    Location:636716
    BRCT; Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo ...
    pfam09309
    Location:716860
    FCP1_C; FCP1, C-terminal
    cl11404
    Location:21111
    Biotinyl_lipoyl_domains; Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl, ...
  3. NM_004715.4NP_004706.3  RNA polymerase II subunit A C-terminal domain phosphatase isoform 1

    See identical proteins and their annotated locations for NP_004706.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the predominant transcript, and encodes the longest isoform (1, also known as FCP1).
    Source sequence(s)
    AA282312, BC047999, BC052576, BM512113, DR001939
    Consensus CDS
    CCDS12017.1
    UniProtKB/Swiss-Prot
    Q9Y5B0
    Related
    ENSP00000484525.1, ENST00000613122.4
    Conserved Domains (4) summary
    TIGR02250
    Location:177323
    FCP1_euk; FCP1-like phosphatase, phosphatase domain
    cd00027
    Location:636716
    BRCT; Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo ...
    pfam09309
    Location:716961
    FCP1_C; FCP1, C-terminal
    cl11404
    Location:21111
    Biotinyl_lipoyl_domains; Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl, ...
  4. NM_048368.3NP_430255.2  RNA polymerase II subunit A C-terminal domain phosphatase isoform 2

    See identical proteins and their annotated locations for NP_430255.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) is missing a coding exon in the 3' region compared to variant 1. This results in a frame-shift and a shorter isoform (2, also known as FCP1b) with a distinct C-terminus (lacking the carboxy-terminal TFIIF-binding protein domain) compared to isoform 1.
    Source sequence(s)
    AA282312, BC047999, BC052576, BM512113, DR001939
    Consensus CDS
    CCDS12018.1
    UniProtKB/Swiss-Prot
    Q9Y5B0
    Related
    ENSP00000075430.7, ENST00000075430.11
    Conserved Domains (4) summary
    TIGR02250
    Location:177323
    FCP1_euk; FCP1-like phosphatase, phosphatase domain
    cd00027
    Location:636716
    BRCT; Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo ...
    pfam09309
    Location:716806
    FCP1_C; FCP1, C-terminal
    cl11404
    Location:21111
    Biotinyl_lipoyl_domains; Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl, ...

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_000018.10 Reference GRCh38.p12 Primary Assembly

    Range
    79679801..79754510
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011526261.1XP_011524563.1  RNA polymerase II subunit A C-terminal domain phosphatase isoform X1

    Conserved Domains (4) summary
    TIGR02250
    Location:177323
    FCP1_euk; FCP1-like phosphatase, phosphatase domain
    cd00027
    Location:636716
    BRCT; Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo ...
    pfam09309
    Location:716851
    FCP1_C; FCP1, C-terminal
    cl11404
    Location:21111
    Biotinyl_lipoyl_domains; Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl, ...
  2. XM_017026078.1XP_016881567.1  RNA polymerase II subunit A C-terminal domain phosphatase isoform X2

Reference GRCh38.p12 ALT_REF_LOCI_1

Genomic

  1. NT_187617.1 Reference GRCh38.p12 ALT_REF_LOCI_1

    Range
    122434..160679
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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