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SEC13 (SEC13 homolog, nuclear pore and COPII coat complex component)

Identity

Alias_namesD3S1231E
SEC13L1
SEC13 (S. cerevisiae)-like 1
SEC13-like 1 (S. cerevisiae)
SEC13 homolog (S. cerevisiae)
Alias_symbol (synonym)SEC13R
npp-20
Other alias
HGNC (Hugo) SEC13
LocusID (NCBI) 6396
Atlas_Id 73079
Location 3p25.3  [Link to chromosome band 3p25]
Location_base_pair Starts at 10300929 and ends at 10321188 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)
ITGA9 (3p22.2) / SEC13 (3p25.3)KHNYN (14q12) / SEC13 (3p25.3)MRPS10 (6p21.1) / SEC13 (3p25.3)
TOMM7 (7p15.3) / SEC13 (3p25.3)

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)SEC13   10697
Cards
Entrez_Gene (NCBI)SEC13  6396  SEC13 homolog, nuclear pore and COPII coat complex component
AliasesD3S1231E; SEC13L1; SEC13R; npp-20
GeneCards (Weizmann)SEC13
Ensembl hg19 (Hinxton)ENSG00000157020 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000157020 [Gene_View]  chr3:10300929-10321188 [Contig_View]  SEC13 [Vega]
ICGC DataPortalENSG00000157020
TCGA cBioPortalSEC13
AceView (NCBI)SEC13
Genatlas (Paris)SEC13
WikiGenes6396
SOURCE (Princeton)SEC13
Genetics Home Reference (NIH)SEC13
Genomic and cartography
GoldenPath hg38 (UCSC)SEC13  -     chr3:10300929-10321188 -  3p25.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SEC13  -     3p25.3   [Description]    (hg19-Feb_2009)
EnsemblSEC13 - 3p25.3 [CytoView hg19]  SEC13 - 3p25.3 [CytoView hg38]
Mapping of homologs : NCBISEC13 [Mapview hg19]  SEC13 [Mapview hg38]
OMIM600152   
Gene and transcription
Genbank (Entrez)AA682381 AB209554 AF052155 AK095629 AK223019
RefSeq transcript (Entrez)NM_001136026 NM_001136232 NM_001278946 NM_030673 NM_183352
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SEC13
Cluster EST : UnigeneHs.672979 [ NCBI ]
CGAP (NCI)Hs.672979
Alternative Splicing GalleryENSG00000157020
Gene ExpressionSEC13 [ NCBI-GEO ]   SEC13 [ EBI - ARRAY_EXPRESS ]   SEC13 [ SEEK ]   SEC13 [ MEM ]
Gene Expression Viewer (FireBrowse)SEC13 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6396
GTEX Portal (Tissue expression)SEC13
Human Protein AtlasENSG00000157020-SEC13 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP55735   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP55735  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP55735
Splice isoforms : SwissVarP55735
PhosPhoSitePlusP55735
Domaine pattern : Prosite (Expaxy)WD_REPEATS_2 (PS50082)    WD_REPEATS_REGION (PS50294)   
Domains : Interpro (EBI)WD40/YVTN_repeat-like_dom    WD40_repeat    WD40_repeat_dom   
Domain families : Pfam (Sanger)WD40 (PF00400)   
Domain families : Pfam (NCBI)pfam00400   
Domain families : Smart (EMBL)WD40 (SM00320)  
Conserved Domain (NCBI)SEC13
DMDM Disease mutations6396
Blocks (Seattle)SEC13
PDB (SRS)3BG0    3BG1    5A9Q   
PDB (PDBSum)3BG0    3BG1    5A9Q   
PDB (IMB)3BG0    3BG1    5A9Q   
PDB (RSDB)3BG0    3BG1    5A9Q   
Structural Biology KnowledgeBase3BG0    3BG1    5A9Q   
SCOP (Structural Classification of Proteins)3BG0    3BG1    5A9Q   
CATH (Classification of proteins structures)3BG0    3BG1    5A9Q   
SuperfamilyP55735
Human Protein Atlas [tissue]ENSG00000157020-SEC13 [tissue]
Peptide AtlasP55735
HPRD02538
IPIIPI00479141   IPI00845335   IPI00375370   IPI00853598   IPI00789755   IPI00793447   IPI00792860   IPI00852874   IPI00852657   IPI00853116   IPI00791226   IPI00924744   
Protein Interaction databases
DIP (DOE-UCLA)P55735
IntAct (EBI)P55735
FunCoupENSG00000157020
BioGRIDSEC13
STRING (EMBL)SEC13
ZODIACSEC13
Ontologies - Pathways
QuickGOP55735
Ontology : AmiGOGolgi membrane  kinetochore  antigen processing and presentation of peptide antigen via MHC class I  protein binding  nuclear envelope  nucleoplasm  lysosomal membrane  endoplasmic reticulum membrane  cytosol  intracellular protein transport  sister chromatid cohesion  ER to Golgi transport vesicle membrane  antigen processing and presentation of exogenous peptide antigen via MHC class II  nuclear pore outer ring  nuclear pore outer ring  positive regulation of TOR signaling  identical protein binding  intracellular membrane-bounded organelle  COPII vesicle coating  mRNA transport  GATOR2 complex  extracellular exosome  
Ontology : EGO-EBIGolgi membrane  kinetochore  antigen processing and presentation of peptide antigen via MHC class I  protein binding  nuclear envelope  nucleoplasm  lysosomal membrane  endoplasmic reticulum membrane  cytosol  intracellular protein transport  sister chromatid cohesion  ER to Golgi transport vesicle membrane  antigen processing and presentation of exogenous peptide antigen via MHC class II  nuclear pore outer ring  nuclear pore outer ring  positive regulation of TOR signaling  identical protein binding  intracellular membrane-bounded organelle  COPII vesicle coating  mRNA transport  GATOR2 complex  extracellular exosome  
Pathways : KEGGRNA transport    Protein processing in endoplasmic reticulum   
NDEx NetworkSEC13
Atlas of Cancer Signalling NetworkSEC13
Wikipedia pathwaysSEC13
Orthology - Evolution
OrthoDB6396
GeneTree (enSembl)ENSG00000157020
Phylogenetic Trees/Animal Genes : TreeFamSEC13
HOVERGENP55735
HOGENOMP55735
Homologs : HomoloGeneSEC13
Homology/Alignments : Family Browser (UCSC)SEC13
Gene fusions - Rearrangements
Tumor Fusion PortalSEC13
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSEC13 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SEC13
dbVarSEC13
ClinVarSEC13
1000_GenomesSEC13 
Exome Variant ServerSEC13
ExAC (Exome Aggregation Consortium)ENSG00000157020
GNOMAD BrowserENSG00000157020
Genetic variants : HAPMAP6396
Genomic Variants (DGV)SEC13 [DGVbeta]
DECIPHERSEC13 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSEC13 
Mutations
ICGC Data PortalSEC13 
TCGA Data PortalSEC13 
Broad Tumor PortalSEC13
OASIS PortalSEC13 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSEC13  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSEC13
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 SEC13
DgiDB (Drug Gene Interaction Database)SEC13
DoCM (Curated mutations)SEC13 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SEC13 (select a term)
intoGenSEC13
Cancer3DSEC13(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM600152   
Orphanet
DisGeNETSEC13
MedgenSEC13
Genetic Testing Registry SEC13
NextProtP55735 [Medical]
TSGene6396
GENETestsSEC13
Target ValidationSEC13
Huge Navigator SEC13 [HugePedia]
snp3D : Map Gene to Disease6396
BioCentury BCIQSEC13
ClinGenSEC13
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD6396
Chemical/Pharm GKB GenePA35620
Clinical trialSEC13
Miscellaneous
canSAR (ICR)SEC13 (select the gene name)
Probes
Litterature
PubMed60 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSEC13
EVEXSEC13
GoPubMedSEC13
iHOPSEC13
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Nov 21 13:08:57 CET 2017

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