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    Dennd3 DENN domain containing 3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 315055, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Dennd3provided by RGD
    Official Full Name
    DENN domain containing 3provided by RGD
    Primary source
    RGD:1311559
    See related
    EnsemblRapid:ENSRNOG00000010794 AllianceGenome:RGD:1311559
    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
    RGD1311559
    Summary
    Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be involved in endosome to lysosome transport; protein catabolic process; and regulation of Rab protein signal transduction. Predicted to be active in cytoplasmic vesicle. Orthologous to human DENND3 (DENN domain containing 3). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Kidney (RPKM 130.2), Lung (RPKM 129.6) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Dennd3 in Genome Data Viewer
    Location:
    7q34
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 7 NC_086025.1 (107304860..107362573)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 7 NC_051342.1 (105415870..105473583)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 7 NC_005106.4 (114724644..114812471)

    Chromosome 7 - NC_086025.1Genomic Context describing neighboring genes Neighboring gene protein tyrosine kinase 2 Neighboring gene small nucleolar RNA SNORA8 Neighboring gene ribosomal protein L36 like 1 Neighboring gene solute carrier family 45, member 4 Neighboring gene uncharacterized LOC134479924

    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. Small GTPase Rab12 regulates constitutive degradation of transferrin receptor. Matsui T, et al. Traffic, 2011 Oct. PMID 21718402
    2. Family-wide characterization of the DENN domain Rab GDP-GTP exchange factors. Yoshimura S, et al. J Cell Biol, 2010 Oct 18. PMID 20937701, Free PMC Article
    3. 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

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables guanyl-nucleotide exchange factor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in endosome to lysosome transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein catabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of Rab protein signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasmic vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    DENN domain-containing protein 3
    Names
    DENN/MADD domain containing 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_001427258.1 → NP_001414187.1  DENN domain-containing protein 3

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000007
      Related
      ENSRNOP00000078310.2, ENSRNOT00000097499.2

    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_086025.1 Reference GRCr8

      Range
      107304860..107362573
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063263576.1 → XP_063119646.1  DENN domain-containing protein 3 isoform X3

    2. XM_017595246.3 → XP_017450735.1  DENN domain-containing protein 3 isoform X2

      UniProtKB/TrEMBL
      D4A2H4

    3. XM_006241738.4 → XP_006241800.2  DENN domain-containing protein 3 isoform X1

      UniProtKB/TrEMBL
      D4A2H4

    4. XM_039080223.1 → XP_038936151.1  DENN domain-containing protein 3 isoform X4

      UniProtKB/TrEMBL
      A0A8I6G2K6
      Conserved Domains (4) summary
      smart00801
      Location:187 → 249
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      COG2319
      Location:749 → 1028
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:781 → 816
      7WD40; WD40 repeat [structural motif]
      cl11519
      Location:7 → 121
      DENN; DENN (AEX-3) domain

    5. XM_039080224.1 → XP_038936152.1  DENN domain-containing protein 3 isoform X5

      Conserved Domains (4) summary
      smart00801
      Location:127 → 189
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      COG2319
      Location:689 → 968
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:721 → 756
      7WD40; WD40 repeat [structural motif]
      cl11519
      Location:1 → 61
      DENN; DENN (AEX-3) domain

    6. XM_039080225.2 → XP_038936153.1  DENN domain-containing protein 3 isoform X6

      UniProtKB/TrEMBL
      A6HRV6
      Conserved Domains (2) summary
      COG2319
      Location:509 → 788
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:541 → 576
      7WD40; WD40 repeat [structural motif]
    Nucleotide Protein Strain
    Heading Accession and Version

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