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PSD4 (pleckstrin and Sec7 domain containing 4)

Identity

Alias_symbol (synonym)TIC
EFA6B
Other alias
HGNC (Hugo) PSD4
LocusID (NCBI) 23550
Atlas_Id 42559
Location 2q14.1  [Link to chromosome band 2q14]
Location_base_pair Starts at 113173983 and ends at 113203100 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
HLA-DQB1 (6p21.32) / PSD4 (2q13)LOC100129148 (7q34) / PSD4 (2q13)PSD4 (2q13) / ARHGAP6 (Xp22.2)
PSD4 (2q13) / PSD4 (2q13)

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)PSD4   19096
Cards
Entrez_Gene (NCBI)PSD4  23550  pleckstrin and Sec7 domain containing 4
AliasesEFA6B; TIC
GeneCards (Weizmann)PSD4
Ensembl hg19 (Hinxton)ENSG00000125637 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000125637 [Gene_View]  chr2:113173983-113203100 [Contig_View]  PSD4 [Vega]
ICGC DataPortalENSG00000125637
TCGA cBioPortalPSD4
AceView (NCBI)PSD4
Genatlas (Paris)PSD4
WikiGenes23550
SOURCE (Princeton)PSD4
Genetics Home Reference (NIH)PSD4
Genomic and cartography
GoldenPath hg38 (UCSC)PSD4  -     chr2:113173983-113203100 +  2q14.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PSD4  -     2q14.1   [Description]    (hg19-Feb_2009)
EnsemblPSD4 - 2q14.1 [CytoView hg19]  PSD4 - 2q14.1 [CytoView hg38]
Mapping of homologs : NCBIPSD4 [Mapview hg19]  PSD4 [Mapview hg38]
OMIM614442   
Gene and transcription
Genbank (Entrez)AA429250 AB208798 AJ459781 AK023421 AK093556
RefSeq transcript (Entrez)NM_012455
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)PSD4
Cluster EST : UnigeneHs.516306 [ NCBI ]
CGAP (NCI)Hs.516306
Alternative Splicing GalleryENSG00000125637
Gene ExpressionPSD4 [ NCBI-GEO ]   PSD4 [ EBI - ARRAY_EXPRESS ]   PSD4 [ SEEK ]   PSD4 [ MEM ]
Gene Expression Viewer (FireBrowse)PSD4 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)23550
GTEX Portal (Tissue expression)PSD4
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ8NDX1   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ8NDX1  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ8NDX1
Splice isoforms : SwissVarQ8NDX1
PhosPhoSitePlusQ8NDX1
Domaine pattern : Prosite (Expaxy)PH_DOMAIN (PS50003)    SEC7 (PS50190)   
Domains : Interpro (EBI)PH_dom-like    PH_dom-spectrin-type    PH_domain    Sec7_alpha_orthog    Sec7_dom   
Domain families : Pfam (Sanger)Sec7 (PF01369)   
Domain families : Pfam (NCBI)pfam01369   
Domain families : Smart (EMBL)PH (SM00233)  Sec7 (SM00222)  
Conserved Domain (NCBI)PSD4
DMDM Disease mutations23550
Blocks (Seattle)PSD4
SuperfamilyQ8NDX1
Human Protein AtlasENSG00000125637
Peptide AtlasQ8NDX1
HPRD15191
IPIIPI00304670   IPI00787751   IPI00909778   IPI00883878   IPI00916262   
Protein Interaction databases
DIP (DOE-UCLA)Q8NDX1
IntAct (EBI)Q8NDX1
FunCoupENSG00000125637
BioGRIDPSD4
STRING (EMBL)PSD4
ZODIACPSD4
Ontologies - Pathways
QuickGOQ8NDX1
Ontology : AmiGOARF guanyl-nucleotide exchange factor activity  phospholipid binding  plasma membrane  membrane  regulation of ARF protein signal transduction  positive regulation of GTPase activity  
Ontology : EGO-EBIARF guanyl-nucleotide exchange factor activity  phospholipid binding  plasma membrane  membrane  regulation of ARF protein signal transduction  positive regulation of GTPase activity  
Pathways : KEGGEndocytosis   
NDEx NetworkPSD4
Atlas of Cancer Signalling NetworkPSD4
Wikipedia pathwaysPSD4
Orthology - Evolution
OrthoDB23550
GeneTree (enSembl)ENSG00000125637
Phylogenetic Trees/Animal Genes : TreeFamPSD4
HOVERGENQ8NDX1
HOGENOMQ8NDX1
Homologs : HomoloGenePSD4
Homology/Alignments : Family Browser (UCSC)PSD4
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPSD4 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PSD4
dbVarPSD4
ClinVarPSD4
1000_GenomesPSD4 
Exome Variant ServerPSD4
ExAC (Exome Aggregation Consortium)PSD4 (select the gene name)
Genetic variants : HAPMAP23550
Genomic Variants (DGV)PSD4 [DGVbeta]
DECIPHERPSD4 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPSD4 
Mutations
ICGC Data PortalPSD4 
TCGA Data PortalPSD4 
Broad Tumor PortalPSD4
OASIS PortalPSD4 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPSD4  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDPSD4
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 PSD4
DgiDB (Drug Gene Interaction Database)PSD4
DoCM (Curated mutations)PSD4 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PSD4 (select a term)
intoGenPSD4
Cancer3DPSD4(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM614442   
Orphanet
MedgenPSD4
Genetic Testing Registry PSD4
NextProtQ8NDX1 [Medical]
TSGene23550
GENETestsPSD4
Target ValidationPSD4
Huge Navigator PSD4 [HugePedia]
snp3D : Map Gene to Disease23550
BioCentury BCIQPSD4
ClinGenPSD4
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD23550
Chemical/Pharm GKB GenePA134875981
Clinical trialPSD4
Miscellaneous
canSAR (ICR)PSD4 (select the gene name)
Probes
Litterature
PubMed11 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePSD4
EVEXPSD4
GoPubMedPSD4
iHOPPSD4
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Aug 1 17:11:51 CEST 2017

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