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CTDSPL2 CTD small phosphatase like 2 [ Homo sapiens (human) ]

Gene ID: 51496, updated on 3-Nov-2024

Summary

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Official Symbol
CTDSPL2provided by HGNC
Official Full Name
CTD small phosphatase like 2provided by HGNC
Primary source
HGNC:HGNC:26936
See related
Ensembl:ENSG00000137770 MIM:618739; AllianceGenome:HGNC:26936
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
SCP4; HSPC058; HSPC129
Summary
Enables 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 BMP signaling pathway; positive regulation of protein export from nucleus; and protein dephosphorylation. Located in nucleoplasm. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in lymph node (RPKM 7.7), testis (RPKM 7.5) and 25 other tissues See more
Orthologs
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Genomic context

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See CTDSPL2 in Genome Data Viewer
Location:
15q15.3-q21.1
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (44427629..44529038)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (42234989..42336704)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (44719827..44821236)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene golgi membrane protein 2 Neighboring gene glyceraldehyde 3 phosphate dehydrogenase pseudogene 43 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:44695413-44695632 Neighboring gene uncharacterized LOC124903479 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:44718729-44719336 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:44719337-44719944 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:44719945-44720551 Neighboring gene heterogeneous nuclear ribonucleoprotein M pseudogene 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:44828013-44828800 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6395 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6396 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6397 Neighboring gene EIF3J divergent transcript Neighboring gene eukaryotic translation initiation factor 3 subunit J Neighboring gene SPG11 vesicle trafficking associated, spatacsin

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. Hypermethylation of CTDSPL2 prior to necrotizing enterocolitis onset. Klerk DH, et al. Epigenomics, 2023 Apr. PMID 37309586
  2. CTD small phosphatase like 2 (CTDSPL2) can increase ε- and γ-globin gene expression in K562 cells and CD34+ cells derived from umbilical cord blood. Ma YN, et al. BMC Cell Biol, 2010 Oct 9. PMID 20932329, Free PMC Article
  3. C-terminal domain small phosphatase-like 2 promotes epithelial-to-mesenchymal transition via Snail dephosphorylation and stabilization. Zhao Y, et al. Open Biol, 2018 Apr. PMID 29618518, Free PMC Article
  4. The phosphatase CTDSPL2 is phosphorylated in mitosis and a target for restraining tumor growth and motility in pancreatic cancer. Xiao Y, et al. Cancer Lett, 2022 Feb 1. PMID 34813892, Free PMC Article
  5. Human SCP4 is a chromatin-associated CTD phosphatase and exhibits the dynamic translocation during erythroid differentiation. Wani S, et al. J Biochem, 2016 Aug. PMID 26920047

See all (40) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Hypermethylation of CTDSPL2 prior to necrotizing enterocolitis onset.
    Title: Hypermethylation of CTDSPL2 prior to necrotizing enterocolitis onset.
  2. SCP4-STK35/PDIK1L complex is a dual phospho-catalytic signaling dependency in acute myeloid leukemia.
    Title: SCP4-STK35/PDIK1L complex is a dual phospho-catalytic signaling dependency in acute myeloid leukemia.
  3. The phosphatase CTDSPL2 is phosphorylated in mitosis and a target for restraining tumor growth and motility in pancreatic cancer.
    Title: The phosphatase CTDSPL2 is phosphorylated in mitosis and a target for restraining tumor growth and motility in pancreatic cancer.
  4. CTD small phosphatase like 2 plays a critical role in EMT through Snail dephosphorylation and stabilization.
    Title: C-terminal domain small phosphatase-like 2 promotes epithelial-to-mesenchymal transition via Snail dephosphorylation and stabilization.
  5. expression significantly increased in skeletal muscle of chronic kidney disease patients
    Title: The nuclear phosphatase SCP4 regulates FoxO transcription factors during muscle wasting in chronic kidney disease.
  6. SCP4 is a unique chromatin-associated, Ser5-preferential CTD phosphatase that preferentially distributes to transcriptionally silenced gene regions and may participate in gene regulation during erythroid differentiation.
    Title: Human SCP4 is a chromatin-associated CTD phosphatase and exhibits the dynamic translocation during erythroid differentiation.
  7. proteomic screening was conducted to identify binding partners of CTDSPL2 in nuclear extract through immunoprecipitation of CTDSPL2 with its associated.
    Title: A systematic study of nuclear interactome of C-terminal domain small phosphatase-like 2 using inducible expression system and shotgun proteomics.
  8. increases epsilon- and gamma-globin gene expression during erythroid differentiation
    Title: CTD small phosphatase like 2 (CTDSPL2) can increase ε- and γ-globin gene expression in K562 cells and CD34+ cells derived from umbilical cord blood.
Submit: New GeneRIF Correction

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

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

Clone Names

  • FLJ10523

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA polymerase II CTD heptapeptide repeat phosphatase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables phosphoprotein phosphatase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in negative regulation of BMP signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of protein export from nucleus IEA
Inferred from Electronic Annotation
more info
  
involved_in protein export from nucleus 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 nucleoplasm IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
CTD small phosphatase-like protein 2
Names
CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2
CTDSP-like 2
NP_057480.2
XP_005254498.1
XP_006720628.1
XP_011519967.1
XP_016877795.1
XP_047288608.1
XP_047288609.1
XP_047288610.1
XP_047288611.1
XP_054234142.1
XP_054234143.1
XP_054234144.1
XP_054234145.1
XP_054234146.1
XP_054234147.1
XP_054234148.1
XP_054234149.1

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_016396.3 → NP_057480.2  CTD small phosphatase-like protein 2

    See identical proteins and their annotated locations for NP_057480.2

    Status: VALIDATED

    Source sequence(s)
    AC009996, AF161478, BC035744
    Consensus CDS
    CCDS10110.1
    UniProtKB/Swiss-Prot
    Q05D32, Q3ZTU1, Q6AI06, Q8IYI9, Q9NVT2, Q9NZX8, Q9P030
    Related
    ENSP00000260327.4, ENST00000260327.9
    Conserved Domains (1) summary
    TIGR02251
    Location:287 → 448
    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    44427629..44529038
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005254441.3 → XP_005254498.1  CTD small phosphatase-like protein 2 isoform X1

    See identical proteins and their annotated locations for XP_005254498.1

    UniProtKB/Swiss-Prot
    Q05D32, Q3ZTU1, Q6AI06, Q8IYI9, Q9NVT2, Q9NZX8, Q9P030
    Related
    ENSP00000452837.1, ENST00000558966.5
    Conserved Domains (1) summary
    TIGR02251
    Location:287 → 448
    HIF-SF_euk; Dullard-like phosphatase domain

  2. XM_011521665.3 → XP_011519967.1  CTD small phosphatase-like protein 2 isoform X2

    Conserved Domains (1) summary
    TIGR02251
    Location:286 → 447
    HIF-SF_euk; Dullard-like phosphatase domain

  3. XM_006720565.3 → XP_006720628.1  CTD small phosphatase-like protein 2 isoform X1

    See identical proteins and their annotated locations for XP_006720628.1

    UniProtKB/Swiss-Prot
    Q05D32, Q3ZTU1, Q6AI06, Q8IYI9, Q9NVT2, Q9NZX8, Q9P030
    Related
    ENSP00000453051.1, ENST00000558373.5
    Conserved Domains (1) summary
    TIGR02251
    Location:287 → 448
    HIF-SF_euk; Dullard-like phosphatase domain

  4. XM_017022306.3 → XP_016877795.1  CTD small phosphatase-like protein 2 isoform X2

    Conserved Domains (1) summary
    TIGR02251
    Location:286 → 447
    HIF-SF_euk; Dullard-like phosphatase domain

  5. XM_047432652.1 → XP_047288608.1  CTD small phosphatase-like protein 2 isoform X3

  6. XM_047432655.1 → XP_047288611.1  CTD small phosphatase-like protein 2 isoform X4

  7. XM_047432653.1 → XP_047288609.1  CTD small phosphatase-like protein 2 isoform X3

  8. XM_047432654.1 → XP_047288610.1  CTD small phosphatase-like protein 2 isoform X3

RNA

  1. XR_007064454.1 RNA Sequence

  2. XR_007064456.1 RNA Sequence

  3. XR_007064453.1 RNA Sequence

  4. XR_007064452.1 RNA Sequence

  5. XR_007064455.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    42234989..42336704
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054378167.1 → XP_054234142.1  CTD small phosphatase-like protein 2 isoform X1

    UniProtKB/Swiss-Prot
    Q05D32, Q3ZTU1, Q6AI06, Q8IYI9, Q9NVT2, Q9NZX8, Q9P030

  2. XM_054378170.1 → XP_054234145.1  CTD small phosphatase-like protein 2 isoform X2

  3. XM_054378172.1 → XP_054234147.1  CTD small phosphatase-like protein 2 isoform X3

  4. XM_054378169.1 → XP_054234144.1  CTD small phosphatase-like protein 2 isoform X2

  5. XM_054378171.1 → XP_054234146.1  CTD small phosphatase-like protein 2 isoform X3

  6. XM_054378174.1 → XP_054234149.1  CTD small phosphatase-like protein 2 isoform X4

  7. XM_054378173.1 → XP_054234148.1  CTD small phosphatase-like protein 2 isoform X3

  8. XM_054378168.1 → XP_054234143.1  CTD small phosphatase-like protein 2 isoform X1

    UniProtKB/Swiss-Prot
    Q05D32, Q3ZTU1, Q6AI06, Q8IYI9, Q9NVT2, Q9NZX8, Q9P030

RNA

  1. XR_008488961.1 RNA Sequence

  2. XR_008488962.1 RNA Sequence

  3. XR_008488964.1 RNA Sequence

  4. XR_008488960.1 RNA Sequence

  5. XR_008488963.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q05D32.2 GenPept UniProtKB/Swiss-Prot:Q05D32

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