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

Gene ID: 58190, updated on 7-Jun-2020

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

Genomic context

See CTDSP1 in Genome Data Viewer
Location:
2q35
Exon count:
9
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (218398233..218405941)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (219263061..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

NHGRI GWAS Catalog

Description
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
NHGRI GWA Catalog

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
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 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
phosphoprotein phosphatase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
negative regulation of G1/S transition of mitotic cell cycle IEA
Inferred from Electronic Annotation
more info
 
negative regulation of neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of protein phosphorylation IEA
Inferred from Electronic Annotation
more info
 
protein dephosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
extracellular exosome HDA PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
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)

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, ENST00000273062.6
    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.

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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