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CTDSPL (CTD (Carboxy-Terminal Domain, RNA Polymerase II, Polypeptide A) Small Phosphatase-Like)

Written2014-03Shreya Sarkar, Guru Prasad Maiti, Chinmay Kumar Panda
Department of Oncogene Regulation, Chittaranjan National Cancer Institute, 37 S P Mukherjee Road, Kolkata - 700026, West Bengal, India

(Note : for Links provided by Atlas : click)

Identity

Alias_namesC3orf8
chromosome 3 open reading frame 8
CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase-like
Alias_symbol (synonym)HYA22
SCP3
PSR1
RBSP3
Other alias
HGNC (Hugo) CTDSPL
LocusID (NCBI) 10217
Atlas_Id 40189
Location 3p22.2  [Link to chromosome band 3p22]
Location_base_pair Starts at 37862178 and ends at 37984469 bp from pter ( according to hg19-Feb_2009)  [Mapping CTDSPL.png]
Fusion genes
(updated 2016)
ADCY9 (16p13.3) / CTDSPL (3p22.2)CTDSPL (3p22.2) / CTDSPL (3p22.2)CTDSPL (3p22.2) / TMCC1 (3q22.1)
CTDSPL (3p22.2) / WRN (8p12)ITGA9 (3p22.2) / CTDSPL (3p22.2)OXSR1 (3p22.2) / CTDSPL (3p22.2)
PDHX (11p13) / CTDSPL (3p22.2)PRCP (11q14.1) / CTDSPL (3p22.2)

DNA/RNA

 
  Diagram shows the different transcripts of CTDSPL (Brown, Blue, Grey and Maroon boxes). Beginning of boxes represents transcription start sites. Filled areas represent translated regions. The larger form, CTDSPL B is shown as CTDSPL 001, whereas the smaller form, CTDSPL A is shown as CTDSPL 002. Image adapted from Ensembl.org.
Description Located in the short (p) arm of chromosome 3, the length of the CTDSPL gene is about 122.5Kb, contains 8 exons and is arranged in a telomere to centromere orientation.
Transcription The full length transcript of CTDSLP is 4459 bp (Ensembl,Transcript ID ENST00000443503). A total of 8 transcripts can be generated, out of which 5 are protein coding, 1 undergoes nonsense mediated decay, while the rest 2 do not code for a protein product. However, two splice variants of CTDSPL, the smaller CTDSPL A (lacking exon 3, therefore short of 33 bp, 11 amino acids) and the full length CTDSPL B were identified by Kashuba et al., 2004.
Interesting observation: The transcription start site for CTDSPL A and CTDSPL B are different (from ensemble.org). While the larger B form has a shorter 5'UTR, the smaller A form has a larger 5'UTR, although their translation start sites remain common. Difference in the size of the 5'UTR may account for differential splicing between the isoforms.
Pseudogene None reported.

Protein

 
  Schematic diagram of full length RBSP3 protein, showing different domains. Adapted from PDB O15194. Data origin/ Colour codes: Data in Green originates from UniProtKB; Data in Yellow originates from Pfam, by interacting with the HMMER3 website; Data in Grey has been calculated using BioJava. Protein disorder predictions are based on JRONN, a Java implementation of RONN. (a. Red- Potentially disordered region. b. Blue- Probably ordered region. Hydropathy has been calculated using a sliding window of 15 residues and summing up scored from standard hydrophobicity tables. a. Red- Hydrophobic. b. Blue- Hydrophilic); Data in blue originates from PDB. Secstruc- Secondary structure projected from representative PDB entries onto the UniProt sequence. (a. Red box - Helix. b. Yellow box - Sheet. c. Grey tube- Coil); Data in red indicates combined ranges of Homology Models from SBKB and the Protein Model Portal.
Description The full length CTDSPL protein (CTDSPL B) is 276 amino acids in length, with a molecular weight of 31KD. The smaller protein, CTDSPL A is 265 amino acids in length (amino acids 79- 89 missing) and 29.9 KD in weight. Amino acids 102-260 contain the FCP1 homology domain, which contains an essential protein serine phosphatase that dephosphorylates the C-terminal domain (CTD) of RNA polymerase II.
 
  CTDSPL Protein expression data from MOPED1, PaxDb2 and MAXQB3. 1. MOPED - Eugene Kolker, Bioinformatics & High-throughput Analysis Lab, Seattle Children's Research Institute. 2. PaxDb - Christian von Mering, Bioinformatics Group, Institute of Molecular Life Sciences, University of Zurich. 3. MAXQB - Matthias Mann, Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Germany. The data was normalized as follows: 1. For each sample, ppm protein values were calculated, if not provided so by data sources. For each sample from MAXQB, iBAQ expression values were divided by sum of values of each sample, and multiplied by 1000000. For all samples, data was gene centrically aggregated by summing expression values of all isoforms for each gene. 2. For better visualization of graphs, expression values are drawn on a root scale, which is an intermediate between log and linear scales as used for our mRNA expression graphs (Safran et al., 2003).
Localisation Both nuclear and cytoplasmic (Maiti et al., 2012; Sarkar et al., 2013).
Function - CTDSPL is a serine phosphatase which regulates cell growth and differentiation. It dephosphorylates RB at serine 807/ 811 (hence called RB1 serine phosphatase from human chromosome 3), thereby increasing RB-E2F interaction and halting the cell cycle at G1/S boundary (Kashuba et al., 2004).
- It also inactivates RNA polymerase-II by preferential dephosphorylation of 'Ser-5' within the tandem 7 residues repeats in the C-terminal domain (CTD) of the largest RNA polymerase II subunit, thus controlling the transcription machinery (hence called carboxy-terminal domain, RNA polymerase II, polypeptide A small phosphatase-like) (Yeo et al., 2003).
- Studies also suggest that CTDSPL/RBSP3 might function as a transcriptional co-repressor, inhibiting transcription of neuronal genes in non-neuronal cells (Yeo et al., 2005), and may also act as a phosphatase of Smad1, Smad2/Smad3 and Snail (Wu et al., 2009; Sapkota et al., 2006).
Homology Chimpanzee, Rhesus monkey, dog, cow, mouse, chicken, zebrafish, S.cerevisiae, K.lactis, E.gossypii, S.pombe, M.oryzae, and N.crassa show conserved RBSP3 gene (Source NCBI homologene).
RBSP3 and miRNAs
1. miRNA 100
- RBSP3 is a bonafide target for miRNA 100.
- miRNA 100 binds to the 3`UTR of RBSP3 in regions conserved in humans, rats and mice.
- RBSP3 expression is inversely co-related with the expression of miRNA 100 in 76.5% AML cases.
2. miRNA 26a (has-miR-26a-1)
- miRNA 26a resides in the intron of RBSP3.
- It is concomitantly expressed with RBSP3 during the cell cycle.
 

Mutations

 
  Mutations and copy number variations in different organs. Red bar: Loss. Grey bar: Gain. Adapted from COSMIC gene analysis.
Germinal None reported.

Implicated in

Note
  
Entity Cervical cancer
Note - High deletion (48%, 45% cases) and methylation (26%, 25% cases) was seen in CIN and CACX respectively (Mitra et al., 2010).
- Reduced mRNA expression was seen in CACX (Mitra et al., 2010).
- RBSP3B (larger, active isoform) was under-expressed in CACX (Mitra et al., 2010).
- In HPV infected cervical cancer, high deletion (42% cases) was observed, with significant variation (p<0.05) between metastatic (64%) and non-metastatic (32%) cases (Anedchenko et al., 2007).
- Altogether, copy number change was seen in 51% cases (Anedchenko et al., 2007).
- Decreased expression was seen in 64% cases, with significant difference between metastatic (83%) and non-metastatic (52%) cases (Anedchenko et al., 2007).
- Increase in expression was also observed in some cases (Anedchenko et al., 2007).
- Altogether, change in expression was in 79% of cases (Anedchenko et al., 2007).
Prognosis RBSP3 alterations (deletion, methylation) were significantly associated with poor patient outcome and posed 4.5-13 times risk of survival (Anedchenko et al., 2007).
Oncogenesis Inactivation of RBSP3 was an early event in cervical carcinogenesis (Mitra et al., 2010).
  
  
Entity Breast cancer
Note - Study population was divided into two groups, Group A (≤40 yrs, early onset) and Group B (>40 yrs, late onset) (Sinha et al., 2008).
- High deletion (30%, 24% cases) and methylation (38%, 32% cases) were observed in Groups A and B respectively (Sinha et al., 2008).
- 28.9 ± 39.1 fold reduction in expression of RBSP3 was observed in about 33 - 40% of the tumors (Sinha et al., 2008).
- Homozygous deletion (10-18%) was observed for RBSP3 (Senchenko et al., 2004).
Prognosis Patients belonging lower to age of onset (≤40 yrs) with alterations of RBSP3 had poor disease outcome (Sinha et al., 2008).
Oncogenesis Higher alterations of RBSP3 were observed in patients belonging to the lower age of onset (Group A) (Sinha et al., 2008).
  
  
Entity Acute lymphoid leukemia (ALL)
Note Promoter methylation was seen in RBSP3 in 24% of ALL patients.
  
  
Entity Prostate cancer
Note GWAS study using Affymetrix 100K SNP GeneChip with GEE model showed that the SNP, rs9311171 (G/ T), located within RBSP3, had a notable GEE p value (1.8x 10 -6).
Oncogenesis GEE p value 1.8x 10 -6 indicates that this SNP within RBSP3 plays a role in tumor progression.
  
  
Entity Non - small cell lung cancer (NSCLC)
Note - Reduction of expression of RBSP3 was obtained for both adenocarcinoma (AC) and squamous cell carcinoma (SCC) (Senchenko et al., 2008).
- Downregulation was both genetic and epigenetic (Senchenko et al., 2008).
- For ACs, decrease in level of expression was in 88% cases and 70% cases of metastatic and non-metastatic tumors respectively, whereas for SCCs, it was in 88% cases for both metastatic and non-metastatic tumors (Senchenko et al., 2008).
- Decrease in mRNA in ACs was due to deletion (25% cases) and promoter methylation (38% cases), whereas for SCCs, it was in 30% and 80% cases for deletion and methylation respectively (Senchenko et al., 2008).
- Fold decrease in expression of RBSP3 in AC and SCC was 78% and 88% respectively, with overall 85% decrease in expression of RBSP3 in NSCLC (Senchenko et al., 2010).
Oncogenesis Deletion and methylation of promoter of RBSP3 are responsible for reduction in expression of the protein and play important roles in progression of NSCLC (Senchenko et al., 2008).
Reduction of expression of RBSP3 is required for development of lung adenocarcinomas (Senchenko et al., 2010).
  
  
Entity Ovarian cancer
Note Deletion/Methylation of RBSP3 were observed in 33% cases.
Oncogenesis RBSP3 deletion/methylation can be used as a biomarker for ovarian cancer in combination with other studied markers.
  
  
Entity Head and neck squamous cell carcinoma (HNSCC)
Note - Deletion of RBSP3 in dysplasia and HNSCC was in 24% and 32% cases respectively (Ghosh et al., 2010).
- Promoter methylation was observed in 39% and 38% cases of dysplasia and HNSCC samples respectively (Ghosh et al., 2010).
- Fold reduction of mRNA in the tumors was 33.6 ± 9.4 (Ghosh et al., 2010).
- While normal tissues expressed the larger RBSP3 B form, tumors either showed no expression of RBSP3, or preferentially expressed the smaller, less active form, RBSP3 A (Ghosh et al., 2010).
Expression of RBSP3 decreases from pre-malignant to malignant lesions (Maiti et al., 2012).
Expression of RBSP3 was seen to be increased from pre-neoadjuvant chemotherapy tumors to post-therapy tumors (Sarkar et al., 2013).
Prognosis Patients with RBSP3 alterations show poor survival (Ghosh et al., 2010).
Oncogenesis Early alteration of RBSP3 takes place in head and neck cancers (Ghosh et al., 2010).
Loss of expression of RBSP3 was seen to be required for progression from malignant to invasive cancer (Maiti et al., 2012).
Regain of expression of RBSP3 in post-therapy tumors may be one of the reasons of shrinkage of tumors due to neoadjuvant chemotherapy (Sarkar et al., 2013).
  
  
Entity Lung, renal, breast, cervical and ovarian cancers
Note High frequencies of somatic mutations in RBSP3 in different cancers suggesting it may underlay the mutator phenotype of cancer.
  
  
Entity Acute myeloid leukemia (AML)
Note RBSP3 might have a crucial role in myeloid cell differentiation towards granulocyte/monocyte lineages through pRB-E2F pathway.
  
  
Entity Cell lines
Note Leukemia cell lines RAJI, BJAB (B cell leukemia) and HL-60 (myeloid leukemia) showed hypermethylation of RBSP3 promoter.
  
  
Entity Hepatocellular carcinoma (HCC) in mouse model system
Note RBSP3 shows increase in expression (RNA, protein) upon treatment with the chemopreventive agent Amarogentin.
Oncogenesis Increase in expression of RBSP3 might play a role in chemoprevention upon treatment with amarogentin.
  

Bibliography

Down-regulation of RBSP3/CTDSPL, NPRL2/G21, RASSF1A, ITGA9, HYAL1 and HYAL2 genes in non-small cell lung cancer
Anedchenko EA, Dmitriev AA, Krasnov GS, Kondrat'eva TT, Kopantsev EP, Vinogradova TV, Zinov'eva MV, Zborovskaia IB, Polotskii( BE, Sakharova OV, Kashuba VI, Zabarovskii( ER, Senchenko VN.
Mol Biol (Mosk). 2008 Nov-Dec;42(6):965-76.
PMID 19140316
 
Frequent alterations of the candidate genes hMLH1, ITGA9 and RBSP3 in early dysplastic lesions of head and neck: clinical and prognostic significance.
Ghosh A, Ghosh S, Maiti GP, Sabbir MG, Zabarovsky ER, Roy A, Roychoudhury S, Panda CK.
Cancer Sci. 2010 Jun;101(6):1511-20. doi: 10.1111/j.1349-7006.2010.01551.x. Epub 2010 Feb 4.
PMID 20412120
 
NotI Microarrays: Novel Epigenetic Markers for Early Detection and Prognosis of High Grade Serous Ovarian Cancer.
Kashuba V, Dmitriev AA, Krasnov GS, Pavlova T, Ignatjev I, Gordiyuk VV, Gerashchenko AV, Braga EA, Yenamandra SP, Lerman M, Senchenko VN, Zabarovsky E.
Int J Mol Sci. 2012 Oct 18;13(10):13352-77. doi: 10.3390/ijms131013352.
PMID 23202957
 
High mutability of the tumor suppressor genes RASSF1 and RBSP3 (CTDSPL) in cancer.
Kashuba VI, Pavlova TV, Grigorieva EV, Kutsenko A, Yenamandra SP, Li J, Wang F, Protopopov AI, Zabarovska VI, Senchenko V, Haraldson K, Eshchenko T, Kobliakova J, Vorontsova O, Kuzmin I, Braga E, Blinov VM, Kisselev LL, Zeng YX, Ernberg I, Lerman MI, Klein G, Zabarovsky ER.
PLoS One. 2009 May 29;4(5):e5231. doi: 10.1371/journal.pone.0005231.
PMID 19478941
 
Reduced expression of LIMD1 in ulcerative oral epithelium associated with tobacco and areca nut.
Maiti GP, Ghosh A, Chatterjee R, Roy A, Sharp TV, Roychoudhury S, Panda CK.
Asian Pac J Cancer Prev. 2012;13(9):4341-6.
PMID 23167340
 
RBSP3 is frequently altered in premalignant cervical lesions: clinical and prognostic significance.
Mitra S, Mazumder Indra D, Bhattacharya N, Singh RK, Basu PS, Mondal RK, Roy A, Zabarovsky ER, Roychoudhury S, Panda CK.
Genes Chromosomes Cancer. 2010 Feb;49(2):155-70. doi: 10.1002/gcc.20726.
PMID 19885927
 
A genome-wide association study of breast and prostate cancer in the NHLBI's Framingham Heart Study.
Murabito JM, Rosenberg CL, Finger D, Kreger BE, Levy D, Splansky GL, Antman K, Hwang SJ.
BMC Med Genet. 2007 Sep 19;8 Suppl 1:S6.
PMID 17903305
 
Prevention of liver carcinogenesis by amarogentin through modulation of G1/S cell cycle check point and induction of apoptosis.
Pal D, Sur S, Mandal S, Das A, Roy A, Das S, Panda CK.
Carcinogenesis. 2012 Dec;33(12):2424-31. doi: 10.1093/carcin/bgs276. Epub 2012 Sep 4.
PMID 22948180
 
An integrated physical and gene map of the 3.5-Mb chromosome 3p21.3 (AP20) region implicated in major human epithelial malignancies.
Protopopov A, Kashuba V, Zabarovska VI, Muravenko OV, Lerman MI, Klein G, Zabarovsky ER.
Cancer Res. 2003 Jan 15;63(2):404-12.
PMID 12543795
 
Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE.
Safran M, Chalifa-Caspi V, Shmueli O, Olender T, Lapidot M, Rosen N, Shmoish M, Peter Y, Glusman G, Feldmesser E, Adato A, Peter I, Khen M, Atarot T, Groner Y, Lancet D.
Nucleic Acids Res. 2003 Jan 1;31(1):142-6.
PMID 12519968
 
Dephosphorylation of the linker regions of Smad1 and Smad2/3 by small C-terminal domain phosphatases has distinct outcomes for bone morphogenetic protein and transforming growth factor-beta pathways.
Sapkota G, Knockaert M, Alarcon C, Montalvo E, Brivanlou AH, Massague J.
J Biol Chem. 2006 Dec 29;281(52):40412-9. Epub 2006 Nov 2.
PMID 17085434
 
Reduction of proliferation and induction of apoptosis are associated with shrinkage of head and neck squamous cell carcinoma due to neoadjuvant chemotherapy.
Sarkar S, Maiti GP, Jha J, Biswas J, Roy A, Roychoudhury S, Sharp T, Panda CK.
Asian Pac J Cancer Prev. 2013;14(11):6419-25.
PMID 24377544
 
Simultaneous down-regulation of tumor suppressor genes RBSP3/CTDSPL, NPRL2/G21 and RASSF1A in primary non-small cell lung cancer.
Senchenko VN, Anedchenko EA, Kondratieva TT, Krasnov GS, Dmitriev AA, Zabarovska VI, Pavlova TV, Kashuba VI, Lerman MI, Zabarovsky ER.
BMC Cancer. 2010 Mar 1;10:75. doi: 10.1186/1471-2407-10-75.
PMID 20193080
 
Silencing of bidirectional promoters by DNA methylation in tumorigenesis.
Shu J, Jelinek J, Chang H, Shen L, Qin T, Chung W, Oki Y, Issa JP.
Cancer Res. 2006 May 15;66(10):5077-84.
PMID 16707430
 
Frequent alterations of hMLH1 and RBSP3/HYA22 at chromosomal 3p22.3 region in early and late-onset breast carcinoma: clinical and prognostic significance.
Sinha S, Singh RK, Alam N, Roy A, Roychoudhury S, Panda CK.
Cancer Sci. 2008 Oct;99(10):1984-91. doi: 10.1111/j.1349-7006.2008.00952.x.
PMID 19016758
 
Small CTD phosphatases function in silencing neuronal gene expression.
Yeo M, Lee SK, Lee B, Ruiz EC, Pfaff SL, Gill GN.
Science. 2005 Jan 28;307(5709):596-600.
PMID 15681389
 
A novel RNA polymerase II C-terminal domain phosphatase that preferentially dephosphorylates serine 5.
Yeo M, Lin PS, Dahmus ME, Gill GN.
J Biol Chem. 2003 Jul 11;278(28):26078-85. Epub 2003 Apr 28.
PMID 12721286
 
MiR-100 regulates cell differentiation and survival by targeting RBSP3, a phosphatase-like tumor suppressor in acute myeloid leukemia.
Zheng YS, Zhang H, Zhang XJ, Feng DD, Luo XQ, Zeng CW, Lin KY, Zhou H, Qu LH, Zhang P, Chen YQ.
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PMID 21643017
 
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Citation

This paper should be referenced as such :
S Sarkar, GP Maiti, CK Panda
CTDSPL (CTD (Carboxy-Terminal Domain, RNA Polymerase II, Polypeptide A) Small Phosphatase-Like)
Atlas Genet Cytogenet Oncol Haematol. 2014;18(11):797-804.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/CTDSPLID40189ch3p22.html


External links

Nomenclature
HGNC (Hugo)CTDSPL   16890
Cards
AtlasCTDSPLID40189ch3p22
Entrez_Gene (NCBI)CTDSPL  10217  CTD small phosphatase like
AliasesC3orf8; HYA22; PSR1; RBSP3; 
SCP3
GeneCards (Weizmann)CTDSPL
Ensembl hg19 (Hinxton)ENSG00000144677 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000144677 [Gene_View]  chr3:37862178-37984469 [Contig_View]  CTDSPL [Vega]
ICGC DataPortalENSG00000144677
TCGA cBioPortalCTDSPL
AceView (NCBI)CTDSPL
Genatlas (Paris)CTDSPL
WikiGenes10217
SOURCE (Princeton)CTDSPL
Genetics Home Reference (NIH)CTDSPL
Genomic and cartography
GoldenPath hg38 (UCSC)CTDSPL  -     chr3:37862178-37984469 +  3p22.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)CTDSPL  -     3p22.2   [Description]    (hg19-Feb_2009)
EnsemblCTDSPL - 3p22.2 [CytoView hg19]  CTDSPL - 3p22.2 [CytoView hg38]
Mapping of homologs : NCBICTDSPL [Mapview hg19]  CTDSPL [Mapview hg38]
OMIM608592   
Gene and transcription
Genbank (Entrez)AI143812 AI192993 AJ575644 AJ575645 AY279532
RefSeq transcript (Entrez)NM_001008392 NM_005808
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)CTDSPL
Cluster EST : UnigeneHs.475963 [ NCBI ]
CGAP (NCI)Hs.475963
Alternative Splicing GalleryENSG00000144677
Gene ExpressionCTDSPL [ NCBI-GEO ]   CTDSPL [ EBI - ARRAY_EXPRESS ]   CTDSPL [ SEEK ]   CTDSPL [ MEM ]
Gene Expression Viewer (FireBrowse)CTDSPL [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)10217
GTEX Portal (Tissue expression)CTDSPL
Protein : pattern, domain, 3D structure
UniProt/SwissProtO15194   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO15194  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO15194
Splice isoforms : SwissVarO15194
Catalytic activity : Enzyme3.1.3.16 [ Enzyme-Expasy ]   3.1.3.163.1.3.16 [ IntEnz-EBI ]   3.1.3.16 [ BRENDA ]   3.1.3.16 [ KEGG ]   
PhosPhoSitePlusO15194
Domaine pattern : Prosite (Expaxy)FCP1 (PS50969)   
Domains : Interpro (EBI)Dullard_phosphatase    FCP1_dom    HAD-like_dom   
Domain families : Pfam (Sanger)NIF (PF03031)   
Domain families : Pfam (NCBI)pfam03031   
Domain families : Smart (EMBL)CPDc (SM00577)  
Conserved Domain (NCBI)CTDSPL
DMDM Disease mutations10217
Blocks (Seattle)CTDSPL
PDB (SRS)2HHL   
PDB (PDBSum)2HHL   
PDB (IMB)2HHL   
PDB (RSDB)2HHL   
Structural Biology KnowledgeBase2HHL   
SCOP (Structural Classification of Proteins)2HHL   
CATH (Classification of proteins structures)2HHL   
SuperfamilyO15194
Human Protein AtlasENSG00000144677
Peptide AtlasO15194
IPIIPI00454757   IPI00024826   IPI00790486   IPI00927335   IPI00927578   IPI00927826   
Protein Interaction databases
DIP (DOE-UCLA)O15194
IntAct (EBI)O15194
FunCoupENSG00000144677
BioGRIDCTDSPL
STRING (EMBL)CTDSPL
ZODIACCTDSPL
Ontologies - Pathways
QuickGOO15194
Ontology : AmiGOnegative regulation of protein phosphorylation  molecular_function  phosphoprotein phosphatase activity  nucleus  protein dephosphorylation  biological_process  metal ion binding  extracellular exosome  negative regulation of G1/S transition of mitotic cell cycle  
Ontology : EGO-EBInegative regulation of protein phosphorylation  molecular_function  phosphoprotein phosphatase activity  nucleus  protein dephosphorylation  biological_process  metal ion binding  extracellular exosome  negative regulation of G1/S transition of mitotic cell cycle  
NDEx NetworkCTDSPL
Atlas of Cancer Signalling NetworkCTDSPL
Wikipedia pathwaysCTDSPL
Orthology - Evolution
OrthoDB10217
GeneTree (enSembl)ENSG00000144677
Phylogenetic Trees/Animal Genes : TreeFamCTDSPL
HOVERGENO15194
HOGENOMO15194
Homologs : HomoloGeneCTDSPL
Homology/Alignments : Family Browser (UCSC)CTDSPL
Gene fusions - Rearrangements
Fusion : MitelmanCTDSPL/TMCC1 [3p22.2/3q22.1]  
Fusion : MitelmanCTDSPL/WRN [3p22.2/8p12]  [t(3;8)(p22;p12)]  
Fusion : MitelmanOXSR1/CTDSPL [3p22.2/3p22.2]  [t(3;3)(p22;p22)]  
Fusion: TCGACTDSPL 3p22.2 TMCC1 3q22.1 BRCA
Fusion: TCGACTDSPL 3p22.2 WRN 8p12 BLCA
Fusion: TCGAOXSR1 3p22.2 CTDSPL 3p22.2 LUAD
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCTDSPL [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)CTDSPL
dbVarCTDSPL
ClinVarCTDSPL
1000_GenomesCTDSPL 
Exome Variant ServerCTDSPL
ExAC (Exome Aggregation Consortium)CTDSPL (select the gene name)
Genetic variants : HAPMAP10217
Genomic Variants (DGV)CTDSPL [DGVbeta]
DECIPHERCTDSPL [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisCTDSPL 
Mutations
ICGC Data PortalCTDSPL 
TCGA Data PortalCTDSPL 
Broad Tumor PortalCTDSPL
OASIS PortalCTDSPL [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICCTDSPL  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDCTDSPL
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch CTDSPL
DgiDB (Drug Gene Interaction Database)CTDSPL
DoCM (Curated mutations)CTDSPL (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)CTDSPL (select a term)
intoGenCTDSPL
NCG5 (London)CTDSPL
Cancer3DCTDSPL(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM608592   
Orphanet
MedgenCTDSPL
Genetic Testing Registry CTDSPL
NextProtO15194 [Medical]
TSGene10217
GENETestsCTDSPL
Target ValidationCTDSPL
Huge Navigator CTDSPL [HugePedia]
snp3D : Map Gene to Disease10217
BioCentury BCIQCTDSPL
ClinGenCTDSPL
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD10217
Chemical/Pharm GKB GenePA128394571
Clinical trialCTDSPL
Miscellaneous
canSAR (ICR)CTDSPL (select the gene name)
Probes
Litterature
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