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Aliases for PSD3 Gene

Aliases for PSD3 Gene

  • Pleckstrin And Sec7 Domain Containing 3 2 3 5
  • Exchange Factor For ADP-Ribosylation Factor Guanine Nucleotide Factor 6 3 4
  • Pleckstrin Homology And SEC7 Domain-Containing Protein 3 3 4
  • Hepatocellular Carcinoma-Associated Antigen 67 3 4
  • Epididymis Tissue Protein Li 20mP 3 4
  • EFA6R 3 4
  • HCA67 3 4
  • ADP-Ribosylation Factor Guanine Nucleotide Factor 6 3
  • PH And SEC7 Domain-Containing Protein 3 3
  • KIAA0942 4
  • EFA6D 3

External Ids for PSD3 Gene

Previous GeneCards Identifiers for PSD3 Gene

  • GC00U916998
  • GC08M016929

Summaries for PSD3 Gene

GeneCards Summary for PSD3 Gene

PSD3 (Pleckstrin And Sec7 Domain Containing 3) is a Protein Coding gene. Among its related pathways are Endocytosis. GO annotations related to this gene include phospholipid binding and ARF guanyl-nucleotide exchange factor activity. An important paralog of this gene is PSD.

UniProtKB/Swiss-Prot for PSD3 Gene

  • Guanine nucleotide exchange factor for ARF6.

Gene Wiki entry for PSD3 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PSD3 Gene

Genomics for PSD3 Gene

Regulatory Elements for PSD3 Gene

Enhancers for PSD3 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
GH08G018845 1.7 FANTOM5 Ensembl ENCODE dbSUPER 19.6 +239.5 239510 3.3 KLF17 BMI1 FEZF1 ZNF121 ETV6 RELB IKZF2 CREM GATAD2B ZNF518A PSD3 ENSG00000283402 GC08P018841
GH08G018850 1.4 Ensembl ENCODE dbSUPER 19.8 +233.9 233893 5.4 ZNF76 ZNF2 RAD21 YY1 ZNF366 SCRT2 FOS ZMIZ1 ZNF398 REST PSD3 PCM1 ENSG00000283402 ENSG00000278886
GH08G019139 1.6 FANTOM5 Ensembl ENCODE dbSUPER 10.8 -54.5 -54527 3.7 KLF1 TAF1 ZIC2 ZNF664 ZNF316 ZFHX2 NFE2 FOS MAFK EGR2 PSD3 LOC105379301 GC08P019197
GH08G019181 1.4 Ensembl ENCODE dbSUPER 9.8 -96.5 -96516 2.9 FOXA2 MLX ZFP64 SIN3A RARA RCOR1 FOS CEBPB MIER3 CEBPA PSD3 GC08P019197 LOC105379301
GH08G019200 1.3 FANTOM5 Ensembl ENCODE dbSUPER 10.4 -114.1 -114107 1.3 JUND JUN FOS PSD3 SH2D4A ENSG00000271654 GC08P019197 LOC442382
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PSD3 on UCSC Golden Path with GeneCards custom track

Genomic Location for PSD3 Gene

Chromosome:
8
Start:
18,527,301 bp from pter
End:
19,086,921 bp from pter
Size:
559,621 bases
Orientation:
Minus strand

Genomic View for PSD3 Gene

Genes around PSD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PSD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PSD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PSD3 Gene

Proteins for PSD3 Gene

  • Protein details for PSD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NYI0-PSD3_HUMAN
    Recommended name:
    PH and SEC7 domain-containing protein 3
    Protein Accession:
    Q9NYI0
    Secondary Accessions:
    • A6NFQ4
    • E9KL50
    • Q6B003
    • Q9Y2F1

    Protein attributes for PSD3 Gene

    Size:
    1048 amino acids
    Molecular mass:
    116034 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAF61269.2; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=AAH75044.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=AAH75045.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAA76786.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for PSD3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PSD3 Gene

Post-translational modifications for PSD3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PSD3 Gene

Domains & Families for PSD3 Gene

Gene Families for PSD3 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PSD3: view

No data available for UniProtKB/Swiss-Prot for PSD3 Gene

Function for PSD3 Gene

Molecular function for PSD3 Gene

UniProtKB/Swiss-Prot Function:
Guanine nucleotide exchange factor for ARF6.

Gene Ontology (GO) - Molecular Function for PSD3 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 PSD3: view
genes like me logo Genes that share phenotypes with PSD3: view

Animal Model Products

CRISPR Products

miRNA for PSD3 Gene

miRTarBase miRNAs that target PSD3

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PSD3 Gene

Localization for PSD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PSD3 Gene

Cell junction, synapse, postsynaptic cell membrane, postsynaptic density.

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 PSD3 gene
Compartment Confidence
plasma membrane 4
nucleus 3
cytosol 3

Gene Ontology (GO) - Cellular Components for PSD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0014069 postsynaptic density IEA --
GO:0016020 membrane IEA --
GO:0030054 cell junction IEA --
GO:0032587 ruffle membrane ISS --
genes like me logo Genes that share ontologies with PSD3: view

Pathways & Interactions for PSD3 Gene

SuperPathway Contained pathways
1 Endocytosis
genes like me logo Genes that share pathways with PSD3: view

Pathways by source for PSD3 Gene

1 KEGG pathway for PSD3 Gene

Gene Ontology (GO) - Biological Process for PSD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
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 PSD3: view

No data available for SIGNOR curated interactions for PSD3 Gene

Drugs & Compounds for PSD3 Gene

(3) Drugs for PSD3 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 PSD3: view

Transcripts for PSD3 Gene

Unigene Clusters for PSD3 Gene

Pleckstrin and Sec7 domain containing 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for PSD3 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5a · 5b · 5c ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11a · 11b ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20
SP1: -
SP2: -
SP3:
SP4: -
SP5:
SP6: - -
SP7:
SP8:
SP9:

Relevant External Links for PSD3 Gene

GeneLoc Exon Structure for
PSD3
ECgene alternative splicing isoforms for
PSD3

Expression for PSD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PSD3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PSD3 Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x6.3) and Brain - Cerebellum (x5.0).

Protein differential expression in normal tissues from HIPED for PSD3 Gene

This gene is overexpressed in Frontal cortex (38.5) and Brain (19.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PSD3 Gene



NURSA nuclear receptor signaling pathways regulating expression of PSD3 Gene:

PSD3

SOURCE GeneReport for Unigene cluster for PSD3 Gene:

Hs.434255

mRNA Expression by UniProt/SwissProt for PSD3 Gene:

Q9NYI0-PSD3_HUMAN
Tissue specificity: Isoform 2 is expressed in epididymis (at protein level).

Evidence on tissue expression from TISSUES for PSD3 Gene

  • Nervous system(5)
  • Liver(4.3)
genes like me logo Genes that share expression patterns with PSD3: view

Primer Products

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for PSD3 Gene

Orthologs for PSD3 Gene

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

Orthologs for PSD3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PSD3 34 35
  • 99.17 (n)
mouse
(Mus musculus)
Mammalia Psd3 34 16 35
  • 88.22 (n)
dog
(Canis familiaris)
Mammalia PSD3 34 35
  • 86.76 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 86 (a)
OneToMany
-- 35
  • 65 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Psd3 34
  • 82.38 (n)
cow
(Bos Taurus)
Mammalia PSD3 34 35
  • 82.07 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 74 (a)
OneToMany
-- 35
  • 60 (a)
OneToMany
-- 35
  • 46 (a)
OneToMany
chicken
(Gallus gallus)
Aves PSD3 34 35
  • 67.58 (n)
lizard
(Anolis carolinensis)
Reptilia PSD3 35
  • 85 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia psd3 34
  • 67.47 (n)
Str.16491 34
zebrafish
(Danio rerio)
Actinopterygii psd3l 34 35
  • 67.95 (n)
fruit fly
(Drosophila melanogaster)
Insecta Efa6 35
  • 20 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea efa-6 35
  • 28 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GEA2 35
  • 9 (a)
ManyToMany
GEA1 35
  • 8 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 24 (a)
OneToMany
Species where no ortholog for PSD3 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)
  • wheat (Triticum aestivum)

Evolution for PSD3 Gene

ENSEMBL:
Gene Tree for PSD3 (if available)
TreeFam:
Gene Tree for PSD3 (if available)

Paralogs for PSD3 Gene

Variants for PSD3 Gene

Sequence variations from dbSNP and Humsavar for PSD3 Gene

SNP ID Clin Chr 08 pos Sequence Context AA Info Type
rs1000004579 -- 18,819,549(+) AAATA(C/T)TTCAA intron-variant
rs1000009809 -- 18,864,800(+) AAGGA(C/T)AGGCT intron-variant
rs1000015489 -- 18,599,868(+) TCTCC(C/T)ATACA intron-variant
rs1000019441 -- 18,619,398(+) CCAGC(A/C)TTTTG intron-variant
rs1000024662 -- 18,627,239(+) TGAGT(A/T)GAGGA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PSD3 Gene

Variant ID Type Subtype PubMed ID
dgv12047n54 CNV loss 21841781
dgv12048n54 CNV loss 21841781
dgv12049n54 CNV loss 21841781
dgv12050n54 CNV loss 21841781
dgv12051n54 CNV loss 21841781
dgv2056e212 CNV gain 25503493
dgv2057e212 CNV loss 25503493
dgv2058e212 CNV loss 25503493
dgv2059e212 CNV loss 25503493
dgv3788n106 CNV deletion 24896259
dgv3789n106 CNV deletion 24896259
dgv3790n106 CNV deletion 24896259
dgv465e215 CNV deletion 23714750
dgv7126n100 CNV loss 25217958
dgv7127n100 CNV loss 25217958
dgv7128n100 CNV loss 25217958
dgv878n27 CNV loss 19166990
esv1011194 CNV deletion 20482838
esv1270304 CNV deletion 17803354
esv1416189 CNV deletion 17803354
esv1660982 CNV deletion 17803354
esv2190840 CNV deletion 18987734
esv2421371 CNV deletion 20811451
esv2509063 CNV insertion 19546169
esv25125 CNV loss 19812545
esv2531026 CNV deletion 19546169
esv2659994 CNV deletion 23128226
esv2675406 CNV deletion 23128226
esv2676844 CNV deletion 23128226
esv2736701 CNV deletion 23290073
esv2736702 CNV deletion 23290073
esv2736703 CNV deletion 23290073
esv2759601 CNV loss 17122850
esv2761214 CNV gain+loss 21179565
esv2764110 CNV loss 21179565
esv3273162 CNV deletion 24192839
esv3273273 CNV deletion 24192839
esv3273385 CNV deletion 24192839
esv32805 CNV gain 17666407
esv3360605 CNV insertion 20981092
esv3543164 CNV deletion 23714750
esv3543166 CNV deletion 23714750
esv3543168 CNV deletion 23714750
esv3572611 CNV loss 25503493
esv3572612 CNV loss 25503493
esv3572613 CNV loss 25503493
esv3572624 CNV loss 25503493
esv3616522 CNV loss 21293372
esv3616523 CNV loss 21293372
esv3616524 CNV loss 21293372
esv3616525 CNV loss 21293372
esv3616527 CNV loss 21293372
esv3616529 CNV loss 21293372
esv3616530 CNV loss 21293372
esv3616531 CNV loss 21293372
esv3616532 CNV gain 21293372
esv3616533 CNV gain 21293372
esv3616534 CNV loss 21293372
esv3616535 CNV loss 21293372
esv3891367 CNV gain 25118596
esv3891369 CNV gain 25118596
esv5150 CNV loss 18987735
esv5427 CNV loss 18987735
esv5821 CNV loss 19470904
esv6653 CNV loss 19470904
esv989363 CNV deletion 20482838
esv997949 CNV deletion 20482838
esv998126 CNV deletion 20482838
nsv1016482 CNV gain 25217958
nsv1023241 CNV loss 25217958
nsv1026091 CNV gain 25217958
nsv1026366 CNV gain 25217958
nsv1028621 CNV gain 25217958
nsv1029785 CNV loss 25217958
nsv1033377 CNV gain 25217958
nsv1073799 CNV deletion 25765185
nsv1074752 CNV deletion 25765185
nsv1076067 CNV deletion 25765185
nsv1115072 CNV deletion 24896259
nsv1124326 CNV deletion 24896259
nsv1126848 CNV deletion 24896259
nsv1148837 CNV deletion 26484159
nsv1153063 CNV deletion 26484159
nsv1161741 CNV deletion 26073780
nsv397362 CNV deletion 16902084
nsv428196 CNV gain 18775914
nsv442101 CNV loss 18776908
nsv465596 CNV gain 19166990
nsv470201 CNV gain 18288195
nsv507446 OTHER sequence alteration 20534489
nsv512033 CNV loss 21212237
nsv512034 CNV loss 21212237
nsv514482 CNV loss 21397061
nsv517395 CNV loss 19592680
nsv518488 CNV loss 19592680
nsv519028 CNV loss 19592680
nsv519244 CNV loss 19592680
nsv519382 CNV loss 19592680
nsv519585 CNV loss 19592680
nsv520348 CNV loss 19592680
nsv521053 CNV gain 19592680
nsv521368 CNV loss 19592680
nsv525714 CNV loss 19592680
nsv526122 CNV loss 19592680
nsv527228 CNV loss 19592680
nsv6100 CNV insertion 18451855
nsv610718 CNV gain 21841781
nsv610719 CNV loss 21841781
nsv610720 CNV gain 21841781
nsv610721 CNV gain 21841781
nsv610742 CNV loss 21841781
nsv610743 CNV loss 21841781
nsv610746 CNV loss 21841781
nsv818614 CNV loss 17921354
nsv8309 CNV loss 18304495
nsv8310 CNV loss 18304495
nsv831252 CNV gain 17160897
nsv831253 CNV gain 17160897
nsv831254 CNV gain 17160897
nsv831255 CNV gain 17160897
nsv957673 CNV deletion 24416366
nsv957674 CNV deletion 24416366
nsv981918 CNV duplication 23825009
nsv982123 CNV deletion 23825009

Variation tolerance for PSD3 Gene

Residual Variation Intolerance Score: 56.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.03; 68.59% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PSD3 Gene

Human Gene Mutation Database (HGMD)
PSD3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PSD3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PSD3 Gene

Disorders for PSD3 Gene

Relevant External Links for PSD3

Genetic Association Database (GAD)
PSD3
Human Genome Epidemiology (HuGE) Navigator
PSD3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PSD3

No disorders were found for PSD3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PSD3 Gene

Publications for PSD3 Gene

  1. Duffy-null-associated low neutrophil counts influence HIV-1 susceptibility in high-risk South African black women. (PMID: 21507922) Ramsuran V. … Ndung'u T. (Clin. Infect. Dis. 2011) 3 46 64
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  3. Systematic mapping and functional analysis of a family of human epididymal secretory sperm-located proteins. (PMID: 20736409) Li J. … Liu Y. (Mol. Cell. Proteomics 2010) 3 4 64
  4. Inherited genetic variant predisposes to aggressive but not indolent prostate cancer. (PMID: 20080650) Xu J. … Isaacs W.B. (Proc. Natl. Acad. Sci. U.S.A. 2010) 3 46 64
  5. Replication of a genome-wide case-control study of esophageal squamous cell carcinoma. (PMID: 18649358) Ng D. … Taylor P.R. (Int. J. Cancer 2008) 3 46 64

Products for PSD3 Gene

Sources for PSD3 Gene

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