Atlas of Genetics and Cytogenetics in Oncology and Haematology

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SSB (Sjogren syndrome antigen B)

Identity

Alias_namesSjogren syndrome antigen B (autoantigen La)
Alias_symbol (synonym)LARP3
La
La/SSB
Other alias
HGNC (Hugo) SSB
LocusID (NCBI) 6741
Atlas_Id 43885
Location 2q31.1  [Link to chromosome band 2q31]
Location_base_pair Starts at 169798812 and ends at 169812061 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)		Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
SSB (2q31.1) / SSB (2q31.1)TLK1 (2q31.1) / SSB (2q31.1)TLK1 2q31.1 / SSB 2q31.1

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

 

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 1 ]
  TLK1/SSB (2q31)

External links

Nomenclature
HGNC (Hugo)SSB   11316
Cards
Entrez_Gene (NCBI)SSB  6741  Sjogren syndrome antigen B
AliasesLARP3; La; La/SSB
GeneCards (Weizmann)SSB
Ensembl hg19 (Hinxton)ENSG00000138385 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000138385 [Gene_View]  ENSG00000138385 [Sequence]  chr2:169798812-169812061 [Contig_View]  SSB [Vega]
ICGC DataPortalENSG00000138385
TCGA cBioPortalSSB
AceView (NCBI)SSB
Genatlas (Paris)SSB
WikiGenes6741
SOURCE (Princeton)SSB
Genetics Home Reference (NIH)SSB
Genomic and cartography
GoldenPath hg38 (UCSC)SSB  -     chr2:169798812-169812061 +  2q31.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SSB  -     2q31.1   [Description]    (hg19-Feb_2009)
EnsemblSSB - 2q31.1 [CytoView hg19]  SSB - 2q31.1 [CytoView hg38]
Mapping of homologs : NCBISSB [Mapview hg19]  SSB [Mapview hg38]
OMIM109090   
Gene and transcription
Genbank (Entrez)AB451228 AB451351 AH001540 AH001540 AH001540
RefSeq transcript (Entrez)NM_001294145 NM_003142
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SSB
Cluster EST : UnigeneHs.632535 [ NCBI ]
CGAP (NCI)Hs.632535
Alternative Splicing GalleryENSG00000138385
Gene ExpressionSSB [ NCBI-GEO ]   SSB [ EBI - ARRAY_EXPRESS ]   SSB [ SEEK ]   SSB [ MEM ]
Gene Expression Viewer (FireBrowse)SSB [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6741
GTEX Portal (Tissue expression)SSB
Human Protein AtlasENSG00000138385-SSB [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP05455   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP05455  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP05455
Splice isoforms : SwissVarP05455
PhosPhoSitePlusP05455
Domaine pattern : Prosite (Expaxy)HTH_LA (PS50961)    RRM (PS50102)   
Domains : Interpro (EBI)La_HTH    La_RRM    Lupus_La    Nucleotide-bd_a/b_plait_sf    RBD_domain_sf    RRM_dom    WH-like_DNA-bd_sf    WH_DNA-bd_sf   
Domain families : Pfam (Sanger)La (PF05383)    RRM_1 (PF00076)    RRM_3 (PF08777)   
Domain families : Pfam (NCBI)pfam05383    pfam00076    pfam08777   
Domain families : Smart (EMBL)LA (SM00715)  RRM (SM00360)  
Conserved Domain (NCBI)SSB
DMDM Disease mutations6741
Blocks (Seattle)SSB
PDB (RSDB)1OWX    1S79    1S7A    1YTY    1ZH5    2VOD    2VON    2VOO    2VOP   
PDB Europe1OWX    1S79    1S7A    1YTY    1ZH5    2VOD    2VON    2VOO    2VOP   
PDB (PDBSum)1OWX    1S79    1S7A    1YTY    1ZH5    2VOD    2VON    2VOO    2VOP   
PDB (IMB)1OWX    1S79    1S7A    1YTY    1ZH5    2VOD    2VON    2VOO    2VOP   
Structural Biology KnowledgeBase1OWX    1S79    1S7A    1YTY    1ZH5    2VOD    2VON    2VOO    2VOP   
SCOP (Structural Classification of Proteins)1OWX    1S79    1S7A    1YTY    1ZH5    2VOD    2VON    2VOO    2VOP   
CATH (Classification of proteins structures)1OWX    1S79    1S7A    1YTY    1ZH5    2VOD    2VON    2VOO    2VOP   
SuperfamilyP05455
Human Protein Atlas [tissue]ENSG00000138385-SSB [tissue]
Peptide AtlasP05455
HPRD00168
IPIIPI00009032   IPI00916802   IPI00916922   IPI00917386   IPI00917205   
Protein Interaction databases
DIP (DOE-UCLA)P05455
IntAct (EBI)P05455
FunCoupENSG00000138385
BioGRIDSSB
STRING (EMBL)SSB
ZODIACSSB
Ontologies - Pathways
QuickGOP05455
Ontology : AmiGOtRNA binding  nuclear chromosome, telomeric region  tRNA 5'-leader removal  RNA binding  RNA binding  mRNA binding  protein binding  nucleus  cytoplasm  tRNA modification  tRNA export from nucleus  tRNA processing  poly(U) RNA binding  histone mRNA metabolic process  tRNA 3'-end processing  protein homodimerization activity  nuclear histone mRNA catabolic process  IRES-dependent viral translational initiation  protein localization to cytoplasmic stress granule  sequence-specific mRNA binding  ribonucleoprotein complex  
Ontology : EGO-EBItRNA binding  nuclear chromosome, telomeric region  tRNA 5'-leader removal  RNA binding  RNA binding  mRNA binding  protein binding  nucleus  cytoplasm  tRNA modification  tRNA export from nucleus  tRNA processing  poly(U) RNA binding  histone mRNA metabolic process  tRNA 3'-end processing  protein homodimerization activity  nuclear histone mRNA catabolic process  IRES-dependent viral translational initiation  protein localization to cytoplasmic stress granule  sequence-specific mRNA binding  ribonucleoprotein complex  
Pathways : KEGGSystemic lupus erythematosus   
NDEx NetworkSSB
Atlas of Cancer Signalling NetworkSSB
Wikipedia pathwaysSSB
Orthology - Evolution
OrthoDB6741
GeneTree (enSembl)ENSG00000138385
Phylogenetic Trees/Animal Genes : TreeFamSSB
HOGENOMP05455
Homologs : HomoloGeneSSB
Homology/Alignments : Family Browser (UCSC)SSB
Gene fusions - Rearrangements
Fusion : MitelmanTLK1/SSB [2q31.1/2q31.1]  [t(2;2)(q31;q31)]  
Fusion PortalTLK1 2q31.1 SSB 2q31.1 BRCA
Fusion : QuiverSSB
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSSB [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SSB
dbVarSSB
ClinVarSSB
1000_GenomesSSB 
Exome Variant ServerSSB
ExAC (Exome Aggregation Consortium)ENSG00000138385
GNOMAD BrowserENSG00000138385
Varsome BrowserSSB
Genetic variants : HAPMAP6741
Genomic Variants (DGV)SSB [DGVbeta]
DECIPHERSSB [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSSB 
Mutations
ICGC Data PortalSSB 
TCGA Data PortalSSB 
Broad Tumor PortalSSB
OASIS PortalSSB [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSSB  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSSB
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 SSB
DgiDB (Drug Gene Interaction Database)SSB
DoCM (Curated mutations)SSB (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SSB (select a term)
intoGenSSB
Cancer3DSSB(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM109090   
Orphanet
DisGeNETSSB
MedgenSSB
Genetic Testing Registry SSB
NextProtP05455 [Medical]
TSGene6741
GENETestsSSB
Target ValidationSSB
Huge Navigator SSB [HugePedia]
snp3D : Map Gene to Disease6741
BioCentury BCIQSSB
ClinGenSSB
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD6741
Chemical/Pharm GKB GenePA36140
Clinical trialSSB
Miscellaneous
canSAR (ICR)SSB (select the gene name)
DataMed IndexSSB
Probes
Litterature
PubMed177 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSSB
EVEXSSB
GoPubMedSSB
iHOPSSB
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Thu Feb 14 16:59:33 CET 2019
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