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    Dennd5a DENN domain containing 5A [ Rattus norvegicus (Norway rat) ]

    Gene ID: 308942, updated on 30-Mar-2024

    Summary

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    Official Symbol
    Dennd5aprovided by RGD
    Official Full Name
    DENN domain containing 5Aprovided by RGD
    Primary source
    RGD:1306759
    See related
    Ensembl:ENSRNOG00000012206 AllianceGenome:RGD:1306759
    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
    Rab6ip1
    Summary
    Predicted to enable guanyl-nucleotide exchange factor activity and small GTPase binding activity. Involved in negative regulation of neuron projection development. Predicted to be located in trans-Golgi network. Predicted to be part of retromer complex. Human ortholog(s) of this gene implicated in developmental and epileptic encephalopathy 49. Orthologous to human DENND5A (DENN domain containing 5A). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Brain (RPKM 622.0), Heart (RPKM 405.0) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Dennd5a in Genome Data Viewer
    Location:
    1q33
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (173362959..173428973, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (163928183..163994207, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (174524047..174588553, complement)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134483771 Neighboring gene signal peptide, CUB domain and EGF like domain containing 2 Neighboring gene transfer RNA serine (anticodon AGA) 46 Neighboring gene U2 spliceosomal RNA Neighboring gene transmembrane protein 41B Neighboring gene NHP2 ribonucleoprotein, pseudogene 5

    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. Epileptic Encephalopathy Caused by Mutations in the Guanine Nucleotide Exchange Factor DENND5A. Han C, et al. Am J Hum Genet, 2016 Dec 1. PMID 27866705, Free PMC Article
    2. Common sequence and structural features in the heat-shock factor and Ets families of DNA-binding domains. Landsman D, et al. Trends Biochem Sci, 1995 Jun. PMID 7631419
    3. Structural basis for recruitment of Rab6-interacting protein 1 to Golgi via a RUN domain. Recacha R, et al. Structure, 2009 Jan 14. PMID 19141279
    4. The retromer coat complex coordinates endosomal sorting and dynein-mediated transport, with carrier recognition by the trans-Golgi network. Wassmer T, et al. Dev Cell, 2009 Jul. PMID 19619496, Free PMC Article
    5. 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

    See all (8) citations in PubMed

    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 IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 small GTPase binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables small GTPase binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables small GTPase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in negative regulation of neuron projection development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in retrograde transport, endosome to Golgi IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in retrograde transport, endosome to Golgi ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in Golgi membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of retromer complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in trans-Golgi network IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in trans-Golgi network ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    DENN domain-containing protein 5A
    Names
    DENN/MADD domain containing 5A
    Rab6 interacting 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_001107546.2 → NP_001101016.2  DENN domain-containing protein 5A

      See identical proteins and their annotated locations for NP_001101016.2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000001
      UniProtKB/Swiss-Prot
      G3V7Q0
      Related
      ENSRNOP00000017485.4, ENSRNOT00000017485.7
      Conserved Domains (5) summary
      smart00801
      Location:513 → 588
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:12 → 138
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      cd01757
      Location:954 → 1062
      PLAT_RAB6IP1; PLAT/LH2 domain present in RAB6 interacting protein 1 (Rab6IP1)_like family. PLAT/LH2 domains consists of an eight stranded beta-barrel. In RabIP1 this domain may participate in lipid-mediated modulation of Rab6IP1's function via it's generally proposed ...
      pfam02141
      Location:202 → 390
      DENN; DENN (AEX-3) domain
      cl02689
      Location:795 → 942
      RUN; RUN 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
      173362959..173428973 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017589204.3 → XP_017444693.1  DENN domain-containing protein 5A isoform X1

      UniProtKB/TrEMBL
      A0A8I6AMA0
      Related
      ENSRNOP00000096686.1

    2. XM_039078190.2 → XP_038934118.1  DENN domain-containing protein 5A isoform X2

      Conserved Domains (3) summary
      smart00801
      Location:513 → 588
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:12 → 138
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      pfam02141
      Location:202 → 390
      DENN; DENN (AEX-3) domain
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    G3V7Q0.1 GenPept UniProtKB/Swiss-Prot:G3V7Q0

    Gene LinkOut

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