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    PSD4 pleckstrin and Sec7 domain containing 4 [ Homo sapiens (human) ]

    Gene ID: 23550, updated on 2-Nov-2024

    Summary

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    Official Symbol
    PSD4provided by HGNC
    Official Full Name
    pleckstrin and Sec7 domain containing 4provided by HGNC
    Primary source
    HGNC:HGNC:19096
    See related
    Ensembl:ENSG00000125637 MIM:614442; AllianceGenome:HGNC:19096
    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
    TIC; EFA6B
    Summary
    Predicted to enable guanyl-nucleotide exchange factor activity and phospholipid binding activity. Predicted to be involved in regulation of ARF protein signal transduction. Located in ruffle membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in lymph node (RPKM 21.5), spleen (RPKM 20.1) and 22 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PSD4 in Genome Data Viewer
    Location:
    2q14.1
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (113173971..113209391)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (113600541..113635966)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (113931548..113966968)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 10370 Neighboring gene RNA, U6 small nuclear 1180, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16410 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16411 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16412 Neighboring gene interleukin 1 receptor antagonist Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11878 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11879 Neighboring gene Sharpr-MPRA regulatory region 7144 Neighboring gene uncharacterized LOC124907872 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:113929890-113930390 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:113930391-113930891 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16413 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16414 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16415 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11880 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16416 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16417 Neighboring gene Sharpr-MPRA regulatory region 2961 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16418 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11881 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:113998497-113999696 Neighboring gene paired box 8 Neighboring gene PAX8 antisense RNA 1 Neighboring gene PAX8 promoter region Neighboring gene uncharacterized LOC105373567 Neighboring gene long intergenic non-protein coding RNA 2966

    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 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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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. DDR1 promotes hepatocellular carcinoma metastasis through recruiting PSD4 to ARF6.
      Title: DDR1 promotes hepatocellular carcinoma metastasis through recruiting PSD4 to ARF6.
    2. TNF-alpha/NF-kappaB signaling epigenetically represses PSD4 transcription to promote alcohol-related hepatocellular carcinoma progression.
      Title: TNF-α/NF-κB signaling epigenetically represses PSD4 transcription to promote alcohol-related hepatocellular carcinoma progression.
    3. EFA6B regulates a stop signal for collective invasion in breast cancer.
      Title: EFA6B regulates a stop signal for collective invasion in breast cancer.
    4. results identify EFA6B as a novel antagonist in breast cancer and they point to its regulatory and signaling pathways as rational therapeutic targets in aggressive forms of this disease
      Title: EFA6B antagonizes breast cancer.
    5. One of the cytohesin family of guanine nucleotide exchange factors, Tic may act on the ARF family of GTP-binding proteins. A PH domain with similar sequence and relative position to those in other cytohesins may allow association with phosphoinositides.
      Title: Cytohesins and centaurins: mediators of PI 3-kinase-regulated Arf signaling.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ36237, FLJ37279

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables guanyl-nucleotide exchange factor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 regulation of ARF protein signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    NOT located_in cleavage furrow IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in membrane HDA PubMed 
    is_active_in ruffle membrane IBA
    Inferred from Biological aspect of Ancestor
    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 4
    Names
    ADP-ribosylation factor guanine nucleotide-exchange factor 6
    SEC7 homolog
    exchange factor for ADP-ribosylation factor guanine nucleotide factor 6 B
    exchange factor for ADP-ribosylation factor guanine nucleotide factor 6B
    exchange factor for ARF6 B
    pleckstrin homology and SEC7 domain-containing protein 4
    telomeric of interleukin-1 cluster protein

    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_012455.3 → NP_036587.2  PH and SEC7 domain-containing protein 4

      See identical proteins and their annotated locations for NP_036587.2

      Status: VALIDATED

      Source sequence(s)
      AC016683
      Consensus CDS
      CCDS33276.1
      UniProtKB/Swiss-Prot
      A6NEG7, A8K1Y0, O95621, Q4ZG34, Q6GPH8, Q8IYP4, Q8NDX1
      Related
      ENSP00000245796.6, ENST00000245796.11
      Conserved Domains (3) summary
      cd00171
      Location:570 → 738
      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:772 → 900
      PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain
      pfam00169
      Location:794 → 892
      PH; PH domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      113173971..113209391
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      113600541..113635966
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054341224.1 → XP_054197199.1  PH and SEC7 domain-containing protein 4 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NDX1.2 GenPept UniProtKB/Swiss-Prot:Q8NDX1

    Gene LinkOut

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

    Chemical Information
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