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 cel... See more...

Aliases for CTDSP1 Gene

Aliases for CTDSP1 Gene

  • CTD Small Phosphatase 1 2 3 5
  • NLIIF 2 3 4
  • SCP1 2 3 4
  • CTD (Carboxy-Terminal Domain, RNA Polymerase II, Polypeptide A) Small Phosphatase 1 2 3
  • Carboxy-Terminal Domain RNA Polymerase II Polypeptide A Small Phosphatase 1 3 4
  • Nuclear LIM Interactor-Interacting Factor 3 3 4
  • Small C-Terminal Domain Phosphatase 1 3 4
  • NLI-Interacting Factor 3 3 4
  • Small CTD Phosphatase 1 2 4
  • EC 3.1.3.16 4 50
  • NLI-IF 3 4
  • NIF3 3 4
  • Nuclear LIM Interactor-Interacting Factor 2
  • CTDSP1 5

External Ids for CTDSP1 Gene

Previous GeneCards Identifiers for CTDSP1 Gene

  • GC02P219467
  • GC02P219091
  • GC02P218972
  • GC02P219262
  • GC02P211117

Summaries for CTDSP1 Gene

Entrez Gene Summary for CTDSP1 Gene

  • 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]

GeneCards Summary for CTDSP1 Gene

CTDSP1 (CTD Small Phosphatase 1) is a Protein Coding gene. Diseases associated with CTDSP1 include Carnitine-Acylcarnitine Translocase Deficiency. Among its related pathways are Regulation of cytoplasmic and nuclear SMAD2/3 signaling and Coregulation of Androgen receptor activity. Gene Ontology (GO) annotations related to this gene include phosphatase activity and RNA polymerase II CTD heptapeptide repeat phosphatase activity. An important paralog of this gene is CTDSPL.

UniProtKB/Swiss-Prot Summary for CTDSP1 Gene

  • Preferentially catalyzes the dephosphorylation of 'Ser-5' within the tandem 7 residue repeats in the C-terminal domain (CTD) of the largest RNA polymerase II subunit POLR2A. Negatively regulates RNA polymerase II transcription, possibly by controlling the transition from initiation/capping to processive transcript elongation. Recruited by REST to neuronal genes that contain RE-1 elements, leading to neuronal gene silencing in non-neuronal cells.

Gene Wiki entry for CTDSP1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CTDSP1 Gene

Genomics for CTDSP1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CTDSP1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CTDSP1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CTDSP1

Top Transcription factor binding sites by QIAGEN in the CTDSP1 gene promoter:
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • Roaz

Genomic Locations for CTDSP1 Gene

Latest Assembly
chr2:218,398,233-218,405,941
(GRCh38/hg38)
Size:
7,709 bases
Orientation:
Plus strand

Previous Assembly
chr2:219,262,956-219,270,664
(GRCh37/hg19 by Entrez Gene)
Size:
7,709 bases
Orientation:
Plus strand

chr2:219,262,979-219,270,664
(GRCh37/hg19 by Ensembl)
Size:
7,686 bases
Orientation:
Plus strand

Genomic View for CTDSP1 Gene

Genes around CTDSP1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CTDSP1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CTDSP1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CTDSP1 Gene

Proteins for CTDSP1 Gene

  • Protein details for CTDSP1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9GZU7-CTDS1_HUMAN
    Recommended name:
    Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
    Protein Accession:
    Q9GZU7
    Secondary Accessions:
    • C9IYG0
    • Q7Z5Q3
    • Q7Z5Q4

    Protein attributes for CTDSP1 Gene

    Size:
    261 amino acids
    Molecular mass:
    29203 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • Monomer (By similarity). Interacts with GTF2F1. Interacts with REST.
    SequenceCaution:
    • Sequence=AAP34398.1; Type=Frameshift; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for CTDSP1 Gene

    Alternative splice isoforms for CTDSP1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CTDSP1 Gene

Selected DME Specific Peptides for CTDSP1 Gene

Q9GZU7:
  • DNSPASY
  • HQVYVLKRP
  • GNYVKDL
  • DLDETLVHSSFK
  • FTASLAKYADPV

Post-translational modifications for CTDSP1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for CTDSP1 Gene

Gene Families for CTDSP1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for CTDSP1 Gene

InterPro:
Blocks:
  • NLI interacting factor

Suggested Antigen Peptide Sequences for CTDSP1 Gene

GenScript: Design optimal peptide antigens:
  • Small C-terminal domain phosphatase 1 (CTDS1_HUMAN)
genes like me logo Genes that share domains with CTDSP1: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for CTDSP1 Gene

Function for CTDSP1 Gene

Molecular function for CTDSP1 Gene

UniProtKB/Swiss-Prot Function:
Preferentially catalyzes the dephosphorylation of 'Ser-5' within the tandem 7 residue repeats in the C-terminal domain (CTD) of the largest RNA polymerase II subunit POLR2A. Negatively regulates RNA polymerase II transcription, possibly by controlling the transition from initiation/capping to processive transcript elongation. Recruited by REST to neuronal genes that contain RE-1 elements, leading to neuronal gene silencing in non-neuronal cells.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=H2O + O-phospho-L-seryl-[protein] = L-seryl-[protein] + phosphate; Xref=Rhea:RHEA:20629, Rhea:RHEA-COMP:9863, Rhea:RHEA-COMP:11604, ChEBI:CHEBI:15377, ChEBI:CHEBI:29999, ChEBI:CHEBI:43474, ChEBI:CHEBI:83421; EC=3.1.3.16; Evidence={ECO:0000269|PubMed:12721286, ECO:0000269|PubMed:17157258};.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=H2O + O-phospho-L-threonyl-[protein] = L-threonyl-[protein] + phosphate; Xref=Rhea:RHEA:47004, Rhea:RHEA-COMP:11060, Rhea:RHEA-COMP:11605, ChEBI:CHEBI:15377, ChEBI:CHEBI:30013, ChEBI:CHEBI:43474, ChEBI:CHEBI:61977; EC=3.1.3.16; Evidence={ECO:0000269|PubMed:12721286, ECO:0000269|PubMed:17157258};.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
pH dependence: Optimum pH is 5. {ECO:0000269|PubMed:12721286};
UniProtKB/Swiss-Prot EnzymeRegulation:
Stimulated by GTF2F1. Inhibited by beryllofluoride anions.

Enzyme Numbers (IUBMB) for CTDSP1 Gene

Phenotypes From GWAS Catalog for CTDSP1 Gene

Gene Ontology (GO) - Molecular Function for CTDSP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004721 phosphoprotein phosphatase activity IBA 21873635
GO:0004722 protein serine/threonine phosphatase activity IEA --
GO:0005515 protein binding IPI 12721286
GO:0008420 RNA polymerase II CTD heptapeptide repeat phosphatase activity IEA,IDA 12721286
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with CTDSP1: view
genes like me logo Genes that share phenotypes with CTDSP1: view

Animal Models for CTDSP1 Gene

MGI Knock Outs for CTDSP1:
  • Ctdsp1 Ctdsp1<tm1b(EUCOMM)Wtsi>

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CTDSP1

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CTDSP1 Gene

Localization for CTDSP1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CTDSP1 Gene

Nucleus. Note=Colocalizes with RNA polymerase II.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CTDSP1 gene
Compartment Confidence
nucleus 5
extracellular 4
cytosol 2
plasma membrane 1
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for CTDSP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus TAS 10967134
GO:0005654 nucleoplasm IDA --
GO:0070062 extracellular exosome HDA 23533145
genes like me logo Genes that share ontologies with CTDSP1: view

Pathways & Interactions for CTDSP1 Gene

genes like me logo Genes that share pathways with CTDSP1: view

SIGNOR curated interactions for CTDSP1 Gene

Activates:
Inactivates:

Gene Ontology (GO) - Biological Process for CTDSP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001933 negative regulation of protein phosphorylation IEA --
GO:0006357 regulation of transcription by RNA polymerase II IDA 12721286
GO:0006470 protein dephosphorylation IEA,IDA 12721286
GO:0016311 dephosphorylation IEA --
GO:0045665 negative regulation of neuron differentiation IEA --
genes like me logo Genes that share ontologies with CTDSP1: view

Drugs & Compounds for CTDSP1 Gene

(5) Drugs for CTDSP1 Gene - From: DrugBank and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Citric acid Approved, Vet_approved Nutra Target 1606
Water Approved Pharma 0
Aspartate beryllium trifluoride Experimental Pharma Target 0
Phosphate Experimental Pharma 0
Calcium Nutra 6959
genes like me logo Genes that share compounds with CTDSP1: view

Transcripts for CTDSP1 Gene

mRNA/cDNA for CTDSP1 Gene

4 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
15 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CTDSP1

Alternative Splicing Database (ASD) splice patterns (SP) for CTDSP1 Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11a · 11b · 11c ^ 12a · 12b ^ 13a · 13b · 13c · 13d · 13e
SP1: - - - - - - - - -
SP2: - - - -
SP3: - - - -
SP4: - -
SP5: - - - - - - -
SP6:
SP7: - - - - - - - - - -
SP8: - - - - - - -
SP9: - - - - -
SP10: - -
SP11: -

Relevant External Links for CTDSP1 Gene

GeneLoc Exon Structure for
CTDSP1

Expression for CTDSP1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CTDSP1 Gene

mRNA differential expression in normal tissues according to GTEx for CTDSP1 Gene

This gene is overexpressed in Whole Blood (x4.9).

Protein differential expression in normal tissues from HIPED for CTDSP1 Gene

This gene is overexpressed in NK cells (22.2), Bone (15.5), and Breast (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CTDSP1 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CTDSP1

SOURCE GeneReport for Unigene cluster for CTDSP1 Gene:

Hs.444468

mRNA Expression by UniProt/SwissProt for CTDSP1 Gene:

Q9GZU7-CTDS1_HUMAN
Tissue specificity: Expression is restricted to non-neuronal tissues. Highest expression in skeletal muscle, spleen, lung and placenta.

Evidence on tissue expression from TISSUES for CTDSP1 Gene

  • Skin(2.4)
  • Nervous system(2.3)
  • Blood(2.3)
  • Muscle(2.3)
  • Lung(2.2)
  • Heart(2.2)
  • Intestine(2.2)
  • Kidney(2.1)
genes like me logo Genes that share expression patterns with CTDSP1: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for CTDSP1 Gene

Orthologs for CTDSP1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for CTDSP1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia CTDSP1 29 30
  • 99.62 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Ctdsp1 29 16 30
  • 92.34 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia CTDSP1 29 30
  • 91.95 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia CTDSP1 29 30
  • 91.41 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Ctdsp1 29
  • 90.8 (n)
Oppossum
(Monodelphis domestica)
Mammalia CTDSP1 30
  • 82 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 30
  • 16 (a)
ManyToMany
Chicken
(Gallus gallus)
Aves CTDSP1 29 30
  • 79.83 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia CTDSP1 30
  • 78 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia ctdsp1 29
  • 73.46 (n)
Zebrafish
(Danio rerio)
Actinopterygii ctdsp1 30
  • 75 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011422 29
  • 65.28 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG5830 29 30
  • 60.64 (n)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea scpl-1 29 30
  • 57.29 (n)
OneToMany
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PSR2 30
  • 29 (a)
ManyToMany
PSR1 30
  • 26 (a)
ManyToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 75 (a)
OneToMany
Bread mold
(Neurospora crassa)
Ascomycetes NCU08380 29
  • 55.22 (n)
Species where no ortholog for CTDSP1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for CTDSP1 Gene

ENSEMBL:
Gene Tree for CTDSP1 (if available)
TreeFam:
Gene Tree for CTDSP1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CTDSP1: view image
Alliance of Genome Resources:
Additional Orthologs for CTDSP1

Paralogs for CTDSP1 Gene

Paralogs for CTDSP1 Gene

(4) SIMAP similar genes for CTDSP1 Gene using alignment to 4 proteins:

  • CTDS1_HUMAN
  • H7C1Z7_HUMAN
  • H7C270_HUMAN
  • H7C3E0_HUMAN
genes like me logo Genes that share paralogs with CTDSP1: view

Variants for CTDSP1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CTDSP1 Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
rs2227249 Benign: not provided 218,401,662(+) G/Ap.Ala56Thr
NM_021198.3(CTDSP1):c.166G>A (p.Ala56Thr)
MISSENSE
rs2227250 Benign: not provided 218,401,670(+) C/T
NM_021198.3(CTDSP1):c.174C>T (p.Ser58=)
SYNONYMOUS

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CTDSP1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for CTDSP1 Gene

Variant ID Type Subtype PubMed ID
nsv1073011 CNV deletion 25765185
nsv3166 CNV insertion 18451855
nsv519829 CNV loss 19592680

Variation tolerance for CTDSP1 Gene

Residual Variation Intolerance Score: 32.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.73; 46.70% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CTDSP1 Gene

Human Gene Mutation Database (HGMD)
CTDSP1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CTDSP1
Leiden Open Variation Database (LOVD)
CTDSP1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CTDSP1 Gene

Disorders for CTDSP1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for CTDSP1 Gene - From: COP

Disorder Aliases PubMed IDs
carnitine-acylcarnitine translocase deficiency
  • cactd
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for CTDSP1

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with CTDSP1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CTDSP1 Gene

Publications for CTDSP1 Gene

  1. A novel RNA polymerase II C-terminal domain phosphatase that preferentially dephosphorylates serine 5. (PMID: 12721286) Yeo M … Gill GN (The Journal of biological chemistry 2003) 2 3 4 22
  2. 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. (PMID: 11950066) Ma X … Graviss E (Journal of human genetics 2002) 2 3 22
  3. Complete nucleotide sequence and genomic structure of the human NRAMP1 gene region on chromosome region 2q35. (PMID: 10967134) Marquet S … Schurr E (Mammalian genome : official journal of the International Mammalian Genome Society 2000) 3 4 22
  4. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 40
  5. Determinants for dephosphorylation of the RNA polymerase II C-terminal domain by Scp1. (PMID: 17157258) Zhang Y … Noel JP (Molecular cell 2006) 4 22

Products for CTDSP1 Gene

Sources for CTDSP1 Gene