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Aliases for PSD Gene

Aliases for PSD Gene

  • Pleckstrin And Sec7 Domain Containing 2 3 5
  • Pleckstrin Homology And SEC7 Domain-Containing Protein 1 3 4
  • Exchange Factor For ARF6 3 4
  • EFA6 3 4
  • PSD1 3 4
  • TYL 3 4
  • PH And SEC7 Domain-Containing Protein 1 3
  • Pleckstrin And Sec7 Domain Protein 2
  • Pleckstrin-Sec7 Domains-Containing 3
  • KIAA2011 4
  • EFA6A 3

External Ids for PSD Gene

Previous GeneCards Identifiers for PSD Gene

  • GC10M103055
  • GC10M103396
  • GC10M104293
  • GC10M103826
  • GC10M104152
  • GC10M097795

Summaries for PSD Gene

Entrez Gene Summary for PSD Gene

  • This gene encodes a Plekstrin homology and SEC7 domains-containing protein that functions as a guanine nucleotide exchange factor. The encoded protein regulates signal transduction by activating ADP-ribosylation factor 6. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]

GeneCards Summary for PSD Gene

PSD (Pleckstrin And Sec7 Domain Containing) is a Protein Coding gene. Diseases associated with PSD include Branch Retinal Artery Occlusion. Among its related pathways are Endocytosis. GO annotations related to this gene include signal transducer activity and ARF guanyl-nucleotide exchange factor activity. An important paralog of this gene is PSD2.

UniProtKB/Swiss-Prot for PSD Gene

  • Guanine nucleotide exchange factor for ARF6. Induces cytoskeletal remodeling (By similarity).

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PSD Gene

Genomics for PSD Gene

Regulatory Elements for PSD Gene

Enhancers for PSD Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH10G102595 1.9 FANTOM5 Ensembl ENCODE dbSUPER 10.5 -179.1 -179132 11.2 FOXA2 MLX ARID4B DMAP1 ZNF2 YY1 ZNF766 ZNF143 FOS SP5 MFSD13A SFXN2 ACTR1A SUFU C10orf95 PSD FBXL15 CUEDC2 MIR146B ARL3
GH10G102342 1.2 FANTOM5 Ensembl ENCODE 10.3 +78.1 78123 2.3 SCRT1 TEAD4 CBX2 ETS1 FOXA1 BCL11A GATA2 POLR2A SCRT2 POU5F1 PITX3 GBF1 ELOVL3 NOLC1 PSD FBXL15 C10orf95 MFSD13A ACTR1A GC10P102289
GH10G102169 1.2 Ensembl ENCODE 10.3 +251.8 251842 1.0 ATF1 ARID4B SIN3A ZNF2 ZNF121 ZNF143 DEK REST ZNF518A ZNF579 GBF1 ELOVL3 HPS6 PITX3 PPRC1 NFKB2 PSD FBXL15 NOLC1
GH10G102501 1.1 ENCODE 11 -81.9 -81850 4.6 HDGF PKNOX1 FOXA2 ARNT CREB3L1 WRNIP1 ARID4B SIN3A DMAP1 ZNF2 MFSD13A PDCD11 PPRC1 RNU6-43P C10orf95 MGEA5 PSD FBXL15 RPARP-AS1 GC10P102507
GH10G102467 1 Ensembl ENCODE 11.1 -47.3 -47336 2.7 HDAC1 KLF1 ZBTB40 ADNP ZNF600 NR2F1 ELF4 CEBPB ELF1 DPF2 MFSD13A MIR146B CUEDC2 SUFU NFKB2 RNU6-43P PSD FBXL15 ELOVL3 RPARP-AS1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PSD on UCSC Golden Path with GeneCards custom track

Promoters for PSD Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000261172 39 2201 HDGF MLX CREB3L1 ARNT AGO1 ZFP64 WRNIP1 ARID4B SIN3A FEZF1
ENSR00000032737 1839 201 HDAC1 SIN3A ARID4B ZNF76 ZSCAN9 RARA GLIS2 ZNF143 THAP11 SMARCC1

Genomic Location for PSD Gene

Chromosome:
10
Start:
102,402,617 bp from pter
End:
102,421,539 bp from pter
Size:
18,923 bases
Orientation:
Minus strand

Genomic View for PSD Gene

Genes around PSD on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for PSD Gene

Proteins for PSD Gene

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

    Protein Symbol:
    A5PKW4-PSD1_HUMAN
    Recommended name:
    PH and SEC7 domain-containing protein 1
    Protein Accession:
    A5PKW4
    Secondary Accessions:
    • B1AKX7
    • D3DR87
    • Q15673
    • Q8IVG0

    Protein attributes for PSD Gene

    Size:
    1024 amino acids
    Molecular mass:
    109543 Da
    Quaternary structure:
    • Interacts with ACTN1. Interacts (ARF6-bound form) with KCNK1; does not interact with KCNK1 in the absence of ARF6 (By similarity).
    SequenceCaution:
    • Sequence=BAC23107.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for PSD Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PSD Gene

Post-translational modifications for PSD Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PSD Gene

Domains & Families for PSD Gene

Gene Families for PSD Gene

Protein Domains for PSD Gene

Suggested Antigen Peptide Sequences for PSD Gene

Graphical View of Domain Structure for InterPro Entry

A5PKW4

UniProtKB/Swiss-Prot:

PSD1_HUMAN :
  • Belongs to the PSD family.
Family:
  • Belongs to the PSD family.
genes like me logo Genes that share domains with PSD: view

Function for PSD Gene

Molecular function for PSD Gene

GENATLAS Biochemistry:
pleckstrin-Sec 7 domains protein,71kDa,with three alternatively spliced forms the larger in the brain,tightly linked to NKF2,in tail to tail orientation
UniProtKB/Swiss-Prot Function:
Guanine nucleotide exchange factor for ARF6. Induces cytoskeletal remodeling (By similarity).

Gene Ontology (GO) - Molecular Function for PSD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004871 signal transducer activity NAS 9417912
GO:0005085 guanyl-nucleotide exchange factor activity IEA --
GO:0005086 ARF guanyl-nucleotide exchange factor activity IEA,IDA 23603394
GO:0005515 protein binding IPI 20339350
GO:0005543 phospholipid binding IEA --
genes like me logo Genes that share ontologies with PSD: view
genes like me logo Genes that share phenotypes with PSD: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for PSD Gene

Localization for PSD Gene

Subcellular locations from UniProtKB/Swiss-Prot for PSD Gene

Cell membrane. Cell projection, ruffle.

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 PSD gene
Compartment Confidence
plasma membrane 5
nucleus 3
cytosol 3
endosome 3
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for PSD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0014069 postsynaptic density IEA --
GO:0016020 membrane IEA --
GO:0032154 cleavage furrow IDA 23603394
GO:0032587 ruffle membrane IDA 23603394
genes like me logo Genes that share ontologies with PSD: view

Pathways & Interactions for PSD Gene

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

Pathways by source for PSD Gene

1 KEGG pathway for PSD Gene

Gene Ontology (GO) - Biological Process for PSD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007165 signal transduction NAS 9417912
GO:0031175 neuron projection development IEA --
GO:0032012 regulation of ARF protein signal transduction IEA --
GO:0043547 positive regulation of GTPase activity IEA --
genes like me logo Genes that share ontologies with PSD: view

No data available for SIGNOR curated interactions for PSD Gene

Drugs & Compounds for PSD Gene

(3) Drugs for PSD Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Guanosine diphosphate Experimental Pharma 0
Guanosine monophosphate Experimental Pharma 0
Guanosine triphosphate Experimental Pharma 0
genes like me logo Genes that share compounds with PSD: view

Transcripts for PSD Gene

Unigene Clusters for PSD Gene

Pleckstrin and Sec7 domain containing:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b · 9c ^ 10 ^ 11a · 11b ^ 12a · 12b ^ 13a · 13b ^ 14 ^ 15a · 15b · 15c · 15d · 15e ^ 16 ^ 17a ·
SP1: - - - - -
SP2: - - - - - -
SP3: - - - - - -
SP4: - - - - - -
SP5: -
SP6: - -
SP7:
SP8:
SP9: - - - - -
SP10: - - - -
SP11: - - -
SP12: - -
SP13:
SP14:
SP15:

ExUns: 17b ^ 18a · 18b · 18c · 18d ^ 19a · 19b ^ 20a · 20b
SP1:
SP2:
SP3:
SP4:
SP5: -
SP6: -
SP7: - -
SP8: - -
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:

Relevant External Links for PSD Gene

GeneLoc Exon Structure for
PSD
ECgene alternative splicing isoforms for
PSD

Expression for PSD Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Brain - Nucleus accumbens (basal ganglia) (x5.6), Brain - Hippocampus (x4.8), Brain - Putamen (basal ganglia) (x4.6), Brain - Amygdala (x4.5), Brain - Cortex (x4.4), and Brain - Caudate (basal ganglia) (x4.3).

Protein differential expression in normal tissues from HIPED for PSD Gene

This gene is overexpressed in Plasma (38.7), Fetal Brain (18.2), and Platelet (7.0).

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



Protein tissue co-expression partners for PSD Gene

NURSA nuclear receptor signaling pathways regulating expression of PSD Gene:

PSD

SOURCE GeneReport for Unigene cluster for PSD Gene:

Hs.154658

mRNA Expression by UniProt/SwissProt for PSD Gene:

A5PKW4-PSD1_HUMAN
Tissue specificity: Isoform 2 is expressed in the brain.

Evidence on tissue expression from TISSUES for PSD Gene

  • Nervous system(4.9)
genes like me logo Genes that share expression patterns with PSD: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for PSD Gene

Orthologs for PSD Gene

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

Orthologs for PSD Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PSD 34 35
  • 98.48 (n)
dog
(Canis familiaris)
Mammalia PSD 34 35
  • 93.29 (n)
cow
(Bos Taurus)
Mammalia PSD 34 35
  • 91.98 (n)
mouse
(Mus musculus)
Mammalia Psd 34 16 35
  • 89.74 (n)
rat
(Rattus norvegicus)
Mammalia Psd 34
  • 89.47 (n)
oppossum
(Monodelphis domestica)
Mammalia PSD 35
  • 79 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PSD 35
  • 69 (a)
OneToOne
chicken
(Gallus gallus)
Aves PSD 35 34
  • 67.37 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PSD 35
  • 60 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia psd 34
  • 62.06 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.33589 34
zebrafish
(Danio rerio)
Actinopterygii LOC570918 34
  • 65.08 (n)
PSD (1 of 3) 35
  • 54 (a)
OneToMany
PSD (2 of 3) 35
  • 29 (a)
OneToMany
CABZ01075947.1 35
  • 23 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta Efa6 35
  • 19 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea Y55D9A.1a 36
  • 37 (a)
Y55D9A.1b 36
  • 37 (a)
efa-6 35
  • 26 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GEA2 35
  • 8 (a)
ManyToMany
GEA1 35
  • 7 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 24 (a)
OneToMany
Species where no ortholog for PSD was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • wheat (Triticum aestivum)

Evolution for PSD Gene

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

Paralogs for PSD Gene

Paralogs for PSD Gene

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

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

Variants for PSD Gene

Sequence variations from dbSNP and Humsavar for PSD Gene

SNP ID Clin Chr 10 pos Sequence Context AA Info Type
rs397514331 Pathogenic 102,402,144(+) GAGAC(-/A)AGCTG downstream-variant-500B, reference, frameshift-variant
rs397514332 Pathogenic 102,402,138(+) AAACC(C/T)GAGAC downstream-variant-500B, reference, stop-gained
rs727502786 Pathogenic 102,402,137(+) GAAAC(-/CCGAGACA)AGCTG downstream-variant-500B, reference, frameshift-variant
rs727502787 Pathogenic 102,402,267(+) GGAAG(A/G)CAGTG downstream-variant-500B, reference, missense
rs727502788 Pathogenic 102,402,273(+) CAGTG(C/T)GTACG downstream-variant-500B, reference, missense

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

Variant ID Type Subtype PubMed ID
nsv1159761 CNV deletion 26073780
nsv525546 CNV loss 19592680
nsv552058 CNV loss 21841781
nsv951006 CNV deletion 24416366

Variation tolerance for PSD Gene

Residual Variation Intolerance Score: 31.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.31; 53.30% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PSD Gene

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

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

Disorders for PSD Gene

MalaCards: The human disease database

(1) MalaCards diseases for PSD Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
branch retinal artery occlusion
  • arterial retinal branch occlusion
- elite association - COSMIC cancer census association via MalaCards
Search PSD in MalaCards View complete list of genes associated with diseases

Relevant External Links for PSD

Genetic Association Database (GAD)
PSD
Human Genome Epidemiology (HuGE) Navigator
PSD
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PSD
genes like me logo Genes that share disorders with PSD: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PSD Gene

Publications for PSD Gene

  1. Identification of a novel gene, PSD, adjacent to NFKB2/lyt-10, which contains Sec7 and pleckstrin-homology domains. (PMID: 9417912) Perletti L. … Neri A. (Genomics 1997) 2 3 4 64
  2. Association between genetic variants in VEGF, ERCC3 and occupational benzene haematotoxicity. (PMID: 19773279) Hosgood H.D. … Lan Q. (Occup Environ Med 2009) 3 46 64
  3. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. (PMID: 16385451) Grupe A. … Goate A. (Am. J. Hum. Genet. 2006) 3 46 64
  4. Class I Arfs (Arf1 and Arf3) and Arf6 are localized to the Flemming body and play important roles in cytokinesis. (PMID: 26330566) Hanai A. … Nakayama K. (J. Biochem. 2016) 3 64
  5. The Pleckstrin and Sec7 domain-containing gene as a novel epigenetic modification marker in human gastric cancer and its clinical significance. (PMID: 25355626) Zhu X. … Dai D. (Int. J. Oncol. 2015) 3 64

Products for PSD Gene

Sources for PSD Gene

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