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

    Gene ID: 58190, updated on 2-Nov-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
    mouse all
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    Genomic context

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    See CTDSP1 in Genome Data Viewer
    Location:
    2q35
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (218396351..218405941)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (218882480..218892071)
    RS_2024_09 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 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. 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
    2. 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
    3. 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
    4. Ethnic divergence and linkage disequilibrium of novel SNPs in the human NLI-IF gene: evidence of human origin and lack of association with tuberculosis susceptibility. Ma X, et al. J Hum Genet, 2002. PMID 11950066
    5. 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

    See all (47) 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 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_2024_08

    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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