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Aliases for CTDSP1 Gene

Aliases for CTDSP1 Gene

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

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. Among its related pathways are Coregulation of Androgen receptor activity and Regulation of cytoplasmic and nuclear SMAD2/3 signaling. Gene Ontology (GO) annotations related to this gene include phosphatase activity and CTD phosphatase activity. An important paralog of this gene is CTDSPL.

UniProtKB/Swiss-Prot 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

Additional gene information for CTDSP1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CTDSP1 Gene

Genomics for CTDSP1 Gene

GeneHancer (GH) Regulatory Elements for CTDSP1 Gene

Promoters and enhancers for CTDSP1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02J218393 Promoter/Enhancer 2.9 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 650.7 +2.8 2751 14.4 CLOCK MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 E2F8 ZNF143 SP3 CTDSP1 ENSG00000273361 MIR26B GC02P218403 CNOT9 AAMP USP37 RNF25 NHEJ1 ZNF142
GH02J218281 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 12 -108.0 -108018 17.9 MLX DMAP1 IRF4 YY1 ZNF143 SP3 NFYC MEF2D GLIS1 RCOR2 TMBIM1 ENSG00000261338 SLC11A1 ANKZF1 CTDSP1 MIR26B CNOT9 ARPC2 PNKD CATIP-AS1
GH02J218269 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 10.6 -125.6 -125616 7.1 MLX DMAP1 YY1 SLC30A9 E2F8 ZNF143 SP3 NFYC SSRP1 ZNF610 AAMP PNKD USP37 ENSG00000261338 NHEJ1 CNPPD1 SLC23A3 CTDSP1 ARPC2 CNOT9
GH02J219277 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 10.5 +881.4 881377 4.5 MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF143 SP3 NFYC TUBA4A PIR48822 GC02P219281 DNAJB2 NHEJ1 USP37 PTPRN DNPEP CNPPD1 OBSL1
GH02J218710 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 10.5 +313.0 312956 2.4 HDGF PKNOX1 FOXA2 CLOCK MLX ARNT ARID4B SIN3A DMAP1 ZNF2 TTLL4 AAMP CNOT9 NHEJ1 SLC23A3 USP37 STK36 ANKZF1 LINC00608 RNF25
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CTDSP1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CTDSP1 gene promoter:

Genomic Locations for CTDSP1 Gene

Genomic Locations for CTDSP1 Gene
chr2:218,398,256-218,405,941
(GRCh38/hg38)
Size:
7,686 bases
Orientation:
Plus strand
chr2:219,262,979-219,270,664
(GRCh37/hg19)

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; Positions=72; 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

Post-translational modifications for CTDSP1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CTDSP1 Gene

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

Suggested Antigen Peptide Sequences for CTDSP1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

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

No data available for 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:
[a protein]-serine/threonine phosphate + H(2)O = [a protein]-serine/threonine + phosphate.
UniProtKB/Swiss-Prot EnzymeRegulation:
Stimulated by GTF2F1. Inhibited by beryllofluoride anions.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
pH dependence: Optimum pH is 5. {ECO:0000269 PubMed:12721286};

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,IEA --
GO:0005515 protein binding IPI 12721286
GO:0008420 CTD phosphatase activity IDA 12721286
GO:0016787 hydrolase activity IEA --
GO:0016791 phosphatase 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>

Animal Model Products

Clone Products

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
extracellular 5
nucleus 5
cytosol 2

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

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 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 Agonist, Activator, Target 1243
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
calcium Approved Nutra 0
Aspartate Beryllium Trifluoride Experimental Pharma Target 0

(1) Additional Compounds for CTDSP1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Phosphate
  • [po(OH)3]
  • Acide phosphorique
  • Acidum phosphoricum
  • H3PO4
  • Orthophosphoric acid
14265-44-2
genes like me logo Genes that share compounds with CTDSP1: view

Transcripts for CTDSP1 Gene

Unigene Clusters for CTDSP1 Gene

CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1:
Representative Sequences:

Clone Products

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
ECgene alternative splicing isoforms for
CTDSP1

Expression for CTDSP1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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



NURSA nuclear receptor signaling pathways regulating expression of CTDSP1 Gene:

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

  • Lung(2.2)
genes like me logo Genes that share expression patterns with CTDSP1: view

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 34 33
  • 99.62 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Ctdsp1 16 34 33
  • 92.34 (n)
dog
(Canis familiaris)
Mammalia CTDSP1 34 33
  • 91.95 (n)
OneToOne
cow
(Bos Taurus)
Mammalia CTDSP1 34 33
  • 91.41 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Ctdsp1 33
  • 90.8 (n)
oppossum
(Monodelphis domestica)
Mammalia CTDSP1 34
  • 82 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 16 (a)
ManyToMany
chicken
(Gallus gallus)
Aves CTDSP1 34 33
  • 79.83 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CTDSP1 34
  • 78 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ctdsp1 33
  • 73.46 (n)
zebrafish
(Danio rerio)
Actinopterygii ctdsp1 34
  • 75 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011422 33
  • 65.28 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG5830 34 33
  • 60.64 (n)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea scpl-1 34 33
  • 57.29 (n)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PSR2 34
  • 29 (a)
ManyToMany
PSR1 34
  • 26 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 75 (a)
OneToMany
bread mold
(Neurospora crassa)
Ascomycetes NCU08380 33
  • 55.22 (n)
Species where no ortholog for CTDSP1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 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

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 from dbSNP and Humsavar for CTDSP1 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs1000027061 -- 218,404,221(+) G/A downstream_transcript_variant, genic_downstream_transcript_variant, intron_variant
rs1000081277 -- 218,401,932(+) C/G intron_variant
rs1000637242 -- 218,397,793(+) TAACTAACTA/TAACTA/TAACTAACTAACTA upstream_transcript_variant
rs1000668580 -- 218,397,682(+) G/A upstream_transcript_variant
rs1000921583 -- 218,405,326(+) T/C 3_prime_UTR_variant, genic_downstream_transcript_variant

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

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

Disorders for CTDSP1 Gene

Additional Disease Information for CTDSP1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for CTDSP1 Gene.

No data available for MalaCards , 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 58
  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 58
  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 58
  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 44 58
  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 58

Products for CTDSP1 Gene

Sources for CTDSP1 Gene