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

Gene ID: 58190, updated on 3-Apr-2024

Summary

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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; AllianceGenome:HGNC:21614
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

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Location:
2q35
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (218396351..218405941)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (218882480..218892071)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (219261074..219270664)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene CATIP antisense RNA 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:219221475-219221986 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12315 Neighboring gene ribosomal protein L19 pseudogene 5 Neighboring gene CATIP antisense RNA 1 Neighboring gene ciliogenesis associated TTC17 interacting protein Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:219257303-219257972 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:219258642-219259310 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:219259311-219259979 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12316 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17122 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12317 Neighboring gene solute carrier family 11 member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12318 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12319 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12320 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12321 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17123 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17124 Neighboring gene microRNA 26b Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:219289129-219289629 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:219290512-219290729 Neighboring gene villin 1 Neighboring gene Sharpr-MPRA regulatory region 3568 Neighboring gene ubiquitin specific peptidase 37 Neighboring gene RN7SK pseudogene 38

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. C-terminal domain small phosphatase 1 (CTDSP1) regulates growth factor expression and axonal regeneration in peripheral nerve tissue. Gervasi NM, et al. Sci Rep, 2021 Jul 14. PMID 34262056, Free PMC Article
  2. In vivo putative O-GlcNAcylation of human SCP1 and evidence for possible role of its N-terminal disordered structure. Koo J, et al. BMB Rep, 2014 Oct. PMID 25081999, Free PMC Article
  3. A study of substrate specificity for a CTD phosphatase, SCP1, by proteomic screening of binding partners. Kim YJ, et al. Biochem Biophys Res Commun, 2014 May 30. PMID 24769477
  4. Selective inactivation of a human neuronal silencing phosphatase by a small molecule inhibitor. Zhang M, et al. ACS Chem Biol, 2011 May 20. PMID 21348431, Free PMC Article
  5. Structural and functional analysis of the phosphoryl transfer reaction mediated by the human small C-terminal domain phosphatase, Scp1. Zhang M, et al. Protein Sci, 2010 May. PMID 20222012, Free PMC Article

See all (44) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. GPC5 suppresses lung cancer progression and metastasis via intracellular CTDSP1/AhR/ARNT signaling axis and extracellular exosome secretion.
    Title: GPC5 suppresses lung cancer progression and metastasis via intracellular CTDSP1/AhR/ARNT signaling axis and extracellular exosome secretion.
  2. C-terminal domain small phosphatase 1 (CTDSP1) regulates growth factor expression and axonal regeneration in peripheral nerve tissue.
    Title: C-terminal domain small phosphatase 1 (CTDSP1) regulates growth factor expression and axonal regeneration in peripheral nerve tissue.
  3. Deubiquitinase USP29 promotes gastric cancer cell migration by cooperating with phosphatase SCP1 to stabilize Snail protein.
    Title: Deubiquitinase USP29 promotes gastric cancer cell migration by cooperating with phosphatase SCP1 to stabilize Snail protein.
  4. Tumor suppressor properties of the small C-terminal domain phosphatases in non-small cell lung cancer.
    Title: Tumor suppressor properties of the small C-terminal domain phosphatases in non-small cell lung cancer.
  5. REST is a bona fide substrate for SCP1 in vivo and that SCP1 phosphatase activity protects REST against degradation.
    Title: Phosphatase activity of small C-terminal domain phosphatase 1 (SCP1) controls the stability of the key neuronal regulator RE1-silencing transcription factor (REST).
  6. Our results provide a novel mechanistic insight into the activation of Myc by 27-HC via transcriptional repression of PP2A, SCP1 and FBW7 to increase Myc protein stability in breast cancer cells.
    Title: 27-Hydroxycholesterol increases Myc protein stability via suppressing PP2A, SCP1 and FBW7 transcription in MCF-7 breast cancer cells.
  7. SCP1 is the phosphatase that counterregulates the MAPK-mediated phosphorylation of Ser(68)-Twist1.
    Title: The Small C-terminal Domain Phosphatase 1 Inhibits Cancer Cell Migration and Invasion by Dephosphorylating Ser(P)68-Twist1 to Accelerate Twist1 Protein Degradation.
  8. SCP1 regulates c-Myc stability and functions through dephosphorylating c-Myc Serine-62.
    Title: SCP1 regulates c-Myc stability and functions through dephosphorylating c-Myc Ser62.
  9. hSCP1 may be an beta-O-linked N-acetylglucosamine modified protein in vivo.
    Title: In vivo putative O-GlcNAcylation of human SCP1 and evidence for possible role of its N-terminal disordered structure.
  10. CTDSP1 activity stabilizes REST in stem cells and ERK-dependent phosphorylation combined with Pin1 activity promotes REST degradation in neural progenitors.
    Title: C-terminal domain small phosphatase 1 and MAP kinase reciprocally control REST stability and neuronal differentiation.
Submit: New GeneRIF Correction See all GeneRIFs (18)

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

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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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
  
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 myosin phosphatase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in negative regulation of G1/S transition of mitotic cell cycle IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of neurogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of neuron differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of protein phosphorylation IEA
Inferred from Electronic Annotation
more info
  
involved_in protein dephosphorylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
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

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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_001387197.1
NP_001387198.1
NP_001387199.1
NP_001387200.1
NP_001387201.1
NP_001387202.1
NP_001387203.1
NP_001387204.1
NP_001387205.1
NP_067021.1
NP_872580.1
XP_011509871.1
XP_011509872.1
XP_054199220.1
XP_054199221.1

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

  1. NG_030418.1 RefSeqGene

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

mRNA and Protein(s)

  1. NM_001206878.2 → NP_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/TrEMBL
    H7C270
    Conserved Domains (1) summary
    TIGR02251
    Location:89 → 248
    HIF-SF_euk; Dullard-like phosphatase domain

  2. NM_001400268.1 → NP_001387197.1  carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC021016

  3. NM_001400269.1 → NP_001387198.1  carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC021016

  4. NM_001400270.1 → NP_001387199.1  carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 isoform 5

    Status: REVIEWED

    Source sequence(s)
    AC021016

  5. NM_001400271.1 → NP_001387200.1  carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 isoform 6

    Status: REVIEWED

    Source sequence(s)
    AC021016
    Related
    ENSP00000404301.2, ENST00000452977.6

  6. NM_001400272.1 → NP_001387201.1  carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 isoform 7

    Status: REVIEWED

    Source sequence(s)
    AC021016

  7. NM_001400273.1 → NP_001387202.1  carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 isoform 8

    Status: REVIEWED

    Source sequence(s)
    AC021016

  8. NM_001400274.1 → NP_001387203.1  carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 isoform 9

    Status: REVIEWED

    Source sequence(s)
    AC021016

  9. NM_001400275.1 → NP_001387204.1  carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 isoform 10

    Status: REVIEWED

    Source sequence(s)
    AC021016

  10. NM_001400276.1 → NP_001387205.1  carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 isoform 11

    Status: REVIEWED

    Source sequence(s)
    AC021016

  11. NM_021198.3 → NP_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
    C9IYG0, Q7Z5Q3, Q7Z5Q4, Q9GZU7
    UniProtKB/TrEMBL
    H7C270
    Related
    ENSP00000273062.2, ENST00000273062.7
    Conserved Domains (1) summary
    TIGR02251
    Location:90 → 249
    HIF-SF_euk; Dullard-like phosphatase domain

  12. NM_182642.3 → NP_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/TrEMBL
    H7C270
    Related
    ENSP00000518515.1, ENST00000710837.1
    Conserved Domains (1) summary
    TIGR02251
    Location:89 → 248
    HIF-SF_euk; Dullard-like phosphatase domain

RNA

  1. NR_174456.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC021016

  2. NR_174457.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC021016

  3. NR_174458.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC021016
    Related
    ENST00000710828.1

  4. NR_174459.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC021016

  5. NR_174460.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC021016
    Related
    ENST00000491064.6

  6. NR_174461.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC021016
    Related
    ENST00000473420.6

  7. NR_174462.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC021016

  8. NR_174463.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC021016

  9. NR_174464.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC021016

  10. NR_174465.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC021016

  11. NR_174466.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC021016
    Related
    ENST00000498160.6

  12. NR_174467.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC021016

  13. NR_174468.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC021016
    Related
    ENST00000710838.1

  14. NR_174469.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC021016

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    218396351..218405941
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011511569.3 → XP_011509871.1  carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 isoform X1

    Conserved Domains (2) summary
    COG5190
    Location:213 → 387
    FCP1; TFIIF-interacting CTD phosphatase, includes NLI-interacting factor [Transcription]
    TIGR02251
    Location:223 → 382
    HIF-SF_euk; Dullard-like phosphatase domain

  2. XM_011511570.2 → XP_011509872.1  carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 isoform X2

    Conserved Domains (2) summary
    COG5190
    Location:212 → 386
    FCP1; TFIIF-interacting CTD phosphatase, includes NLI-interacting factor [Transcription]
    TIGR02251
    Location:222 → 381
    HIF-SF_euk; Dullard-like phosphatase domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    218882480..218892071
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054343245.1 → XP_054199220.1  carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 isoform X1

  2. XM_054343246.1 → XP_054199221.1  carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 isoform X2

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.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9GZU7.1 GenPept UniProtKB/Swiss-Prot:Q9GZU7

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