Atlas of Genetics and Cytogenetics in Oncology and Haematology


Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA

SMC5 (structural maintenance of chromosomes 5)

Identity

Alias_namesSMC5L1
SMC5 structural maintenance of chromosomes 5-like 1 (yeast)
Alias_symbol (synonym)KIAA0594
Other alias
HGNC (Hugo) SMC5
LocusID (NCBI) 23137
Atlas_Id 45967
Location 9q21.12  [Link to chromosome band 9q21]
Location_base_pair Starts at 70258962 and ends at 70354873 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
NAALADL2 (3q26.31) / SMC5 (9q21.12)SMC5 (9q21.12) / IMMP2L (7q31.1)SMC5 (9q21.12) / MAMDC2 (9q21.12)
SMC5 (9q21.12) / MYH13 (17p13.1)SMC5 (9q21.12) / SMC5 (9q21.12)SMC5 (9q21.12) / XKR6 (8p23.1)
NAALADL2 3q26.31 / SMC5 9q21.12SMC5 9q21.12 / IMMP2L 7q31.1SMC5 9q21.12 / MAMDC2 9q21.12

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


External links

Nomenclature
HGNC (Hugo)SMC5   20465
Cards
Entrez_Gene (NCBI)SMC5  23137  structural maintenance of chromosomes 5
AliasesSMC5L1
GeneCards (Weizmann)SMC5
Ensembl hg19 (Hinxton)ENSG00000198887 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000198887 [Gene_View]  chr9:70258962-70354873 [Contig_View]  SMC5 [Vega]
ICGC DataPortalENSG00000198887
TCGA cBioPortalSMC5
AceView (NCBI)SMC5
Genatlas (Paris)SMC5
WikiGenes23137
SOURCE (Princeton)SMC5
Genetics Home Reference (NIH)SMC5
Genomic and cartography
GoldenPath hg38 (UCSC)SMC5  -     chr9:70258962-70354873 +  9q21.12   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SMC5  -     9q21.12   [Description]    (hg19-Feb_2009)
EnsemblSMC5 - 9q21.12 [CytoView hg19]  SMC5 - 9q21.12 [CytoView hg38]
Mapping of homologs : NCBISMC5 [Mapview hg19]  SMC5 [Mapview hg38]
OMIM609386   
Gene and transcription
Genbank (Entrez)AA709087 AB011166 AJ310550 AK055825 AK304133
RefSeq transcript (Entrez)NM_015110
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SMC5
Cluster EST : UnigeneHs.601181 [ NCBI ]
CGAP (NCI)Hs.601181
Alternative Splicing GalleryENSG00000198887
Gene ExpressionSMC5 [ NCBI-GEO ]   SMC5 [ EBI - ARRAY_EXPRESS ]   SMC5 [ SEEK ]   SMC5 [ MEM ]
Gene Expression Viewer (FireBrowse)SMC5 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)23137
GTEX Portal (Tissue expression)SMC5
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ8IY18   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ8IY18  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ8IY18
Splice isoforms : SwissVarQ8IY18
PhosPhoSitePlusQ8IY18
Domains : Interpro (EBI)P-loop_NTPase    RecF/RecN/SMC_N    SMC5   
Domain families : Pfam (Sanger)SMC_N (PF02463)   
Domain families : Pfam (NCBI)pfam02463   
Conserved Domain (NCBI)SMC5
DMDM Disease mutations23137
Blocks (Seattle)SMC5
SuperfamilyQ8IY18
Human Protein AtlasENSG00000198887
Peptide AtlasQ8IY18
HPRD10241
IPIIPI00413265   
Protein Interaction databases
DIP (DOE-UCLA)Q8IY18
IntAct (EBI)Q8IY18
FunCoupENSG00000198887
BioGRIDSMC5
STRING (EMBL)SMC5
ZODIACSMC5
Ontologies - Pathways
QuickGOQ8IY18
Ontology : AmiGOtelomere maintenance via recombination  double-strand break repair via homologous recombination  chromosome, telomeric region  sex chromosome  protein binding  ATP binding  nucleus  nucleus  nucleoplasm  double-strand break repair via nonhomologous end joining  cellular response to DNA damage stimulus  sister chromatid cohesion  PML body  nuclear speck  cell junction  Smc5-Smc6 complex  positive regulation of maintenance of mitotic sister chromatid cohesion  interchromatin granule  site of double-strand break  cell division  positive regulation of chromosome segregation  cellular senescence  
Ontology : EGO-EBItelomere maintenance via recombination  double-strand break repair via homologous recombination  chromosome, telomeric region  sex chromosome  protein binding  ATP binding  nucleus  nucleus  nucleoplasm  double-strand break repair via nonhomologous end joining  cellular response to DNA damage stimulus  sister chromatid cohesion  PML body  nuclear speck  cell junction  Smc5-Smc6 complex  positive regulation of maintenance of mitotic sister chromatid cohesion  interchromatin granule  site of double-strand break  cell division  positive regulation of chromosome segregation  cellular senescence  
NDEx NetworkSMC5
Atlas of Cancer Signalling NetworkSMC5
Wikipedia pathwaysSMC5
Orthology - Evolution
OrthoDB23137
GeneTree (enSembl)ENSG00000198887
Phylogenetic Trees/Animal Genes : TreeFamSMC5
HOVERGENQ8IY18
HOGENOMQ8IY18
Homologs : HomoloGeneSMC5
Homology/Alignments : Family Browser (UCSC)SMC5
Gene fusions - Rearrangements
Fusion : MitelmanNAALADL2/SMC5 [3q26.31/9q21.12]  [t(3;9)(q26;q21)]  
Fusion : MitelmanSMC5/IMMP2L [9q21.12/7q31.1]  [t(7;9)(q31;q21)]  
Fusion : MitelmanSMC5/MAMDC2 [9q21.12/9q21.12]  [t(9;9)(q21;q21)]  
Fusion: TCGANAALADL2 3q26.31 SMC5 9q21.12 LUSC
Fusion: TCGASMC5 9q21.12 IMMP2L 7q31.1 BRCA
Fusion: TCGASMC5 9q21.12 MAMDC2 9q21.12 BRCA
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSMC5 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SMC5
dbVarSMC5
ClinVarSMC5
1000_GenomesSMC5 
Exome Variant ServerSMC5
ExAC (Exome Aggregation Consortium)SMC5 (select the gene name)
Genetic variants : HAPMAP23137
Genomic Variants (DGV)SMC5 [DGVbeta]
DECIPHERSMC5 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSMC5 
Mutations
ICGC Data PortalSMC5 
TCGA Data PortalSMC5 
Broad Tumor PortalSMC5
OASIS PortalSMC5 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSMC5  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSMC5
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 SMC5
DgiDB (Drug Gene Interaction Database)SMC5
DoCM (Curated mutations)SMC5 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SMC5 (select a term)
intoGenSMC5
Cancer3DSMC5(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM609386   
Orphanet
MedgenSMC5
Genetic Testing Registry SMC5
NextProtQ8IY18 [Medical]
TSGene23137
GENETestsSMC5
Huge Navigator SMC5 [HugePedia]
snp3D : Map Gene to Disease23137
BioCentury BCIQSMC5
ClinGenSMC5
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD23137
Chemical/Pharm GKB GenePA134993662
Clinical trialSMC5
Miscellaneous
canSAR (ICR)SMC5 (select the gene name)
Probes
Litterature
PubMed30 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSMC5
EVEXSMC5
GoPubMedSMC5
iHOPSMC5
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Fri May 19 12:38:11 CEST 2017

Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.