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

SSC5D (scavenger receptor cysteine rich family member with 5 domains)

Identity

Alias_namesscavenger receptor cysteine rich domain containing (5 domains)
Alias_symbol (synonym)FLJ35258
S5D-SRCRB
Other alias
HGNC (Hugo) SSC5D
LocusID (NCBI) 284297
Atlas_Id 74257
Location 19q13.42  [Link to chromosome band 19q13]
Location_base_pair Starts at 55488503 and ends at 55519099 bp from pter ( according to hg38-Dec_2013)

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)SSC5D   26641
Cards
Entrez_Gene (NCBI)SSC5D  284297  scavenger receptor cysteine rich family member with 5 domains
AliasesS5D-SRCRB
GeneCards (Weizmann)SSC5D
Ensembl hg19 (Hinxton)ENSG00000179954 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000179954 [Gene_View]  chr19:55488503-55519099 [Contig_View]  SSC5D [Vega]
ICGC DataPortalENSG00000179954
TCGA cBioPortalSSC5D
AceView (NCBI)SSC5D
Genatlas (Paris)SSC5D
WikiGenes284297
SOURCE (Princeton)SSC5D
Genetics Home Reference (NIH)SSC5D
Genomic and cartography
GoldenPath hg38 (UCSC)SSC5D  -     chr19:55488503-55519099 +  19q13.42   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SSC5D  -     19q13.42   [Description]    (hg19-Feb_2009)
EnsemblSSC5D - 19q13.42 [CytoView hg19]  SSC5D - 19q13.42 [CytoView hg38]
Mapping of homologs : NCBISSC5D [Mapview hg19]  SSC5D [Mapview hg38]
Gene and transcription
Genbank (Entrez)AF086519 AK092577 BC130538 BC130540 DA008417
RefSeq transcript (Entrez)NM_001144950 NM_001195267 NM_182571
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SSC5D
Cluster EST : UnigeneHs.554182 [ NCBI ]
CGAP (NCI)Hs.554182
Alternative Splicing GalleryENSG00000179954
Gene ExpressionSSC5D [ NCBI-GEO ]   SSC5D [ EBI - ARRAY_EXPRESS ]   SSC5D [ SEEK ]   SSC5D [ MEM ]
Gene Expression Viewer (FireBrowse)SSC5D [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)284297
GTEX Portal (Tissue expression)SSC5D
Protein : pattern, domain, 3D structure
UniProt/SwissProtA1L4H1   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtA1L4H1  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProA1L4H1
Splice isoforms : SwissVarA1L4H1
PhosPhoSitePlusA1L4H1
Domaine pattern : Prosite (Expaxy)SRCR_1 (PS00420)    SRCR_2 (PS50287)   
Domains : Interpro (EBI)SRCR    SRCR-like_dom   
Domain families : Pfam (Sanger)SRCR (PF00530)   
Domain families : Pfam (NCBI)pfam00530   
Domain families : Smart (EMBL)SR (SM00202)  
Conserved Domain (NCBI)SSC5D
DMDM Disease mutations284297
Blocks (Seattle)SSC5D
SuperfamilyA1L4H1
Human Protein AtlasENSG00000179954
Peptide AtlasA1L4H1
HPRD11444
IPIIPI00979213   IPI00946928   IPI00168022   
Protein Interaction databases
DIP (DOE-UCLA)A1L4H1
IntAct (EBI)A1L4H1
FunCoupENSG00000179954
BioGRIDSSC5D
STRING (EMBL)SSC5D
ZODIACSSC5D
Ontologies - Pathways
QuickGOA1L4H1
Ontology : AmiGOfibronectin binding  scavenger receptor activity  protein binding  extracellular space  intracellular  cytoplasm  receptor-mediated endocytosis  multicellular organism development  membrane  extracellular matrix  detection of bacterial lipoprotein  laminin binding  innate immune response  defense response to Gram-negative bacterium  defense response to Gram-positive bacterium  extracellular matrix binding  negative regulation of interleukin-8 secretion  
Ontology : EGO-EBIfibronectin binding  scavenger receptor activity  protein binding  extracellular space  intracellular  cytoplasm  receptor-mediated endocytosis  multicellular organism development  membrane  extracellular matrix  detection of bacterial lipoprotein  laminin binding  innate immune response  defense response to Gram-negative bacterium  defense response to Gram-positive bacterium  extracellular matrix binding  negative regulation of interleukin-8 secretion  
NDEx NetworkSSC5D
Atlas of Cancer Signalling NetworkSSC5D
Wikipedia pathwaysSSC5D
Orthology - Evolution
OrthoDB284297
GeneTree (enSembl)ENSG00000179954
Phylogenetic Trees/Animal Genes : TreeFamSSC5D
HOVERGENA1L4H1
HOGENOMA1L4H1
Homologs : HomoloGeneSSC5D
Homology/Alignments : Family Browser (UCSC)SSC5D
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSSC5D [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SSC5D
dbVarSSC5D
ClinVarSSC5D
1000_GenomesSSC5D 
Exome Variant ServerSSC5D
ExAC (Exome Aggregation Consortium)SSC5D (select the gene name)
Genetic variants : HAPMAP284297
Genomic Variants (DGV)SSC5D [DGVbeta]
DECIPHERSSC5D [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSSC5D 
Mutations
ICGC Data PortalSSC5D 
TCGA Data PortalSSC5D 
Broad Tumor PortalSSC5D
OASIS PortalSSC5D [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSSC5D  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSSC5D
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 SSC5D
DgiDB (Drug Gene Interaction Database)SSC5D
DoCM (Curated mutations)SSC5D (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SSC5D (select a term)
intoGenSSC5D
Cancer3DSSC5D(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM
Orphanet
MedgenSSC5D
Genetic Testing Registry SSC5D
NextProtA1L4H1 [Medical]
TSGene284297
GENETestsSSC5D
Target ValidationSSC5D
Huge Navigator SSC5D [HugePedia]
snp3D : Map Gene to Disease284297
BioCentury BCIQSSC5D
ClinGenSSC5D
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD284297
Chemical/Pharm GKB GenePA166048971
Clinical trialSSC5D
Miscellaneous
canSAR (ICR)SSC5D (select the gene name)
Probes
Litterature
PubMed5 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSSC5D
EVEXSSC5D
GoPubMedSSC5D
iHOPSSC5D
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 : Wed May 31 15:44:13 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.