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    Psd4 pleckstrin and Sec7 domain containing 4 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 311785, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Psd4provided by RGD
    Official Full Name
    pleckstrin and Sec7 domain containing 4provided by RGD
    Primary source
    RGD:1310289
    See related
    EnsemblRapid:ENSRNOG00000006079 AllianceGenome:RGD:1310289
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable guanyl-nucleotide exchange factor activity and phospholipid binding activity. Predicted to be involved in regulation of ARF protein signal transduction. Predicted to be located in cell junction. Predicted to be active in ruffle membrane. Orthologous to human PSD4 (pleckstrin and Sec7 domain containing 4). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 465.2), Spleen (RPKM 208.2) and 3 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Psd4 in Genome Data Viewer
    Location:
    3p13
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (27535341..27571850)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (7137069..7173571)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (1478432..1515094)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene interleukin 36, beta Neighboring gene interleukin 1 family member 10 Neighboring gene interleukin 1 receptor antagonist Neighboring gene uncharacterized LOC134486348 Neighboring gene paired box 8 Neighboring gene uncharacterized LOC102549381

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. EFA6 activates Arf6 and participates in its targeting to the Flemming body during cytokinesis. Ueda T, et al. FEBS Lett, 2013 Jun 5. PMID 23603394
    2. Defining the membrane proteome of NK cells. Ghosh D, et al. J Mass Spectrom, 2010 Jan. PMID 19946888
    3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC124698

    Gene Ontology Provided by RGD

    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
    		  
    Process Evidence Code Pubs
    involved_in regulation of ARF protein signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cell junction IEA
    Inferred from Electronic Annotation
    more info
    		  
    NOT located_in cleavage furrow ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in ruffle membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in ruffle membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    PH and SEC7 domain-containing protein 4

    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_001134881.2 → NP_001128353.1  PH and SEC7 domain-containing protein 4

      See identical proteins and their annotated locations for NP_001128353.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000003
      UniProtKB/TrEMBL
      D3ZPP3
      Related
      ENSRNOP00000008161.3, ENSRNOT00000008161.6
      Conserved Domains (2) summary
      cd00171
      Location:536 → 690
      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:724 → 851
      PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain

    2. NM_001434196.1 → NP_001421125.1  PH and SEC7 domain-containing protein 4

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000003
      UniProtKB/TrEMBL
      D3ZPP3

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086021.1 Reference GRCr8

      Range
      27535341..27571850
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006233592.5 → XP_006233654.1  PH and SEC7 domain-containing protein 4 isoform X1

      See identical proteins and their annotated locations for XP_006233654.1

      UniProtKB/TrEMBL
      D3ZPP3
      Conserved Domains (2) summary
      cd00171
      Location:536 → 690
      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:724 → 851
      PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain

    2. XM_063283915.1 → XP_063139985.1  PH and SEC7 domain-containing protein 4 isoform X2

      UniProtKB/TrEMBL
      A0A8I6A7Y6

    3. XM_039105177.2 → XP_038961105.1  PH and SEC7 domain-containing protein 4 isoform X1

      UniProtKB/TrEMBL
      D3ZPP3
      Conserved Domains (2) summary
      cd00171
      Location:536 → 690
      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:724 → 851
      PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain

    4. XM_039105178.2 → XP_038961106.1  PH and SEC7 domain-containing protein 4 isoform X1

      UniProtKB/TrEMBL
      D3ZPP3
      Conserved Domains (2) summary
      cd00171
      Location:536 → 690
      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:724 → 851
      PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain

    5. XM_039105179.2 → XP_038961107.1  PH and SEC7 domain-containing protein 4 isoform X3

      Conserved Domains (2) summary
      cd00171
      Location:536 → 690
      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 ...
      cl17171
      Location:724 → 859
      PH-like; Pleckstrin homology-like domain

    6. XM_039105180.1 → XP_038961108.1  PH and SEC7 domain-containing protein 4 isoform X4

      Conserved Domains (1) summary
      cl00136
      Location:536 → 628
      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 ...

    7. XM_006233591.4 → XP_006233653.1  PH and SEC7 domain-containing protein 4 isoform X1

      Conserved Domains (2) summary
      cd00171
      Location:536 → 690
      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:724 → 851
      PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain

    8. XM_006233593.5 → XP_006233655.1  PH and SEC7 domain-containing protein 4 isoform X2

      UniProtKB/TrEMBL
      A0A8I6A7Y6
      Related
      ENSRNOP00000087791.1, ENSRNOT00000099515.2
      Conserved Domains (3) summary
      cd00171
      Location:533 → 687
      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:721 → 848
      PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain
      pfam00169
      Location:743 → 840
      PH; PH domain

    9. XM_063283916.1 → XP_063139986.1  PH and SEC7 domain-containing protein 4 isoform X5

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001037781.1: Suppressed sequence

      Description
      NM_001037781.1: This RefSeq was suppressed temporarily based on the calculation that the annotated protein was shorter than a protein or proteins from a putative ortholog.
    Nucleotide Protein Strain
    Heading Accession and Version

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