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

    Gene ID: 5662, updated on 22-Jun-2017
    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; Vega:OTTHUMG00000018954
    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]
    Orthologs
    Location:
    10q24.32
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 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

    • 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

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    NHGRI GWAS Catalog

    Description
    Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
    NHGRI GWA Catalog
    • 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...
    Products Interactant Other Gene Complex Source Pubs Description

    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 
    signal transducer activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    neuron projection development IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of GTPase activity 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 of dendrite IEA
    Inferred from Electronic Annotation
    more info
     
    ruffle membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    PH and SEC7 domain-containing protein 1
    Names
    exchange factor for ARF6
    pleckstrin homology and SEC7 domain-containing protein 1
    pleckstrin-Sec7 domains-containing

    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 (3) 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
      pfam00169
      Location:378486
      PH; PH domain
    3. NM_002779.4NP_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, AI936992
      Consensus CDS
      CCDS31272.1
      UniProtKB/Swiss-Prot
      A5PKW4
      Related
      ENSP00000020673.5, OTTHUMP00000020364, ENST00000020673.5, OTTHUMT00000050041
      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_073110.1 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 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000010.11 Reference GRCh38.p7 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_017016434.1XP_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

    Alternate CHM1_1.1

    Genomic

    1. NC_018921.2 Alternate CHM1_1.1

      Range
      104445795..104463129 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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