Atlas of Genetics and Cytogenetics in Oncology and Haematology


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SEPSECS (Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase)

Identity

Alias_symbol (synonym)SLA/LP
SLA
Other aliasLP
PCH2D
HGNC (Hugo) SEPSECS
LocusID (NCBI) 51091
Atlas_Id 56393
Location 4p15.2  [Link to chromosome band 4p15]
Location_base_pair Starts at 25120005 and ends at 25160582 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
NEK4 (3p21.1) / SEPSECS (4p15.2)

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)SEPSECS   30605
Cards
Entrez_Gene (NCBI)SEPSECS  51091  Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase
AliasesLP; PCH2D; SLA; SLA/LP
GeneCards (Weizmann)SEPSECS
Ensembl hg19 (Hinxton)ENSG00000109618 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000109618 [Gene_View]  chr4:25120005-25160582 [Contig_View]  SEPSECS [Vega]
ICGC DataPortalENSG00000109618
TCGA cBioPortalSEPSECS
AceView (NCBI)SEPSECS
Genatlas (Paris)SEPSECS
WikiGenes51091
SOURCE (Princeton)SEPSECS
Genetics Home Reference (NIH)SEPSECS
Genomic and cartography
GoldenPath hg38 (UCSC)SEPSECS  -     chr4:25120005-25160582 -  4p15.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SEPSECS  -     4p15.2   [Description]    (hg19-Feb_2009)
EnsemblSEPSECS - 4p15.2 [CytoView hg19]  SEPSECS - 4p15.2 [CytoView hg38]
Mapping of homologs : NCBISEPSECS [Mapview hg19]  SEPSECS [Mapview hg38]
OMIM613009   613811   
Gene and transcription
Genbank (Entrez)AF146396 AF282065 AJ238617 AJ277541 AK292476
RefSeq transcript (Entrez)NM_001159728 NM_016955
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SEPSECS
Cluster EST : UnigeneHs.253305 [ NCBI ]
CGAP (NCI)Hs.253305
Alternative Splicing GalleryENSG00000109618
Gene ExpressionSEPSECS [ NCBI-GEO ]   SEPSECS [ EBI - ARRAY_EXPRESS ]   SEPSECS [ SEEK ]   SEPSECS [ MEM ]
Gene Expression Viewer (FireBrowse)SEPSECS [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)51091
GTEX Portal (Tissue expression)SEPSECS
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9HD40   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9HD40  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9HD40
Splice isoforms : SwissVarQ9HD40
PhosPhoSitePlusQ9HD40
Domains : Interpro (EBI)Peroxidases_heam-ligand_BS    PyrdxlP-dep_Trfase    PyrdxlP-dep_Trfase_major_sub1    Sec-tRNA_Se_transferase    SepSecS/SepCysS   
Domain families : Pfam (Sanger)SepSecS (PF05889)   
Domain families : Pfam (NCBI)pfam05889   
Conserved Domain (NCBI)SEPSECS
DMDM Disease mutations51091
Blocks (Seattle)SEPSECS
PDB (SRS)3HL2    4ZDL    4ZDO    4ZDP   
PDB (PDBSum)3HL2    4ZDL    4ZDO    4ZDP   
PDB (IMB)3HL2    4ZDL    4ZDO    4ZDP   
PDB (RSDB)3HL2    4ZDL    4ZDO    4ZDP   
Structural Biology KnowledgeBase3HL2    4ZDL    4ZDO    4ZDP   
SCOP (Structural Classification of Proteins)3HL2    4ZDL    4ZDO    4ZDP   
CATH (Classification of proteins structures)3HL2    4ZDL    4ZDO    4ZDP   
SuperfamilyQ9HD40
Human Protein AtlasENSG00000109618
Peptide AtlasQ9HD40
HPRD11561
IPIIPI00302283   IPI00155389   IPI00930339   IPI01015797   IPI00966271   IPI00967753   IPI00967486   
Protein Interaction databases
DIP (DOE-UCLA)Q9HD40
IntAct (EBI)Q9HD40
FunCoupENSG00000109618
BioGRIDSEPSECS
STRING (EMBL)SEPSECS
ZODIACSEPSECS
Ontologies - Pathways
QuickGOQ9HD40
Ontology : AmiGOtRNA binding  selenocysteine incorporation  protein binding  nucleus  cytoplasm  cytosol  selenocysteine metabolic process  selenocysteinyl-tRNA(Sec) biosynthetic process  phosphoseryl-selenocysteinyl-tRNA selenium transferase activity  
Ontology : EGO-EBItRNA binding  selenocysteine incorporation  protein binding  nucleus  cytoplasm  cytosol  selenocysteine metabolic process  selenocysteinyl-tRNA(Sec) biosynthetic process  phosphoseryl-selenocysteinyl-tRNA selenium transferase activity  
Pathways : KEGGSelenocompound metabolism    Aminoacyl-tRNA biosynthesis   
NDEx NetworkSEPSECS
Atlas of Cancer Signalling NetworkSEPSECS
Wikipedia pathwaysSEPSECS
Orthology - Evolution
OrthoDB51091
GeneTree (enSembl)ENSG00000109618
Phylogenetic Trees/Animal Genes : TreeFamSEPSECS
HOVERGENQ9HD40
HOGENOMQ9HD40
Homologs : HomoloGeneSEPSECS
Homology/Alignments : Family Browser (UCSC)SEPSECS
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSEPSECS [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SEPSECS
dbVarSEPSECS
ClinVarSEPSECS
1000_GenomesSEPSECS 
Exome Variant ServerSEPSECS
ExAC (Exome Aggregation Consortium)SEPSECS (select the gene name)
Genetic variants : HAPMAP51091
Genomic Variants (DGV)SEPSECS [DGVbeta]
DECIPHERSEPSECS [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSEPSECS 
Mutations
ICGC Data PortalSEPSECS 
TCGA Data PortalSEPSECS 
Broad Tumor PortalSEPSECS
OASIS PortalSEPSECS [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSEPSECS  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSEPSECS
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
LOVD (Leiden Open Variation Database)MSeqDR-LSDB Mitochondrial Disease Locus Specific Database
BioMutasearch SEPSECS
DgiDB (Drug Gene Interaction Database)SEPSECS
DoCM (Curated mutations)SEPSECS (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SEPSECS (select a term)
intoGenSEPSECS
Cancer3DSEPSECS(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM613009    613811   
Orphanet19511    2334   
MedgenSEPSECS
Genetic Testing Registry SEPSECS
NextProtQ9HD40 [Medical]
TSGene51091
GENETestsSEPSECS
Target ValidationSEPSECS
Huge Navigator SEPSECS [HugePedia]
snp3D : Map Gene to Disease51091
BioCentury BCIQSEPSECS
ClinGenSEPSECS
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD51091
Chemical/Pharm GKB GenePA162402915
Clinical trialSEPSECS
Miscellaneous
canSAR (ICR)SEPSECS (select the gene name)
Probes
Litterature
PubMed25 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSEPSECS
EVEXSEPSECS
GoPubMedSEPSECS
iHOPSEPSECS
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Tue Aug 1 17:14:03 CEST 2017

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