Free for academic non-profit institutions. Other users need a Commercial license

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 D 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
  • Exchange Factor For ARF6 D 3 4
  • EFA6R 3 4
  • EFA6D 3 4
  • HCA67 3 4
  • Exchange Factor For ADP-Ribosylation Factor Guanine Nucleotide Factor 6 3
  • ADP-Ribosylation Factor Guanine Nucleotide Factor 6 3
  • PH And SEC7 Domain-Containing Protein 3 3
  • KIAA0942 4

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. 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.

UniProtKB/Swiss-Prot for PSD3 Gene

  • Guanine nucleotide exchange factor for ARF6.

Gene Wiki entry for PSD3 Gene

Additional gene information 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

GeneHancer (GH) Regulatory Elements for PSD3 Gene

Promoters and enhancers for PSD3 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
GH08I019011 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 559.4 +73.5 73535 3.8 ARNT ARID4B SIN3A FEZF1 DMAP1 GLI4 ZNF2 ZNF48 ZNF121 GLIS2 PSD3 ENSG00000201157 ENSG00000253335 ENSG00000270255
GH08I018808 Promoter/Enhancer 0.9 EPDnew ENCODE 550.1 +277.9 277881 0.7 ZNF629 CREB1 PSD3 PIR47430 GC08P018838
GH08I019086 Enhancer 0.6 ENCODE dbSUPER 555.3 -0.5 -479 1.3 ZNF512 ZNF398 PSD3 LOC105379301 ENSG00000253557
GH08I018850 Promoter/Enhancer 1.7 Ensembl ENCODE dbSUPER 19.8 +233.9 233893 5.4 MZF1 ZNF76 ZNF2 RAD21 YY1 ZNF335 ZNF366 SCRT2 RCOR1 FOS PSD3 PCM1 ENSG00000283402 ENSG00000278886
GH08I018845 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 19.6 +239.5 239510 3.3 KLF17 BMI1 FEZF1 IRF4 ZNF121 ATF7 ETV6 BCLAF1 IKZF2 RUNX3 ENSG00000283402 PSD3 GC08P018841
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PSD3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PSD3 gene promoter:

Genomic Locations for PSD3 Gene

Genomic Locations for PSD3 Gene
chr8:18,527,301-19,086,921
(GRCh38/hg38)
Size:
559,621 bases
Orientation:
Minus strand
chr8:18,384,811-18,942,240
(GRCh37/hg19)

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

No Post-translational modifications

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.

Phenotypes From GWAS Catalog for PSD3 Gene

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

Clone 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 membrane. Cell projection, ruffle membrane. Cell junction, synapse, postsynaptic cell membrane, postsynaptic density. Note=In interphase associated with the plasma membrane, in particular with membrane ruffling regions. {ECO:0000250 UniProtKB:Q2PFD7}.

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

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleus (2)
  • Vesicles (2)
See all subcellular structures

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:0065009 regulation of molecular function 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

Clone 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 33 34
  • 99.17 (n)
mouse
(Mus musculus)
Mammalia Psd3 33 16 34
  • 88.22 (n)
dog
(Canis familiaris)
Mammalia PSD3 33 34
  • 86.76 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 86 (a)
OneToMany
-- 34
  • 65 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Psd3 33
  • 82.38 (n)
cow
(Bos Taurus)
Mammalia PSD3 33 34
  • 82.07 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 74 (a)
OneToMany
-- 34
  • 60 (a)
OneToMany
-- 34
  • 46 (a)
OneToMany
chicken
(Gallus gallus)
Aves PSD3 33 34
  • 67.58 (n)
lizard
(Anolis carolinensis)
Reptilia PSD3 34
  • 85 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia psd3 33
  • 67.47 (n)
Str.16491 33
zebrafish
(Danio rerio)
Actinopterygii psd3l 33 34
  • 67.95 (n)
fruit fly
(Drosophila melanogaster)
Insecta Efa6 34
  • 20 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea efa-6 34
  • 28 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GEA2 34
  • 9 (a)
ManyToMany
GEA1 34
  • 8 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 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 Variation AA Info Type
rs1000004579 -- 18,819,549(-) T/C genic_upstream_transcript_variant, intron_variant
rs1000009809 -- 18,864,800(-) C/T genic_upstream_transcript_variant, intron_variant
rs1000015489 -- 18,599,868(-) T/C genic_downstream_transcript_variant, intron_variant
rs1000019441 -- 18,619,398(-) A/C genic_downstream_transcript_variant, intron_variant
rs1000024662 -- 18,627,239(-) T/A genic_downstream_transcript_variant, intron_variant

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

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

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)

Additional Variant Information 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

Additional Disease Information for PSD3

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

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 (Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2011) 3 44 58
  2. Inherited genetic variant predisposes to aggressive but not indolent prostate cancer. (PMID: 20080650) Xu J … Isaacs WB (Proceedings of the National Academy of Sciences of the United States of America 2010) 3 44 58
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  4. Systematic mapping and functional analysis of a family of human epididymal secretory sperm-located proteins. (PMID: 20736409) Li J … Liu Y (Molecular & cellular proteomics : MCP 2010) 3 4 58
  5. Replication of a genome-wide case-control study of esophageal squamous cell carcinoma. (PMID: 18649358) Ng D … Taylor PR (International journal of cancer 2008) 3 44 58

Products for PSD3 Gene

Sources for PSD3 Gene

Content
Loading form....