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    Dennd4b DENN domain containing 4B [ Rattus norvegicus (Norway rat) ]

    Gene ID: 361987, updated on 13-Apr-2024

    Summary

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    Official Symbol
    Dennd4bprovided by RGD
    Official Full Name
    DENN domain containing 4Bprovided by RGD
    Primary source
    RGD:1560320
    See related
    Ensembl:ENSRNOG00000022373 AllianceGenome:RGD:1560320
    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
    RGD1560320
    Summary
    Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be involved in regulation of Rab protein signal transduction. Predicted to be located in Golgi apparatus and nucleoplasm. Predicted to be active in cytoplasmic vesicle. Orthologous to human DENND4B (DENN domain containing 4B). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Spleen (RPKM 131.4), Muscle (RPKM 86.7) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Dennd4b in Genome Data Viewer
    Location:
    2q34
    Exon count:
    31
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 2 NC_086020.1 (178018095..178034054)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (175720473..175736425)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (189626922..189642732)

    Chromosome 2 - NC_086020.1Genomic Context describing neighboring genes Neighboring gene solute carrier family 39 member 1 Neighboring gene CREB regulated transcription coactivator 2 Neighboring gene uncharacterized LOC102551157 Neighboring gene GATA zinc finger domain containing 2B Neighboring gene solute carrier family 27 member 3

    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. Signal transduction meets vesicle traffic: the software and hardware of GLUT4 translocation. Klip A, et al. Am J Physiol Cell Physiol, 2014 May 15. PMID 24598362
    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 biological_process ND
    No biological Data available
    more info
    		  
    involved_in regulation of Rab protein signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of Rab protein signal transduction ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in cytoplasmic vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    DENN domain-containing protein 4B
    Names
    DENN/MADD domain containing 4B

    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_001427227.1 → NP_001414156.1  DENN domain-containing protein 4B isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000002
      UniProtKB/TrEMBL
      A0A8I6AH06

    2. NM_001427228.1 → NP_001414157.1  DENN domain-containing protein 4B isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000002
      UniProtKB/TrEMBL
      F1LTT7

    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_086020.1 Reference GRCr8

      Range
      178018095..178034054
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039103984.2 → XP_038959912.1  DENN domain-containing protein 4B isoform X2

      Conserved Domains (5) summary
      smart00801
      Location:563 → 636
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:198 → 279
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      sd00004
      Location:813 → 842
      PPR; PPR repeat [structural motif]
      pfam02141
      Location:313 → 497
      DENN; DENN (AEX-3) domain
      pfam13041
      Location:811 → 851
      PPR_2; PPR repeat family

    2. XM_039103985.2 → XP_038959913.1  DENN domain-containing protein 4B isoform X3

      Conserved Domains (5) summary
      smart00801
      Location:524 → 597
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:159 → 240
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      sd00004
      Location:774 → 803
      PPR; PPR repeat [structural motif]
      pfam02141
      Location:274 → 458
      DENN; DENN (AEX-3) domain
      pfam13041
      Location:772 → 812
      PPR_2; PPR repeat family

    3. XM_008761248.4 → XP_008759470.1  DENN domain-containing protein 4B isoform X1

      Conserved Domains (5) summary
      smart00801
      Location:574 → 647
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:209 → 290
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      sd00004
      Location:824 → 853
      PPR; PPR repeat [structural motif]
      pfam02141
      Location:324 → 508
      DENN; DENN (AEX-3) domain
      pfam13041
      Location:822 → 862
      PPR_2; PPR repeat family

    4. XM_039103986.2 → XP_038959914.1  DENN domain-containing protein 4B isoform X3

      Conserved Domains (5) summary
      smart00801
      Location:524 → 597
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:159 → 240
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      sd00004
      Location:774 → 803
      PPR; PPR repeat [structural motif]
      pfam02141
      Location:274 → 458
      DENN; DENN (AEX-3) domain
      pfam13041
      Location:772 → 812
      PPR_2; PPR repeat family

    5. XM_039103988.2 → XP_038959916.1  DENN domain-containing protein 4B isoform X4

      Conserved Domains (4) summary
      smart00801
      Location:189 → 262
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      sd00004
      Location:439 → 468
      PPR; PPR repeat [structural motif]
      pfam02141
      Location:1 → 123
      DENN; DENN (AEX-3) domain
      pfam13041
      Location:437 → 477
      PPR_2; PPR repeat family

    6. XM_039103989.2 → XP_038959917.1  DENN domain-containing protein 4B isoform X4

      Conserved Domains (4) summary
      smart00801
      Location:189 → 262
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      sd00004
      Location:439 → 468
      PPR; PPR repeat [structural motif]
      pfam02141
      Location:1 → 123
      DENN; DENN (AEX-3) domain
      pfam13041
      Location:437 → 477
      PPR_2; PPR repeat family

    7. XM_039103987.2 → XP_038959915.1  DENN domain-containing protein 4B isoform X4

      Conserved Domains (4) summary
      smart00801
      Location:189 → 262
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      sd00004
      Location:439 → 468
      PPR; PPR repeat [structural motif]
      pfam02141
      Location:1 → 123
      DENN; DENN (AEX-3) domain
      pfam13041
      Location:437 → 477
      PPR_2; PPR repeat family
    Nucleotide Protein Strain
    Heading Accession and Version

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