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

    Gene ID: 171381, updated on 6-Jun-2024

    Summary

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    Official Symbol
    Psdprovided by RGD
    Official Full Name
    pleckstrin and Sec7 domain containingprovided by RGD
    Primary source
    RGD:620297
    See related
    Ensembl:ENSRNOG00000019435 AllianceGenome:RGD:620297
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    EFA6
    Summary
    Predicted to enable guanyl-nucleotide exchange factor activity. Involved in neuron differentiation. Is integral component of membrane. Orthologous to human PSD (pleckstrin and Sec7 domain containing). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Brain (RPKM 240.5) and Uterus (RPKM 24.9) See more
    Orthologs
    human mouse all
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    Genomic context

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    See Psd in Genome Data Viewer
    Location:
    1q54
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (255114703..255130151, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (245173279..245188681, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (266059331..266074774, complement)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134484075 Neighboring gene nuclear factor kappa B subunit 2 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: 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 regulates selective polarised transport and axon regeneration from the axon initial segment. Eva R, et al. J Cell Sci, 2017 Nov 1. PMID 28935671, Free PMC Article
    2. Somatodendritic localization of the mRNA for EFA6A, a guanine nucleotide exchange protein for ARF6, in rat hippocampus and its involvement in dendritic formation. Sakagami H, et al. Eur J Neurosci, 2004 Feb. PMID 15009133
    3. ARF6 and EFA6A regulate the development and maintenance of dendritic spines. Choi S, et al. J Neurosci, 2006 May 3. PMID 16672654, Free PMC Article
    4. Localization of mRNAs for subfamily of guanine nucleotide-exchange proteins (GEP) for ARFs (ADP-ribosylation factors) in the brain of developing and mature rats under normal and postaxotomy conditions. Suzuki I, et al. Brain Res Mol Brain Res, 2002 Jan 31. PMID 11834294
    5. EFA6A encodes two isoforms with distinct biological activities in neuronal cells. Sironi C, et al. J Cell Sci, 2009 Jun 15. PMID 19494129

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. EFA6A, an Exchange Factor for Arf6, Regulates NGF-Dependent TrkA Recycling From Early Endosomes and Neurite Outgrowth in PC12 Cells.
      Title: EFA6A, an Exchange Factor for Arf6, Regulates NGF-Dependent TrkA Recycling From Early Endosomes and Neurite Outgrowth in PC12 Cells.
    2. EFA6 regulates selective polarized transport and axon regeneration from the axon initial segment.
      Title: EFA6 regulates selective polarised transport and axon regeneration from the axon initial segment.
    3. EFA6A could participate in neuronal morphogenesis through the regulated expression of two functionally distinct isoforms.
      Title: EFA6A encodes two isoforms with distinct biological activities in neuronal cells.
    4. There is definitive evidence for somatodendritic localization of EFA6 mRNA in both cultured and in vivo hippocampal neurons: during postnatal development, it is dramatically increased.
      Title: Somatodendritic localization of the mRNA for EFA6A, a guanine nucleotide exchange protein for ARF6, in rat hippocampus and its involvement in dendritic formation.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables guanine nucleotide transmembrane transporter activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables guanyl-nucleotide exchange factor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables guanyl-nucleotide exchange factor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables guanyl-nucleotide exchange factor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables phospholipid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in guanine nucleotide transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in guanine transport TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in maintenance of postsynaptic density structure IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in maintenance of postsynaptic density structure IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in neuron differentiation IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in neuron projection development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in neuron projection development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of ARF protein signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of postsynapse assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of postsynapse assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cleavage furrow IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cleavage furrow ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cleavage furrow ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in dendritic spine IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in dendritic spine ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in glutamatergic synapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in glutamatergic synapse IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    located_in postsynaptic density ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in postsynaptic density, intracellular component IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in postsynaptic density, intracellular component ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in ruffle membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in ruffle membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in ruffle membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    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

    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_134370.2 → NP_599197.2  PH and SEC7 domain-containing protein 1

      See identical proteins and their annotated locations for NP_599197.2

      Status: PROVISIONAL

      Source sequence(s)
      CH473986
      UniProtKB/TrEMBL
      A6JHM0, G3V8J5
      Related
      ENSRNOP00000026378.4, ENSRNOT00000026378.5
      Conserved Domains (3) summary
      cd00171
      Location:541 → 707
      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:752 → 876
      PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain
      pfam00169
      Location:756 → 864
      PH; PH domain

    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_086019.1 Reference GRCr8

      Range
      255114703..255130151 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006231432.5 → XP_006231494.1  PH and SEC7 domain-containing protein 1 isoform X1

      See identical proteins and their annotated locations for XP_006231494.1

      UniProtKB/TrEMBL
      A6JHM0, G3V8J5
      Related
      ENSRNOP00000093417.1
      Conserved Domains (3) summary
      cd00171
      Location:541 → 707
      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:752 → 876
      PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain
      pfam00169
      Location:756 → 864
      PH; PH domain

    2. XM_008760396.4 → XP_008758618.1  PH and SEC7 domain-containing protein 1 isoform X1

      See identical proteins and their annotated locations for XP_008758618.1

      UniProtKB/TrEMBL
      A6JHM0, G3V8J5
      Conserved Domains (3) summary
      cd00171
      Location:541 → 707
      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:752 → 876
      PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain
      pfam00169
      Location:756 → 864
      PH; PH domain

    3. XM_008760394.4 → XP_008758616.1  PH and SEC7 domain-containing protein 1 isoform X1

      See identical proteins and their annotated locations for XP_008758616.1

      UniProtKB/TrEMBL
      A6JHM0, G3V8J5
      Conserved Domains (3) summary
      cd00171
      Location:541 → 707
      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:752 → 876
      PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain
      pfam00169
      Location:756 → 864
      PH; PH domain

    4. XM_063275990.1 → XP_063132060.1  PH and SEC7 domain-containing protein 1 isoform X1

      UniProtKB/TrEMBL
      A6JHM0, G3V8J5

    5. XM_063276038.1 → XP_063132108.1  PH and SEC7 domain-containing protein 1 isoform X3

      UniProtKB/TrEMBL
      A0A8I6GKK2

    6. XM_039089045.2 → XP_038944973.1  PH and SEC7 domain-containing protein 1 isoform X2

      Conserved Domains (1) summary
      cd13295
      Location:279 → 403
      PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain

    RNA

    1. XR_005491590.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9ESQ7.1 GenPept UniProtKB/Swiss-Prot:Q9ESQ7

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