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    CTDSP1 CTD small phosphatase 1 [ Homo sapiens (human) ]

    Gene ID: 58190, updated on 5-Sep-2021

    Summary

    Official Symbol
    CTDSP1provided by HGNC
    Official Full Name
    CTD small phosphatase 1provided by HGNC
    Primary source
    HGNC:HGNC:21614
    See related
    Ensembl:ENSG00000144579 MIM:605323
    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
    NIF3; SCP1; NLIIF; NLI-IF
    Summary
    This gene encodes a member of the small C-terminal domain phosphatase (SCP) family of nuclear phosphatases. These proteins play a role in transcriptional regulation through specific dephosphorylation of phosphoserine 5 within tandem heptapeptide repeats of the C-terminal domain of RNA polymerase II. The encoded protein plays a role in neuronal gene silencing in non-neuronal cells, and may also inhibit osteoblast differentiation. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Oct 2011]
    Expression
    Ubiquitous expression in placenta (RPKM 26.9), ovary (RPKM 24.5) and 25 other tissues See more
    Orthologs
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    Genomic context

    See CTDSP1 in Genome Data Viewer
    Location:
    2q35
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (218398233..218405941)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (219262956..219270664)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene CATIP antisense RNA 1 Neighboring gene ciliogenesis associated TTC17 interacting protein Neighboring gene solute carrier family 11 member 1 Neighboring gene microRNA 26b Neighboring gene villin 1 Neighboring gene ubiquitin specific peptidase 37 Neighboring gene RN7SK pseudogene 38

    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?

    Phenotypes

    Associated conditions

    Description Tests
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    GeneReviews: Not available

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    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
    PubMed 
    enables RNA polymerase II CTD heptapeptide repeat phosphatase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables phosphoprotein phosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein serine phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein threonine phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in extracellular exosome HDA PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus TAS
    Traceable Author Statement
    more info
    PubMed 

    General protein information

    Preferred Names
    carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
    Names
    CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1
    NLI-interacting factor 3
    nuclear LIM interactor-interacting factor 3
    small C-terminal domain phosphatase 1
    NP_001193807.1
    NP_067021.1
    NP_872580.1
    XP_011509871.1
    XP_011509872.1
    XP_016860104.1
    XP_016860105.1
    XP_016860106.1
    XP_016860107.1

    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_030418.1 RefSeqGene

      Range
      6531..12604
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001206878.2NP_001193807.1  carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 isoform 3

      See identical proteins and their annotated locations for NP_001193807.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and has multiple differences in the coding region, including the use of an alternate start codon, compared to variant 1. The encoded isoform (3) is shorter and has a distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AC021016, BC012977, BX446444
      Consensus CDS
      CCDS56166.1
      UniProtKB/Swiss-Prot
      Q9GZU7
      Related
      ENSP00000392248.1, ENST00000443891.5
      Conserved Domains (1) summary
      TIGR02251
      Location:89248
      HIF-SF_euk; Dullard-like phosphatase domain
    2. NM_021198.3NP_067021.1  carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 isoform 1

      See identical proteins and their annotated locations for NP_067021.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AF229162, AY279529
      Consensus CDS
      CCDS2416.1
      UniProtKB/Swiss-Prot
      Q9GZU7
      UniProtKB/TrEMBL
      A0A024R461
      Related
      ENSP00000273062.2, ENST00000273062.7
      Conserved Domains (1) summary
      TIGR02251
      Location:90249
      HIF-SF_euk; Dullard-like phosphatase domain
    3. NM_182642.3NP_872580.1  carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 isoform 2

      See identical proteins and their annotated locations for NP_872580.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AF229162, AY279529, BC012977
      UniProtKB/Swiss-Prot
      Q9GZU7
      Related
      ENSP00000404301.1, ENST00000452977.5
      Conserved Domains (1) summary
      TIGR02251
      Location:89248
      HIF-SF_euk; Dullard-like phosphatase domain

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

      Range
      218398233..218405941
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017004617.2XP_016860106.1  carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 isoform X5

    2. XM_017004618.2XP_016860107.1  carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 isoform X6

    3. XM_017004615.2XP_016860104.1  carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 isoform X1

    4. XM_017004616.2XP_016860105.1  carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 isoform X2

    5. XM_011511569.3XP_011509871.1  carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 isoform X3

      Conserved Domains (2) summary
      COG5190
      Location:213387
      FCP1; TFIIF-interacting CTD phosphatase, includes NLI-interacting factor [Transcription]
      TIGR02251
      Location:223382
      HIF-SF_euk; Dullard-like phosphatase domain
    6. XM_011511570.2XP_011509872.1  carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 isoform X4

      Conserved Domains (2) summary
      COG5190
      Location:212386
      FCP1; TFIIF-interacting CTD phosphatase, includes NLI-interacting factor [Transcription]
      TIGR02251
      Location:222381
      HIF-SF_euk; Dullard-like phosphatase domain

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001206879.1: Suppressed sequence

      Description
      NM_001206879.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
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