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    Psd3 pleckstrin and Sec7 domain containing 3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 306380, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Psd3provided by RGD
    Official Full Name
    pleckstrin and Sec7 domain containing 3provided by RGD
    Primary source
    RGD:1559968
    See related
    EnsemblRapid:ENSRNOG00000013884 AllianceGenome:RGD:1559968
    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
    Also known as
    RGD1559968
    Summary
    Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be involved in regulation of ARF protein signal transduction. Predicted to be located in membrane. Predicted to be active in glutamatergic synapse; postsynapse; and ruffle membrane. Orthologous to human PSD3 (pleckstrin and Sec7 domain containing 3). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Brain (RPKM 389.2), Adrenal (RPKM 260.9) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Psd3 in Genome Data Viewer
    Location:
    16p14
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 16 NC_086034.1 (26238595..26802535)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 16 NC_051351.1 (21465643..22035846)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 16 NC_005115.4 (23212165..23789414)

    Chromosome 16 - NC_086034.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134482490 Neighboring gene uncharacterized LOC102551750 Neighboring gene uncharacterized LOC120097406 Neighboring gene small nucleolar RNA SNORA17 Neighboring gene N-acetyltransferase 3 Neighboring gene high mobility group box 2, pseudogene 3 Neighboring gene N-acetyltransferase 2 Neighboring gene N-acetyltransferase 1

    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. Distinct spatiotemporal expression of EFA6D, a guanine nucleotide exchange factor for ARF6, among the EFA6 family in mouse brain. Sakagami H, et al. Brain Res, 2006 Jun 6. PMID 16707115
    3. Sequential Elution Interactome Analysis of the Mind Bomb 1 Ubiquitin Ligase Reveals a Novel Role in Dendritic Spine Outgrowth. Mertz J, et al. Mol Cell Proteomics, 2015 Jul. PMID 25931508, Free PMC Article
    4. 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
    5. 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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables guanyl-nucleotide exchange factor activity ISO
    Inferred from Sequence Orthology
    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
    NOT located_in cleavage furrow ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in glutamatergic synapse ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in postsynapse 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 3

    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_001419764.1 → NP_001406693.1  PH and SEC7 domain-containing protein 3

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000016
      UniProtKB/TrEMBL
      A0A8I5YC85, A6KFK2

    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_086034.1 Reference GRCr8

      Range
      26238595..26802535
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039094961.2 → XP_038950889.1  PH and SEC7 domain-containing protein 3 isoform X12

      Conserved Domains (1) summary
      cd00171
      Location:830 → 973
      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 ...

    2. XM_006253039.5 → XP_006253101.1  PH and SEC7 domain-containing protein 3 isoform X3

      See identical proteins and their annotated locations for XP_006253101.1

      UniProtKB/TrEMBL
      A0A8I5Y8H6
      Related
      ENSRNOP00000078222.1, ENSRNOT00000093876.2
      Conserved Domains (3) summary
      cd00171
      Location:830 → 984
      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:1029 → 1154
      PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain
      pfam00169
      Location:1034 → 1142
      PH; PH domain

    3. XM_063275383.1 → XP_063131453.1  PH and SEC7 domain-containing protein 3 isoform X4

    4. XM_063275393.1 → XP_063131463.1  PH and SEC7 domain-containing protein 3 isoform X14

    5. XM_063275392.1 → XP_063131462.1  PH and SEC7 domain-containing protein 3 isoform X13

    6. XM_063275384.1 → XP_063131454.1  PH and SEC7 domain-containing protein 3 isoform X5

    7. XM_063275381.1 → XP_063131451.1  PH and SEC7 domain-containing protein 3 isoform X1

    8. XM_063275382.1 → XP_063131452.1  PH and SEC7 domain-containing protein 3 isoform X2

    9. XM_063275390.1 → XP_063131460.1  PH and SEC7 domain-containing protein 3 isoform X9

    10. XM_063275391.1 → XP_063131461.1  PH and SEC7 domain-containing protein 3 isoform X10

    11. XM_063275386.1 → XP_063131456.1  PH and SEC7 domain-containing protein 3 isoform X6

    12. XM_063275389.1 → XP_063131459.1  PH and SEC7 domain-containing protein 3 isoform X8

    13. XM_063275387.1 → XP_063131457.1  PH and SEC7 domain-containing protein 3 isoform X6

    14. XM_063275388.1 → XP_063131458.1  PH and SEC7 domain-containing protein 3 isoform X8

    15. XM_039094958.2 → XP_038950886.1  PH and SEC7 domain-containing protein 3 isoform X11

      UniProtKB/TrEMBL
      D3ZFY7
      Conserved Domains (2) summary
      cd00171
      Location:512 → 667
      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:712 → 837
      PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain

    16. XM_039094959.2 → XP_038950887.1  PH and SEC7 domain-containing protein 3 isoform X11

      UniProtKB/TrEMBL
      D3ZFY7
      Related
      ENSRNOP00000062924.5, ENSRNOT00000068177.6
      Conserved Domains (2) summary
      cd00171
      Location:512 → 667
      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:712 → 837
      PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain

    17. XM_063275394.1 → XP_063131464.1  PH and SEC7 domain-containing protein 3 isoform X15

    18. XM_039094954.2 → XP_038950882.1  PH and SEC7 domain-containing protein 3 isoform X7

      UniProtKB/TrEMBL
      A0A8I6A5C3
      Related
      ENSRNOP00000087887.1, ENSRNOT00000112213.2
      Conserved Domains (2) summary
      cd00171
      Location:544 → 699
      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:744 → 869
      PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain

    19. XM_063275398.1 → XP_063131468.1  PH and SEC7 domain-containing protein 3 isoform X20

      Related
      ENSRNOP00000104225.1, ENSRNOT00000164132.1

    20. XM_063275399.1 → XP_063131469.1  PH and SEC7 domain-containing protein 3 isoform X21

    21. XM_063275396.1 → XP_063131466.1  PH and SEC7 domain-containing protein 3 isoform X18

    22. XM_063275406.1 → XP_063131476.1  PH and SEC7 domain-containing protein 3 isoform X28

    23. XM_063275397.1 → XP_063131467.1  PH and SEC7 domain-containing protein 3 isoform X19

    24. XM_006253047.5 → XP_006253109.1  PH and SEC7 domain-containing protein 3 isoform X16

      See identical proteins and their annotated locations for XP_006253109.1

      UniProtKB/TrEMBL
      A0A8I6ANS5, D4A404
      Related
      ENSRNOP00000096277.2, ENSRNOT00000117420.2
      Conserved Domains (3) summary
      cd00171
      Location:51 → 205
      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:250 → 375
      PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain
      pfam00169
      Location:255 → 363
      PH; PH domain

    25. XM_063275395.1 → XP_063131465.1  PH and SEC7 domain-containing protein 3 isoform X17

    26. XM_063275404.1 → XP_063131474.1  PH and SEC7 domain-containing protein 3 isoform X26

    27. XM_063275405.1 → XP_063131475.1  PH and SEC7 domain-containing protein 3 isoform X27

    28. XM_063275403.1 → XP_063131473.1  PH and SEC7 domain-containing protein 3 isoform X25

    29. XM_063275402.1 → XP_063131472.1  PH and SEC7 domain-containing protein 3 isoform X24

    30. XM_063275401.1 → XP_063131471.1  PH and SEC7 domain-containing protein 3 isoform X23

    31. XM_006253053.5 → XP_006253115.1  PH and SEC7 domain-containing protein 3 isoform X22

      See identical proteins and their annotated locations for XP_006253115.1

      Related
      ENSRNOP00000042590.5, ENSRNOT00000041994.8
      Conserved Domains (2) summary
      cd13295
      Location:109 → 234
      PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain
      pfam00169
      Location:114 → 222
      PH; PH domain

    RNA

    1. XR_010058293.1 RNA Sequence

    2. XR_010058294.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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