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

Gene ID: 308942, updated on 2-Nov-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
EnsemblRapid: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 Golgi apparatus. Predicted to be part of retromer complex. Predicted to be active in trans-Golgi network. 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, Nov 2024]
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 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, ENSRNOT00000017485.8
    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, ENSRNOT00000106309.2

  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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