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

    Gene ID: 5662, updated on 17-Jun-2024

    Summary

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    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; AllianceGenome:HGNC:9507
    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
    mouse all
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    Genomic context

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    See PSD in Genome Data Viewer
    Location:
    10q24.32
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (102402619..102419946, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (103287568..103304910, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (104162376..104179703, 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 MPRA-validated peak1080 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:104147078-104147638 Neighboring gene NANOG hESC enhancer GRCh37_chr10:104151284-104151791 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:104151792-104152298 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2755 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3927 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3928 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3929 Neighboring gene Sharpr-MPRA regulatory region 13585 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2756 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:104160632-104161328 Neighboring gene Sharpr-MPRA regulatory region 3575 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2757 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:104169870-104170552 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:104170553-104171234 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2758 Neighboring gene nuclear factor kappa B subunit 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3930 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2759 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3931 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3932 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3934 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3933 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3935 Neighboring gene F-box and leucine rich repeat protein 15 Neighboring gene CUE domain containing 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. The C-terminal domain of EFA6A interacts directly with F-actin and assembles F-actin bundles. Macia E, et al. Sci Rep, 2019 Dec 16. PMID 31844082, Free PMC Article
    2. The Pleckstrin and Sec7 domain-containing gene as a novel epigenetic modification marker in human gastric cancer and its clinical significance. Zhu X, et al. Int J Oncol, 2015 Jan. PMID 25355626
    3. Aberrant methylation of the Pleckstrin and Sec7 domain-containing gene is implicated in ulcerative colitis-associated carcinogenesis through its inhibitory effect on apoptosis. Okada S, et al. Int J Oncol, 2012 Mar. PMID 22002136
    4. The pleckstrin homology domain of the Arf6-specific exchange factor EFA6 localizes to the plasma membrane by interacting with phosphatidylinositol 4,5-bisphosphate and F-actin. Macia E, et al. J Biol Chem, 2008 Jul 11. PMID 18490450
    5. The EFA6 family: guanine nucleotide exchange factors for ADP ribosylation factor 6 at neuronal synapses. Sakagami H. Tohoku J Exp Med, 2008 Mar. PMID 18323689

    See all (32) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The C-terminal domain of EFA6A interacts directly with F-actin and assembles F-actin bundles.
      Title: The C-terminal domain of EFA6A interacts directly with F-actin and assembles F-actin bundles.
    2. EFA6A recruits alpha-actinin 1 (ACTN1) through direct binding.
      Title: EFA6 proteins regulate lumen formation through α-actinin 1.
    3. Arf GTPases are likely to be locally activated by EFA6 and in turn targeted to the Flemming body to complete cytokinesis.
      Title: Class I Arfs (Arf1 and Arf3) and Arf6 are localized to the Flemming body and play important roles in cytokinesis.
    4. PSD expression might be a useful biomarker for epigenetic-based gastric cancer early diagnosis and may lead to the identification of new targets for pharmacological intervention.
      Title: The Pleckstrin and Sec7 domain-containing gene as a novel epigenetic modification marker in human gastric cancer and its clinical significance.
    5. EFA6 is regulated by a negative feedback loop, which is mediated by an allosteric interaction of Arf6-GTP with a domain of EFA6 and monitors the activation of Arf1 and Arf6 differentially
      Title: EFA6 controls Arf1 and Arf6 activation through a negative feedback loop.
    6. EFA6 participates in activation of Arf6 around the cleavage furrow during cytokinesis.
      Title: EFA6 activates Arf6 and participates in its targeting to the Flemming body during cytokinesis.
    7. Aberrant methylation of PSD occurs in UC-associated colorectal mucosa, enabling circumvention of Rac1 immune responses governing neutrophil chemotaxis and apoptosis, and plays a pivotal role in the mechanisms underlying UC-associated carcinogenesis.
      Title: Aberrant methylation of PSD disturbs Rac1-mediated immune responses governing neutrophil chemotaxis and apoptosis in ulcerative colitis-associated carcinogenesis.
    8. Both levels of accumulation of F-actin and apoptosis were significantly decreased in specimens from UC patients with PSD methylation compared to those without PSD methylation.
      Title: Aberrant methylation of the Pleckstrin and Sec7 domain-containing gene is implicated in ulcerative colitis-associated carcinogenesis through its inhibitory effect on apoptosis.
    9. Observational study of gene-disease association. (HuGE Navigator)
      Title: Association between genetic variants in VEGF, ERCC3 and occupational benzene haematotoxicity.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA2011

    Gene Ontology Provided by GOA

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

    General protein information

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

    NCBI Reference Sequences (RefSeq)

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    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_001270965.2 → NP_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, B1AKX7, D3DR87, Q15673, Q8IVG0
      UniProtKB/TrEMBL
      Q86YI3
      Related
      ENSP00000384830.1, ENST00000406432.5
      Conserved Domains (3) summary
      cd00171
      Location:542 → 708
      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:753 → 877
      PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain
      pfam00169
      Location:757 → 865
      PH; PH domain

    2. NM_001270966.2 → NP_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:163 → 329
      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:374 → 498
      PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain

    3. NM_002779.5 → NP_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, B1AKX7, D3DR87, Q15673, Q8IVG0
      UniProtKB/TrEMBL
      Q86YI3
      Related
      ENSP00000020673.5, ENST00000020673.6
      Conserved Domains (3) summary
      cd00171
      Location:542 → 708
      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:753 → 877
      PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain
      pfam00169
      Location:757 → 865
      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: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      102402619..102419946 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      103287568..103304910 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A5PKW4.2 GenPept UniProtKB/Swiss-Prot:A5PKW4

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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