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PSD3 pleckstrin and Sec7 domain containing 3 [ Homo sapiens (human) ]

Gene ID: 23362, updated on 2-Oct-2018

Summary

Official Symbol
PSD3provided by HGNC
Official Full Name
pleckstrin and Sec7 domain containing 3provided by HGNC
Primary source
HGNC:HGNC:19093
See related
Ensembl:ENSG00000156011 MIM:614440; Vega:OTTHUMG00000163711
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
EFA6D; EFA6R; HCA67
Expression
Broad expression in brain (RPKM 17.3), adrenal (RPKM 6.3) and 19 other tissues See more
Orthologs

Genomic context

See PSD3 in Genome Data Viewer
Location:
8p22
Exon count:
29
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 8 NC_000008.11 (18527303..19086909, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (18384813..18871196, complement)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene ribosomal protein L10a pseudogene 11 Neighboring gene N-acetyltransferase 2 Neighboring gene ribosomal protein L35 pseudogene 6 Neighboring gene uncharacterized LOC107986868 Neighboring gene uncharacterized LOC105379303 Neighboring gene uncharacterized LOC105379301 Neighboring gene uncharacterized LOC100128993 Neighboring gene ATPase plasma membrane Ca2+ transporting 1 pseudogene

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Copy number response

Description
Copy number response
Haploinsufficency

No evidence available (Last evaluated (2016-12-07)

ClinGen Genome Curation Page
Triplosensitivity

No evidence available (Last evaluated (2016-12-07)

ClinGen Genome Curation Page

NHGRI GWAS Catalog

Description
Duffy-null-associated low neutrophil counts influence HIV-1 susceptibility in high-risk South African black women.
NHGRI GWA Catalog
Gene network analysis in a pediatric cohort identifies novel lung function genes.
NHGRI GWA Catalog
Genome-wide association study identifies ephrin type A receptors implicated in paclitaxel induced peripheral sensory neuropathy.
NHGRI GWA Catalog
Genome-wide association study of urinary albumin excretion rate in patients with type 1 diabetes.
NHGRI GWA Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog

Pathways from BioSystems

  • Endocytosis, organism-specific biosystem (from KEGG)
    Endocytosis, organism-specific biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...
  • Endocytosis, conserved biosystem (from KEGG)
    Endocytosis, conserved biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • DKFZp761K1423

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ARF guanyl-nucleotide exchange factor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
regulation of ARF protein signal transduction IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cell junction IEA
Inferred from Electronic Annotation
more info
 
postsynaptic density IEA
Inferred from Electronic Annotation
more info
 
postsynaptic membrane IEA
Inferred from Electronic Annotation
more info
 
ruffle membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ruffle membrane ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
PH and SEC7 domain-containing protein 3
Names
ADP-ribosylation factor guanine nucleotide factor 6
epididymis tissue protein Li 20mP
exchange factor for ADP-ribosylation factor guanine nucleotide factor 6
exchange factor for ADP-ribosylation factor guanine nucleotide factor 6 D
exchange factor for ARF6 D
hepatocellular carcinoma-associated antigen 67
pleckstrin homology and SEC7 domain-containing protein 3

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001362819.1NP_001349748.1  PH and SEC7 domain-containing protein 3 isoform c

    Status: VALIDATED

    Source sequence(s)
    AC087821, AC120051, AF243495, AK091317
    Conserved Domains (2) summary
    cd00171
    Location:548702
    Sec7; Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor ...
    cd13295
    Location:747872
    PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain
  2. NM_015310.3NP_056125.3  PH and SEC7 domain-containing protein 3 isoform a

    See identical proteins and their annotated locations for NP_056125.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AC087821, AC120051, AF243495, AK091317
    Consensus CDS
    CCDS43720.1
    UniProtKB/Swiss-Prot
    Q9NYI0
    UniProtKB/TrEMBL
    B3KRC4
    Related
    ENSP00000324127.8, OTTHUMP00000224594, ENST00000327040.12, OTTHUMT00000374867
    Conserved Domains (3) summary
    cd00171
    Location:581735
    Sec7; Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor ...
    cd13295
    Location:780905
    PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain
    pfam00169
    Location:785893
    PH; PH domain
  3. NM_206909.2NP_996792.1  PH and SEC7 domain-containing protein 3 isoform b

    See identical proteins and their annotated locations for NP_996792.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding region compared to variant 1. The resulting isoform (b) is shorter and has distinct N- and C-termini compared to isoform a.
    Source sequence(s)
    AC120051, AF243495, AK091317, DB055312
    Consensus CDS
    CCDS34854.1
    UniProtKB/Swiss-Prot
    Q9NYI0
    UniProtKB/TrEMBL
    B3KRC4
    Related
    ENSP00000286485.8, OTTHUMP00000224595, ENST00000286485.12, OTTHUMT00000374869
    Conserved Domains (2) summary
    cd00171
    Location:47201
    Sec7; Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor ...
    cd13295
    Location:246371
    PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p12 Primary Assembly

    Range
    18527303..19086909 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017013260.1XP_016868749.1  PH and SEC7 domain-containing protein 3 isoform X3

  2. XM_017013258.1XP_016868747.1  PH and SEC7 domain-containing protein 3 isoform X1

  3. XM_017013259.1XP_016868748.1  PH and SEC7 domain-containing protein 3 isoform X2

  4. XM_024447113.1XP_024302881.1  PH and SEC7 domain-containing protein 3 isoform X9

    Related
    ENSP00000430640.1, ENST00000523619.5
    Conserved Domains (2) summary
    cd00171
    Location:516670
    Sec7; Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor ...
    cd13295
    Location:715840
    PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain
  5. XM_017013261.2XP_016868750.1  PH and SEC7 domain-containing protein 3 isoform X4

    Related
    OTTHUMP00000224597
    Conserved Domains (2) summary
    cd00171
    Location:548702
    Sec7; Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor ...
    cd13295
    Location:747872
    PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain
  6. XM_017013265.1XP_016868754.1  PH and SEC7 domain-containing protein 3 isoform X14

  7. XM_011544467.2XP_011542769.1  PH and SEC7 domain-containing protein 3 isoform X6

    Conserved Domains (1) summary
    cd00171
    Location:825969
    Sec7; Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor ...
  8. XM_011544473.2XP_011542775.1  PH and SEC7 domain-containing protein 3 isoform X11

    Conserved Domains (1) summary
    cd00171
    Location:825969
    Sec7; Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor ...
  9. XM_011544468.2XP_011542770.1  PH and SEC7 domain-containing protein 3 isoform X7

    Conserved Domains (1) summary
    cd00171
    Location:825970
    Sec7; Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor ...
  10. XM_017013262.1XP_016868751.1  PH and SEC7 domain-containing protein 3 isoform X5

  11. XM_011544469.2XP_011542771.1  PH and SEC7 domain-containing protein 3 isoform X8

    Conserved Domains (1) summary
    cd00171
    Location:825969
    Sec7; Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor ...
  12. XM_011544471.2XP_011542773.1  PH and SEC7 domain-containing protein 3 isoform X10

    Conserved Domains (1) summary
    cd00171
    Location:825972
    Sec7; Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor ...
  13. XM_017013263.1XP_016868752.1  PH and SEC7 domain-containing protein 3 isoform X12

  14. XM_017013264.1XP_016868753.1  PH and SEC7 domain-containing protein 3 isoform X13

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