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

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; AllianceGenome:HGNC:2498
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: mouse all
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Genomic context

Location:: 18q23

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	18	NC_000018.10 (79676768..79756625)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	18	NC_060942.1 (79950566..80031824)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	18	NC_000018.9 (77439803..77516625)

Chromosome 18 - NC_000018.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Study identifies CTDP1 as an autoantigen specific for Behcet Disease.
Title: Identification of Novel Biomarkers for Behcet Disease Diagnosis Using Human Proteome Microarray Approach.
results demonstrated that CTDP1 was upregulated in human lung cancer tissues. In addition, it implied that CTDP1 played an important role in cell proliferation and may be a useful therapeutic target in human lung cancer.
Title: Lentivirus-mediated knockdown of CTDP1 inhibits lung cancer cell growth in vitro.
Data propose that Fcp1 has a crucial role in the liaison between dephosphorylation and ubiquitination that drives mitosis exit.
Title: Fcp1-dependent dephosphorylation is required for M-phase-promoting factor inactivation at mitosis exit.
although FCP1 is intrinsically disordered, the above 16 residues composing the RAP74 binding surface form nascent alpha-helical structure in the unbound state.
Title: The disordered C-terminus of the RNA polymerase II phosphatase FCP1 is partially helical in the unbound state.
NMR assignments for C terminal region
Title: NMR assignment of the intrinsically disordered C-terminal region of Homo sapiens FCP1 in the unbound state.
NMR and thermodynamic studies further elucidate the complex molecular mechanism by which TFIIF and FCP1 cooperate for RNAPII recycling.
Title: NMR structure of a complex formed by the carboxyl-terminal domain of human RAP74 and a phosphorylated peptide from the central domain of the FCP1 phosphatase.
These data suggest that icariin exerts its potent osteogenic effect through induction of Runx2 expression, production of BMP-4 and activation of BMP signaling.
Title: Human phosphorylated CTD-interacting protein, PCIF1, negatively modulates gene expression by RNA polymerase II.
FCP1 augments tat transactivation of the HIV-1 long-terminal repeat
Title: A protein phosphatase from human T cells augments tat transactivation of the human immunodeficiency virus type 1 long-terminal repeat.
cocrystal structure of the winged-helix domain of human RNA polymerase II-associating protein 74 bound to the alpha-helical C terminus of human FCP1
Title: Molecular mechanism of recruitment of TFIIF- associating RNA polymerase C-terminal domain phosphatase (FCP1) by transcription factor IIF.
FCP1 kinase from HeLa cells is phosphorylated and affects transcription elongation
Title: The C-terminal domain phosphatase and transcription elongation activities of FCP1 are regulated by phosphorylation.

Submit: New GeneRIF Correction See all GeneRIFs (16)

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

Associated conditions

Description	Tests
Congenital cataracts-facial dysmorphism-neuropathy syndrome MedGen: C1858726 OMIM: 604168 GeneReviews: CTDP1-Related Congenital Cataracts, Facial Dysmorphism, and Neuropathy	Compare labs

EBI GWAS Catalog

Description
Genome-wide association study of clinical dimensions of schizophrenia: polygenic effect on disorganized symptoms. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D18S1268 (e-PCR)
- UniSTS:13606

D18S1015 (e-PCR)
- UniSTS:153685

SHGC-145820 (e-PCR)
- UniSTS:183141

D18S1141 (e-PCR), detects polymorphism
- UniSTS:69231

RH98831 (e-PCR)
- UniSTS:89802

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables MAP kinase serine/threonine phosphatase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat phosphatase activity	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II CTD heptapeptide repeat phosphatase activity	IDA Inferred from Direct Assay more info	PubMed
enables TFIIF-class transcription factor complex binding	IPI Inferred from Physical Interaction more info	PubMed
enables Tat protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables calmodulin-dependent protein phosphatase activity	IEA Inferred from Electronic Annotation more info
enables histone H2AXS140 phosphatase activity	IEA Inferred from Electronic Annotation more info
enables myosin phosphatase activity	IEA Inferred from Electronic Annotation more info
enables phosphoprotein phosphatase activity	TAS Traceable Author Statement more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cell division	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in exit from mitosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of cell growth involved in cardiac muscle cell development	IEA Inferred from Electronic Annotation more info
involved_in positive regulation by host of viral transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in protein dephosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in transcription elongation by RNA polymerase II	TAS Traceable Author Statement more info

Component	Evidence Code	Pubs
located_in centrosome	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in midbody	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
part_of protein-containing complex	IMP Inferred from Mutant Phenotype more info	PubMed
located_in spindle	IDA Inferred from Direct Assay more info	PubMed
located_in spindle midzone	IDA Inferred from Direct Assay more info	PubMed
located_in spindle pole	IDA Inferred from Direct Assay more info	PubMed

General protein information

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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

EC 3.1.3.16

NP_001305440.1

EC 3.1.3.16

NP_004706.3

EC 3.1.3.16

NP_430255.2

EC 3.1.3.16

XP_011524563.1

EC 3.1.3.16

XP_016881567.1

EC 3.1.3.16

XP_047293877.1

EC 3.1.3.16

XP_047293878.1

EC 3.1.3.16

XP_047293879.1

EC 3.1.3.16

XP_047293880.1

EC 3.1.3.16

XP_047293881.1

EC 3.1.3.16

XP_047293882.1

EC 3.1.3.16

XP_047293883.1

EC 3.1.3.16

XP_054175319.1

EC 3.1.3.16

XP_054175320.1

EC 3.1.3.16

XP_054175321.1

EC 3.1.3.16

XP_054175322.1

EC 3.1.3.16

XP_054175323.1

EC 3.1.3.16

XP_054175324.1

EC 3.1.3.16

XP_054175325.1

EC 3.1.3.16

XP_054175326.1

EC 3.1.3.16

XP_054175327.1

EC 3.1.3.16

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

NG_007988.1 RefSeqGene

Range

5001..79710

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_236

mRNA and Protein(s)

NM_001202504.1 → NP_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

UniProtKB/TrEMBL

K7EJD2

Conserved Domains (3) summary

TIGR02250
Location:58 → 204

FCP1_euk; FCP1-like phosphatase, phosphatase domain

cd00027
Location:517 → 597

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:597 → 842

FCP1_C; FCP1, C-terminal
NM_001318511.2 → NP_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

UniProtKB/TrEMBL

A0A0J9YWB6

Related

ENSP00000465119.1, ENST00000591598.5

Conserved Domains (4) summary

TIGR02250
Location:177 → 323

FCP1_euk; FCP1-like phosphatase, phosphatase domain

cd00027
Location:636 → 716

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:716 → 860

FCP1_C; FCP1, C-terminal

cl11404
Location:21 → 111

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, ...
NM_004715.5 → NP_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)

BC047999, BC052576, BM512113, DR001939

Consensus CDS

CCDS12017.1

UniProtKB/Swiss-Prot

A8MY97, Q7Z644, Q96BZ1, Q9Y5B0, Q9Y6F5

UniProtKB/TrEMBL

A0A0J9YWB6

Related

ENSP00000484525.2, ENST00000613122.5

Conserved Domains (4) summary

TIGR02250
Location:177 → 323

FCP1_euk; FCP1-like phosphatase, phosphatase domain

cd00027
Location:636 → 716

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:716 → 961

FCP1_C; FCP1, C-terminal

cl11404
Location:21 → 111

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, ...
NM_048368.4 → NP_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, AC021594, BC047999, BC052576, BM512113, DR001939

Consensus CDS

CCDS12018.1

UniProtKB/TrEMBL

A0A0J9YWB6

Related

ENSP00000075430.7, ENST00000075430.11

Conserved Domains (4) summary

TIGR02250
Location:177 → 323

FCP1_euk; FCP1-like phosphatase, phosphatase domain

cd00027
Location:636 → 716

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:716 → 806

FCP1_C; FCP1, C-terminal

cl11404
Location:21 → 111

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: 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

NC_000018.10 Reference GRCh38.p14 Primary Assembly

Range

79676768..79756625

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047437924.1 → XP_047293880.1 RNA polymerase II subunit A C-terminal domain phosphatase isoform X5
XM_047437922.1 → XP_047293878.1 RNA polymerase II subunit A C-terminal domain phosphatase isoform X2
XM_047437926.1 → XP_047293882.1 RNA polymerase II subunit A C-terminal domain phosphatase isoform X6
XM_011526261.2 → XP_011524563.1 RNA polymerase II subunit A C-terminal domain phosphatase isoform X4

UniProtKB/TrEMBL

A0A0J9YWB6

Conserved Domains (4) summary

TIGR02250
Location:177 → 323

FCP1_euk; FCP1-like phosphatase, phosphatase domain

cd00027
Location:636 → 716

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:716 → 851

FCP1_C; FCP1, C-terminal

cl11404
Location:21 → 111

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, ...
XM_047437925.1 → XP_047293881.1 RNA polymerase II subunit A C-terminal domain phosphatase isoform X5
XM_047437923.1 → XP_047293879.1 RNA polymerase II subunit A C-terminal domain phosphatase isoform X3
XM_047437921.1 → XP_047293877.1 RNA polymerase II subunit A C-terminal domain phosphatase isoform X1
XM_047437927.1 → XP_047293883.1 RNA polymerase II subunit A C-terminal domain phosphatase isoform X7
XM_017026078.2 → XP_016881567.1 RNA polymerase II subunit A C-terminal domain phosphatase isoform X8

UniProtKB/TrEMBL

K7EJD2

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

NT_187617.1 Reference GRCh38.p14 ALT_REF_LOCI_1

Range

122436..160679

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060942.1 Alternate T2T-CHM13v2.0

Range

79950566..80031824

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054319348.1 → XP_054175323.1 RNA polymerase II subunit A C-terminal domain phosphatase isoform X5
XM_054319345.1 → XP_054175320.1 RNA polymerase II subunit A C-terminal domain phosphatase isoform X2
XM_054319350.1 → XP_054175325.1 RNA polymerase II subunit A C-terminal domain phosphatase isoform X6
XM_054319347.1 → XP_054175322.1 RNA polymerase II subunit A C-terminal domain phosphatase isoform X4
XM_054319349.1 → XP_054175324.1 RNA polymerase II subunit A C-terminal domain phosphatase isoform X5
XM_054319346.1 → XP_054175321.1 RNA polymerase II subunit A C-terminal domain phosphatase isoform X3
XM_054319351.1 → XP_054175326.1 RNA polymerase II subunit A C-terminal domain phosphatase isoform X7
XM_054319344.1 → XP_054175319.1 RNA polymerase II subunit A C-terminal domain phosphatase isoform X5
XM_054319352.1 → XP_054175327.1 RNA polymerase II subunit A C-terminal domain phosphatase isoform X8