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Aliases for PSD2 Gene

Aliases for PSD2 Gene

  • Pleckstrin And Sec7 Domain Containing 2 2 3 5
  • Exchange Factor For ADP-Ribosylation Factor Guanine Nucleotide Factor 6 C 3 4
  • Pleckstrin Homology And SEC7 Domain-Containing Protein 2 3 4
  • Exchange Factor For ARF6 C 3 4
  • EFA6C 3 4
  • PH And SEC7 Domain-Containing Protein 2 3
  • EC 2.5.1.6 56
  • EC 3.6.1 56

External Ids for PSD2 Gene

Previous GeneCards Identifiers for PSD2 Gene

  • GC00U916997
  • GC05P139155
  • GC05P134332
  • GC05P139175
  • GC05P139795

Summaries for PSD2 Gene

GeneCards Summary for PSD2 Gene

PSD2 (Pleckstrin And Sec7 Domain Containing 2) is a Protein Coding gene. Among its related pathways are Endocytosis. Gene Ontology (GO) annotations related to this gene include phospholipid binding and ARF guanyl-nucleotide exchange factor activity. An important paralog of this gene is PSD.

Additional gene information for PSD2 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PSD2 Gene

Genomics for PSD2 Gene

GeneHancer (GH) Regulatory Elements for PSD2 Gene

Promoters and enhancers for PSD2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05I139795 Promoter 0.9 EPDnew 550.2 +73.9 73886 0.1 KLF1 MAZ SP2 ZNF398 ZBTB8A ZNF148 POLR2A VEZF1 ZNF341 CTBP2 PSD2 ENSG00000251387 ENSG00000250692
GH05I139796 Promoter 0.8 EPDnew 550.2 +74.4 74364 0.1 ZNF335 MXI1 RFX1 BMI1 EZH2 PSD2 ENSG00000251387 ENSG00000250692
GH05I139763 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 20.7 +43.2 43181 2.6 HDGF ARNT ARID4B SIN3A ZNF2 ZBTB7B SLC30A9 ZNF213 E2F8 ZNF207 PSD2 CXXC5 DNAJC18 IGIP NRG2 PIR36769 ENSG00000271792
GH05I139633 Promoter/Enhancer 2.9 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 8.1 -68.5 -68537 40.3 CLOCK MLX ZFP64 YBX1 FEZF1 DMAP1 IRF4 YY1 ZNF213 E2F8 CXXC5 ANKHD1 TMCO6 IK TMEM173 LOC101929719 APBB3 PSD2 DNAJC18 LOC105379194
GH05I139744 Enhancer 1.5 Ensembl ENCODE dbSUPER 11.7 +24.5 24497 4.7 HDGF PKNOX1 SMAD1 FEZF1 DMAP1 YBX1 ZNF2 YY1 ZNF213 ZNF416 PSD2-AS1 HARS2 ANKHD1 WDR55 IK TMCO6 MALINC1 PSD2 PURA LOC101929719
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PSD2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PSD2 gene promoter:

Genomic Locations for PSD2 Gene

Genomic Locations for PSD2 Gene
chr5:139,721,903-139,844,466
(GRCh38/hg38)
Size:
122,564 bases
Orientation:
Plus strand
chr5:139,175,406-139,224,051
(GRCh37/hg19)

Genomic View for PSD2 Gene

Genes around PSD2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PSD2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PSD2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PSD2 Gene

Proteins for PSD2 Gene

  • Protein details for PSD2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BQI7-PSD2_HUMAN
    Recommended name:
    PH and SEC7 domain-containing protein 2
    Protein Accession:
    Q9BQI7
    Secondary Accessions:
    • D3DQD3
    • Q8N3J8

    Protein attributes for PSD2 Gene

    Size:
    771 amino acids
    Molecular mass:
    84660 Da
    Quaternary structure:
    No Data Available

neXtProt entry for PSD2 Gene

Selected DME Specific Peptides for PSD2 Gene

Q9BQI7:
  • KRTPRGR
  • AHRLARRL

Post-translational modifications for PSD2 Gene

No Post-translational modifications

Other Protein References for PSD2 Gene

Domains & Families for PSD2 Gene

Gene Families for PSD2 Gene

Suggested Antigen Peptide Sequences for PSD2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9BQI7

UniProtKB/Swiss-Prot:

PSD2_HUMAN :
  • Belongs to the PSD family.
Family:
  • Belongs to the PSD family.
genes like me logo Genes that share domains with PSD2: view

Function for PSD2 Gene

Enzyme Numbers (IUBMB) for PSD2 Gene

Phenotypes From GWAS Catalog for PSD2 Gene

Gene Ontology (GO) - Molecular Function for PSD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005086 ARF guanyl-nucleotide exchange factor activity IEA --
GO:0005543 phospholipid binding IEA --
genes like me logo Genes that share ontologies with PSD2: view
genes like me logo Genes that share phenotypes with PSD2: view

Animal Model Products

Clone Products

No data available for Molecular function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PSD2 Gene

Localization for PSD2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PSD2 Gene

Cell membrane; Single-pass membrane protein. Cell projection, ruffle membrane. Cleavage furrow. Note=In interphase associated with the plasma membrane, in particular with membrane ruffling regions. In cells undergoing cytokinesis, transiently found around the ingressing cleavage furrow. Not detected at the midbody ring/Flemming body. {ECO:0000250 UniProtKB:Q6P1I6}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PSD2 gene
Compartment Confidence
plasma membrane 4
nucleus 3
cytosol 3
mitochondrion 1

Gene Ontology (GO) - Cellular Components for PSD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030425 dendrite IEA --
GO:0032154 cleavage furrow ISS --
genes like me logo Genes that share ontologies with PSD2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PSD2 Gene

Pathways & Interactions for PSD2 Gene

SuperPathway Contained pathways
1 Endocytosis
genes like me logo Genes that share pathways with PSD2: view

Pathways by source for PSD2 Gene

1 KEGG pathway for PSD2 Gene

Gene Ontology (GO) - Biological Process for PSD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0032012 regulation of ARF protein signal transduction IEA --
GO:0065009 regulation of molecular function IEA --
genes like me logo Genes that share ontologies with PSD2: view

No data available for SIGNOR curated interactions for PSD2 Gene

Drugs & Compounds for PSD2 Gene

No Compound Related Data Available

Transcripts for PSD2 Gene

mRNA/cDNA for PSD2 Gene

Unigene Clusters for PSD2 Gene

Pleckstrin and Sec7 domain containing 2:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PSD2 Gene

No ASD Table

Relevant External Links for PSD2 Gene

GeneLoc Exon Structure for
PSD2
ECgene alternative splicing isoforms for
PSD2

Expression for PSD2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PSD2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PSD2 Gene

This gene is overexpressed in Brain - Caudate (basal ganglia) (x6.4), Brain - Putamen (basal ganglia) (x5.9), Brain - Nucleus accumbens (basal ganglia) (x5.5), Brain - Amygdala (x5.2), and Brain - Cortex (x4.3).

Protein differential expression in normal tissues from HIPED for PSD2 Gene

This gene is overexpressed in Fetal Brain (46.8) and Esophagus (17.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for PSD2 Gene



Protein tissue co-expression partners for PSD2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PSD2 Gene:

PSD2

SOURCE GeneReport for Unigene cluster for PSD2 Gene:

Hs.21963

Evidence on tissue expression from TISSUES for PSD2 Gene

  • Nervous system(4.7)
genes like me logo Genes that share expression patterns with PSD2: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PSD2 Gene

Orthologs for PSD2 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for PSD2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PSD2 33 34
  • 99.74 (n)
dog
(Canis familiaris)
Mammalia PSD2 33 34
  • 88.85 (n)
cow
(Bos Taurus)
Mammalia PSD2 33 34
  • 88.63 (n)
rat
(Rattus norvegicus)
Mammalia Psd2 33
  • 85.83 (n)
mouse
(Mus musculus)
Mammalia Psd2 33 16 34
  • 85.71 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PSD2 34
  • 80 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PSD2 34
  • 67 (a)
OneToOne
chicken
(Gallus gallus)
Aves PSD2 33 34
  • 73.54 (n)
lizard
(Anolis carolinensis)
Reptilia PSD2 34
  • 64 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii LOC557199 33
  • 69.18 (n)
BX005008.2 34
  • 56 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Efa6 34
  • 18 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea efa-6 34
  • 24 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GEA1 34
  • 7 (a)
ManyToMany
GEA2 34
  • 7 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 23 (a)
OneToMany
Species where no ortholog for PSD2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for PSD2 Gene

ENSEMBL:
Gene Tree for PSD2 (if available)
TreeFam:
Gene Tree for PSD2 (if available)

Paralogs for PSD2 Gene

(3) SIMAP similar genes for PSD2 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with PSD2: view

Variants for PSD2 Gene

Sequence variations from dbSNP and Humsavar for PSD2 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs1000012757 -- 139,684,938(+) G/A 5_prime_UTR_variant, genic_upstream_transcript_variant
rs1000015850 -- 139,789,923(+) T/C genic_upstream_transcript_variant, intron_variant
rs1000016351 -- 139,806,279(+) C/T intron_variant
rs1000048690 -- 139,772,029(+) C/T genic_upstream_transcript_variant, intron_variant
rs1000048847 -- 139,698,793(+) C/T genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PSD2 Gene

Variant ID Type Subtype PubMed ID
nsv830506 CNV loss 17160897
nsv519808 CNV loss 19592680
nsv474629 CNV novel sequence insertion 20440878
nsv471051 CNV gain 18288195
esv3606942 CNV loss 21293372
esv3570450 CNV loss 25503493
dgv1650e212 CNV loss 25503493

Variation tolerance for PSD2 Gene

Residual Variation Intolerance Score: 46.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.71; 46.36% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PSD2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PSD2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PSD2 Gene

Disorders for PSD2 Gene

Additional Disease Information for PSD2

No disorders were found for PSD2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PSD2 Gene

Publications for PSD2 Gene

  1. Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PMID: 11230166) Wiemann S … Poustka A (Genome research 2001) 3 4 58
  2. Early-Onset Alzheimer Disease and Candidate Risk Genes Involved in Endolysosomal Transport. (PMID: 28738127) Kunkle BW … Pericak-Vance MA (JAMA neurology 2017) 3 58
  3. Association Between Brain Gene Expression, DNA Methylation, and Alteration of Ex Vivo Magnetic Resonance Imaging Transverse Relaxation in Late-Life Cognitive Decline. (PMID: 29084334) Yu L … Bennett DA (JAMA neurology 2017) 3 58
  4. The full-ORF clone resource of the German cDNA Consortium. (PMID: 17974005) Bechtel S … Schupp I (BMC genomics 2007) 4 58
  5. Characterization of the interactome of the human MutL homologues MLH1, PMS1, and PMS2. (PMID: 17148452) Cannavo E … Jiricny J (The Journal of biological chemistry 2007) 3 58

Products for PSD2 Gene

Sources for PSD2 Gene

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