U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

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

    Gene ID: 9150, updated on 17-Jun-2024

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CTDP1 in Genome Data Viewer
    Location:
    18q23
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (79676768..79756625)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (79950566..80031824)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (77439803..77516625)

    Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904335 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77350417-77351256 Neighboring gene CRISPR/Cas9-targeted silencer 8 Neighboring gene uncharacterized LOC284240 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77358253-77359146 Neighboring gene uncharacterized LOC105372228 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77371029-77371622 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77371623-77372215 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr18:77378514-77379195 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr18:77379196-77379876 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77386241-77386740 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77386889-77387390 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77390729-77391230 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:77404966-77405480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77416983-77417518 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77417519-77418054 Neighboring gene CTDP1 divergent transcript Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:77438928-77439435 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:77439436-77439944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77441560-77442068 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77442069-77442575 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77457803-77458304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77458305-77458804 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:77471187-77471379 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_50709 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77557221-77557817 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77576519-77577020 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77577021-77577520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13545 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr18:77585975-77587174 Neighboring gene potassium voltage-gated channel modifier subfamily G member 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77601626-77602126 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9578 Neighboring gene Sharpr-MPRA regulatory region 1017 Neighboring gene Sharpr-MPRA regulatory region 1467 Neighboring gene Sharpr-MPRA regulatory region 11655 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:77664167-77664802 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77672372-77673288 Neighboring gene solute carrier family 66 member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9579 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9580 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9581 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9582

    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 Functions

    What's a GeneRIF?

    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 PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    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 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 
    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

    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
    XP_047293877.1
    XP_047293878.1
    XP_047293879.1
    XP_047293880.1
    XP_047293881.1
    XP_047293882.1
    XP_047293883.1
    XP_054175319.1
    XP_054175320.1
    XP_054175321.1
    XP_054175322.1
    XP_054175323.1
    XP_054175324.1
    XP_054175325.1
    XP_054175326.1
    XP_054175327.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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
      UniProtKB/TrEMBL
      K7EJD2
      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_001318511.2NP_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: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_004715.5NP_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: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_048368.4NP_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: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: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000018.10 Reference GRCh38.p14 Primary Assembly

      Range
      79676768..79756625
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047437924.1XP_047293880.1  RNA polymerase II subunit A C-terminal domain phosphatase isoform X5

      UniProtKB/TrEMBL
      K7EJD2
    2. XM_047437922.1XP_047293878.1  RNA polymerase II subunit A C-terminal domain phosphatase isoform X2

      UniProtKB/TrEMBL
      K7EJD2
    3. XM_047437926.1XP_047293882.1  RNA polymerase II subunit A C-terminal domain phosphatase isoform X6

      UniProtKB/TrEMBL
      A0A0J9YWJ4
    4. XM_011526261.2XP_011524563.1  RNA polymerase II subunit A C-terminal domain phosphatase isoform X4

      UniProtKB/TrEMBL
      A0A0J9YWB6
      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, ...
    5. XM_047437925.1XP_047293881.1  RNA polymerase II subunit A C-terminal domain phosphatase isoform X5

      UniProtKB/TrEMBL
      K7EJD2
    6. XM_047437923.1XP_047293879.1  RNA polymerase II subunit A C-terminal domain phosphatase isoform X3

      UniProtKB/TrEMBL
      K7EJD2
    7. XM_047437921.1XP_047293877.1  RNA polymerase II subunit A C-terminal domain phosphatase isoform X1

      UniProtKB/TrEMBL
      K7EJD2
    8. XM_047437927.1XP_047293883.1  RNA polymerase II subunit A C-terminal domain phosphatase isoform X7

      UniProtKB/TrEMBL
      A0A0J9YWJ4
    9. XM_017026078.2XP_016881567.1  RNA polymerase II subunit A C-terminal domain phosphatase isoform X8

      UniProtKB/TrEMBL
      K7EJD2

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NT_187617.1 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      122436..160679
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060942.1 Alternate T2T-CHM13v2.0

      Range
      79950566..80031824
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054319348.1XP_054175323.1  RNA polymerase II subunit A C-terminal domain phosphatase isoform X5

      UniProtKB/TrEMBL
      K7EJD2
    2. XM_054319345.1XP_054175320.1  RNA polymerase II subunit A C-terminal domain phosphatase isoform X2

      UniProtKB/TrEMBL
      K7EJD2
    3. XM_054319350.1XP_054175325.1  RNA polymerase II subunit A C-terminal domain phosphatase isoform X6

      UniProtKB/TrEMBL
      A0A0J9YWJ4
    4. XM_054319347.1XP_054175322.1  RNA polymerase II subunit A C-terminal domain phosphatase isoform X4

      UniProtKB/TrEMBL
      A0A0J9YWB6
    5. XM_054319349.1XP_054175324.1  RNA polymerase II subunit A C-terminal domain phosphatase isoform X5

      UniProtKB/TrEMBL
      K7EJD2
    6. XM_054319346.1XP_054175321.1  RNA polymerase II subunit A C-terminal domain phosphatase isoform X3

      UniProtKB/TrEMBL
      K7EJD2
    7. XM_054319351.1XP_054175326.1  RNA polymerase II subunit A C-terminal domain phosphatase isoform X7

      UniProtKB/TrEMBL
      A0A0J9YWJ4
    8. XM_054319344.1XP_054175319.1  RNA polymerase II subunit A C-terminal domain phosphatase isoform X5

      UniProtKB/TrEMBL
      K7EJD2
    9. XM_054319352.1XP_054175327.1  RNA polymerase II subunit A C-terminal domain phosphatase isoform X8

      UniProtKB/TrEMBL
      K7EJD2