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

Gene ID: 5662, updated on 11-Sep-2019

Summary

Official Symbol
PSDprovided by HGNC
Official Full Name
pleckstrin and Sec7 domain containingprovided by HGNC
Primary source
HGNC:HGNC:9507
See related
Ensembl:ENSG00000059915 MIM:602327
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
TYL; EFA6; PSD1; EFA6A
Summary
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]
Expression
Biased expression in brain (RPKM 23.5), endometrium (RPKM 9.6) and 8 other tissues See more
Orthologs

Genomic context

See PSD in Genome Data Viewer
Location:
10q24.32
Exon count:
22
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 10 NC_000010.11 (102402617..102420164, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (104162374..104179691, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene golgi brefeldin A resistant guanine nucleotide exchange factor 1 Neighboring gene uncharacterized LOC107984263 Neighboring gene nuclear factor kappa B subunit 2 Neighboring gene F-box and leucine rich repeat protein 15 Neighboring gene CUE domain containing 2 Neighboring gene microRNA 146b

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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
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

  • KIAA2011

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ARF guanyl-nucleotide exchange factor activity IDA
Inferred from Direct Assay
more info
PubMed 
phospholipid binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
neuron projection development IEA
Inferred from Electronic Annotation
more info
 
regulation of ARF protein signal transduction IEA
Inferred from Electronic Annotation
more info
 
signal transduction NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
cleavage furrow IDA
Inferred from Direct Assay
more info
PubMed 
dendritic spine IEA
Inferred from Electronic Annotation
more info
 
extrinsic component of postsynaptic endosome membrane IEA
Inferred from Electronic Annotation
more info
 
postsynaptic density, intracellular component IEA
Inferred from Electronic Annotation
more info
 
ruffle membrane IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
PH and SEC7 domain-containing protein 1
Names
exchange factor for ADP-ribosylation factor guanine nucleotide factor 6
exchange factor for ARF6
exchange factor for ARF6 A
pleckstrin homology and SEC7 domain-containing protein 1
pleckstrin-Sec7 domains-containing

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_001270965.1NP_001257894.1  PH and SEC7 domain-containing protein 1 isoform 1

    See identical proteins and their annotated locations for NP_001257894.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Both variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AI936992, AL121928, BC142643
    Consensus CDS
    CCDS31272.1
    UniProtKB/Swiss-Prot
    A5PKW4
    Related
    ENSP00000384830.1, ENST00000406432.5
    Conserved Domains (3) summary
    cd00171
    Location:542708
    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:753877
    PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain
    pfam00169
    Location:757865
    PH; PH domain
  2. NM_001270966.1NP_001257895.1  PH and SEC7 domain-containing protein 1 isoform 2

    See identical proteins and their annotated locations for NP_001257895.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AI936992, AL121928, BC039259, BC142643
    Consensus CDS
    CCDS73187.1
    UniProtKB/Swiss-Prot
    A5PKW4
    UniProtKB/TrEMBL
    Q86YI3
    Related
    ENSP00000481250.1, ENST00000611678.4
    Conserved Domains (2) summary
    cd00171
    Location:163329
    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:374498
    PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain
  3. NM_002779.5NP_002770.3  PH and SEC7 domain-containing protein 1 isoform 1

    See identical proteins and their annotated locations for NP_002770.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1). Both variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AB095931
    Consensus CDS
    CCDS31272.1
    UniProtKB/Swiss-Prot
    A5PKW4
    Related
    ENSP00000020673.5, ENST00000020673.6
    Conserved Domains (3) summary
    cd00171
    Location:542708
    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:753877
    PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain
    pfam00169
    Location:757865
    PH; PH domain

RNA

  1. NR_073110.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4, also known as EFA6As) lacks multiple exons in the 5' region but includes an alternate 5' exon, compared to variant 1. This variant is represented as non-coding due to the presence of an upstream ORF that is predicted to interfere with translation of the longest ORF; translation of the upstream ORF renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AI936992, BC142643, BM920983, DB505450

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.p13 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p13 Primary Assembly

    Range
    102402617..102420164 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011539969.2XP_011538271.1  PH and SEC7 domain-containing protein 1 isoform X1

    See identical proteins and their annotated locations for XP_011538271.1

    UniProtKB/Swiss-Prot
    A5PKW4
    Conserved Domains (3) summary
    cd00171
    Location:542708
    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:753877
    PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain
    pfam00169
    Location:757865
    PH; PH domain
  2. XM_017016434.2XP_016871923.1  PH and SEC7 domain-containing protein 1 isoform X1

    UniProtKB/Swiss-Prot
    A5PKW4
    Conserved Domains (3) summary
    cd00171
    Location:542708
    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:753877
    PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain
    pfam00169
    Location:757865
    PH; PH domain
  3. XM_011539968.1XP_011538270.1  PH and SEC7 domain-containing protein 1 isoform X1

    See identical proteins and their annotated locations for XP_011538270.1

    UniProtKB/Swiss-Prot
    A5PKW4
    Conserved Domains (3) summary
    cd00171
    Location:542708
    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:753877
    PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain
    pfam00169
    Location:757865
    PH; PH domain
  4. XM_017016433.1XP_016871922.1  PH and SEC7 domain-containing protein 1 isoform X1

    UniProtKB/Swiss-Prot
    A5PKW4
    Conserved Domains (3) summary
    cd00171
    Location:542708
    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:753877
    PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain
    pfam00169
    Location:757865
    PH; PH domain
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