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CTDSPL CTD small phosphatase like [ Homo sapiens (human) ]

Gene ID: 10217, updated on 2-Nov-2024

Summary

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Official Symbol
CTDSPLprovided by HGNC
Official Full Name
CTD small phosphatase likeprovided by HGNC
Primary source
HGNC:HGNC:16890
See related
Ensembl:ENSG00000144677 MIM:608592; AllianceGenome:HGNC:16890
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PSR1; SCP3; HYA22; RBSP3; C3orf8
Summary
Predicted to enable RNA polymerase II CTD heptapeptide repeat phosphatase activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within negative regulation of G1/S transition of mitotic cell cycle and negative regulation of protein phosphorylation. Located in extracellular exosome. Biomarker of lung non-small cell carcinoma. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in skin (RPKM 20.1), gall bladder (RPKM 14.9) and 25 other tissues See more
Orthologs
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Genomic context

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See CTDSPL in Genome Data Viewer
Location:
3p22.2
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (37861880..37984469)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (37866043..37988649)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (37903371..38025960)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene integrin subunit alpha 9 Neighboring gene VISTA enhancer hs1961 Neighboring gene ribosomal protein L21 pseudogene 135 Neighboring gene ITGA9 antisense RNA 1 Neighboring gene NADH:ubiquinone oxidoreductase complex assembly factor 4 pseudogene 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:37904633-37905134 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:37905135-37905634 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:37945100-37945826 Neighboring gene Sharpr-MPRA regulatory region 2528 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19674 Neighboring gene HNF1 motif-containing MPRA enhancer 248 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:38003356-38003967 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:38010565-38011128 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:38011129-38011690 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:38028477-38028654 Neighboring gene Sharpr-MPRA regulatory region 12639 Neighboring gene Sharpr-MPRA regulatory region 7921 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38035775-38036392 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38039104-38039674 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14200 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14201 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38047479-38047979 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38050723-38051473 Neighboring gene microRNA 26a-1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14202 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14203 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14204 Neighboring gene villin like Neighboring gene phospholipase C delta 1

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. RBSP3 (HYA22) is a tumor suppressor gene implicated in major epithelial malignancies. Kashuba VI, et al. Proc Natl Acad Sci U S A, 2004 Apr 6. PMID 15051889, Free PMC Article
  2. RBSP3 is frequently altered in premalignant cervical lesions: clinical and prognostic significance. Mitra S, et al. Genes Chromosomes Cancer, 2010 Feb. PMID 19885927
  3. The miR-181 family promotes cell cycle by targeting CTDSPL, a phosphatase-like tumor suppressor in uveal melanoma. Zhang L, et al. J Exp Clin Cancer Res, 2018 Jan 30. PMID 29382357, Free PMC Article
  4. High mutability of the tumor suppressor genes RASSF1 and RBSP3 (CTDSPL) in cancer. Kashuba VI, et al. PLoS One, 2009 May 29. PMID 19478941, Free PMC Article
  5. Sequence analysis of a 685-kb genomic region on chromosome 3p22-p21.3 that is homozygously deleted in a lung carcinoma cell line. Ishikawa S, et al. DNA Res, 1997 Feb 28. PMID 9179494

See all (44) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Hsa-miR-503-5p regulates CTDSPL to accelerate cisplatin resistance and angiogenesis of lung adenocarcinoma cells.
    Title: Hsa-miR-503-5p regulates CTDSPL to accelerate cisplatin resistance and angiogenesis of lung adenocarcinoma cells.
  2. 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.
  3. we have presented herein the novel finding that miR-181b contributes to cell cycle progression through depressing the expression of CTDSPL, which in turn activates the downstream effector E2F1 and promotes S-phase entry.
    Title: The miR-181 family promotes cell cycle by targeting CTDSPL, a phosphatase-like tumor suppressor in uveal melanoma.
  4. our data also suggests the importance ofLIMD1 and CDC25A in conjunction with HPV for use as diagnostic and prognostic markers of HNSCC, whereas RBSP3 as a prognostic marker only.
    Title: Differential transmission of the molecular signature of RBSP3, LIMD1 and CDC25A in basal/ parabasal versus spinous of normal epithelium during head and neck tumorigenesis: A mechanistic study.
  5. data suggest that overexpression of p-RB1 in basal-parabasal layers of normal cervical epithelium was due to methylation/low functional-linked non-synonimous SNPs of P16 and RBSP3. This pattern was maintained during cervical carcinogenesis by additional deletion/mutation
    Title: Association of P16-RBSP3 inactivation with phosphorylated RB1 overexpression in basal-parabasal layers of normal cervix unchanged during CACX development.
  6. CTDSPL and Rb directly interact and can be involved in the common mechanism of cell cycle regulation.
    Title: [Interaction of two tumor suppressors: Phosphatase CTDSPL and Rb protein].
  7. identified RBSP3, a phosphatase-like tumor suppressor, as a bona fide target of miR-100 and validated that RBSP3 was involved in cell differentiation and survival in acute myeloid leukemia
    Title: MiR-100 regulates cell differentiation and survival by targeting RBSP3, a phosphatase-like tumor suppressor in acute myeloid leukemia.
  8. tumor suppressor genes RBSP3/CTDSPL, NPRL2/G21 and RASSF1A are downregulated in primary non-small cell lung cancer
    Title: Simultaneous down-regulation of tumor suppressor genes RBSP3/CTDSPL, NPRL2/G21 and RASSF1A in primary non-small cell lung cancer.
  9. dysregulation of hMLH1, ITGA9, and RBSP3 associated multiple cellular pathways are needed for the development of early dysplastic lesions of the head and neck.
    Title: Frequent alterations of the candidate genes hMLH1, ITGA9 and RBSP3 in early dysplastic lesions of head and neck: clinical and prognostic significance.
  10. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Submit: New GeneRIF Correction See all GeneRIFs (17)

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
A genome-wide association study of breast and prostate cancer in the NHLBI's Framingham Heart Study.
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

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 metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables molecular_function ND
No biological Data available
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 biological_process ND
No biological Data available
more info
  
involved_in negative regulation of G1/S transition of mitotic cell cycle IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in extracellular exosome HDA PubMed 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
CTD small phosphatase-like protein
Names
CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase-like
CTDSP-like
NIF-like protein
NLI-interacting factor 1
RB protein serine phosphatase from chromosome 3
carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 3
nuclear LIM interactor-interacting factor 1
small C-terminal domain phosphatase 3
small CTD phosphatase 3
NP_001008393.1
NP_005799.2
XP_016861008.1
XP_016861009.1
XP_047303138.1
XP_054200880.1
XP_054200881.1
XP_054200882.1

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.

mRNA and Protein(s)

  1. NM_001008392.2 → NP_001008393.1  CTD small phosphatase-like protein isoform 1

    See identical proteins and their annotated locations for NP_001008393.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC093415, AC105752, AI143812, AJ575645
    Consensus CDS
    CCDS33734.1
    UniProtKB/Swiss-Prot
    O15194, Q3ZTU0, Q70KI4, Q7Z5Q2
    Related
    ENSP00000273179.5, ENST00000273179.10
    Conserved Domains (1) summary
    TIGR02251
    Location:106 → 265
    HIF-SF_euk; Dullard-like phosphatase domain

  2. NM_005808.3 → NP_005799.2  CTD small phosphatase-like protein isoform 2

    See identical proteins and their annotated locations for NP_005799.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon, compared to variant 1, resulting in a shorter protein (isoform 2) compared to isoform 1.
    Source sequence(s)
    AC093415, AC105752, AI192993, AJ575644
    Consensus CDS
    CCDS33735.1
    UniProtKB/Swiss-Prot
    O15194
    Related
    ENSP00000398288.2, ENST00000443503.6
    Conserved Domains (1) summary
    TIGR02251
    Location:95 → 254
    HIF-SF_euk; Dullard-like phosphatase domain

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    37861880..37984469
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017005519.2 → XP_016861008.1  CTD small phosphatase-like protein isoform X1

    UniProtKB/TrEMBL
    H7C353
    Related
    ENSP00000409600.2, ENST00000436654.2
    Conserved Domains (1) summary
    TIGR02251
    Location:106 → 265
    HIF-SF_euk; Dullard-like phosphatase domain

  2. XM_047447182.1 → XP_047303138.1  CTD small phosphatase-like protein isoform X2

  3. XM_017005520.2 → XP_016861009.1  CTD small phosphatase-like protein isoform X3

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791771.1 Reference GRCh38.p14 PATCHES

    Range
    434537..434935
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    37866043..37988649
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054344905.1 → XP_054200880.1  CTD small phosphatase-like protein isoform X1

    UniProtKB/TrEMBL
    H7C353

  2. XM_054344906.1 → XP_054200881.1  CTD small phosphatase-like protein isoform X2

  3. XM_054344907.1 → XP_054200882.1  CTD small phosphatase-like protein isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O15194.2 GenPept UniProtKB/Swiss-Prot:O15194

Gene LinkOut

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