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    denn-4 DENN domain type RAB GEF [ Caenorhabditis elegans ]

    Gene ID: 186100, updated on 9-Dec-2024

    Summary

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    Official Symbol
    denn-4
    Official Full Name
    DENN domain type RAB GEF
    Primary source
    WormBase:WBGene00018681
    Locus tag
    CELE_F52C12.4
    See related
    AllianceGenome:WB:WBGene00018681
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Caenorhabditis elegans (strain: Bristol N2)
    Lineage
    Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
    Summary
    Predicted to be involved in regulation of Rab protein signal transduction. Predicted to be located in cytoplasm. Predicted to be active in cytoplasmic vesicle. Is expressed in nervous system. Orthologous to several human genes including DENND4B (DENN domain containing 4B) and DENND4C (DENN domain containing 4C). [provided by Alliance of Genome Resources, Dec 2024]
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    Genomic context

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    See denn-4 in Genome Data Viewer
    Location:
    chromosome: IV
    Exon count:
    22
    Sequence:
    Chromosome: IV; NC_003282.8 (1924001..1948080)

    Chromosome IV - NC_003282.8Genomic Context describing neighboring genes Neighboring gene Putative transcription factor egl-18 Neighboring gene Transcription factor elt-6 Neighboring gene tRNA-splicing endonuclease subunit Sen54 N-terminal domain-containing protein Neighboring gene 18S rRNA aminocarboxypropyltransferase

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003282.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Age-associated decline in RAB-10 efficacy impairs intestinal barrier integrity. Zhang J, et al. Nat Aging, 2023 Sep. PMID 37640905
    2. LET-413/Erbin acts as a RAB-5 effector to promote RAB-10 activation during endocytic recycling. Liu H, et al. J Cell Biol, 2018 Jan 2. PMID 29079669, Free PMC Article
    3. Novel LOTUS-domain proteins are organizational hubs that recruit C. elegans Vasa to germ granules. Cipriani PG, et al. Elife, 2021 Jul 5. PMID 34223818, Free PMC Article
    4. OrthoList: a compendium of C. elegans genes with human orthologs. Shaye DD, et al. PLoS One, 2011. PMID 21647448, Free PMC Article
    5. OrthoList 2: A New Comparative Genomic Analysis of Human and Caenorhabditis elegans Genes. Kim W, et al. Genetics, 2018 Oct. PMID 30120140, Free PMC Article

    See all (6) 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 WormBase

    Process Evidence Code Pubs
    involved_in regulation of Rab protein signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 type RAB GEF
    NP_001294384.1
    • Confirmed by transcript evidence
    NP_001294385.1
    • Confirmed by transcript evidence
    NP_001294386.1
    • Confirmed by transcript evidence
    NP_001294387.1
    • Confirmed by transcript evidence
    NP_001294388.1
    • Confirmed by transcript evidence
    NP_001294389.1
    • Confirmed by transcript evidence
    NP_001294390.1
    • Confirmed by transcript evidence
    NP_001294391.1
    • Confirmed by transcript evidence

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference assembly

    Genomic

    1. NC_003282.8 Reference assembly

      Range
      1924001..1948080
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001307456.3 → NP_001294385.1  DENN domain type RAB GEF [Caenorhabditis elegans]

      See identical proteins and their annotated locations for NP_001294385.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      U4PEG5
      Conserved Domains (6) summary
      smart00801
      Location:582 → 656
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:199 → 286
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      sd00004
      Location:839 → 868
      PPR; PPR repeat [structural motif]
      pfam02141
      Location:329 → 514
      DENN; DENN (AEX-3) domain
      pfam10240
      Location:51 → 205
      DUF2464; Protein of unknown function (DUF2464)
      pfam13041
      Location:838 → 879
      PPR_2; PPR repeat family

    2. NM_001307459.4 → NP_001294388.1  DENN domain type RAB GEF [Caenorhabditis elegans]

      See identical proteins and their annotated locations for NP_001294388.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      U4PM26
      Conserved Domains (6) summary
      smart00801
      Location:580 → 654
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:199 → 286
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      sd00004
      Location:835 → 864
      PPR; PPR repeat [structural motif]
      pfam02141
      Location:327 → 512
      DENN; DENN (AEX-3) domain
      pfam10240
      Location:51 → 205
      DUF2464; Protein of unknown function (DUF2464)
      pfam13041
      Location:834 → 875
      PPR_2; PPR repeat family

    3. NM_001307461.3 → NP_001294390.1  DENN domain type RAB GEF [Caenorhabditis elegans]

      See identical proteins and their annotated locations for NP_001294390.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      U4PEG9
      Conserved Domains (6) summary
      smart00801
      Location:580 → 654
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:199 → 286
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      sd00004
      Location:848 → 877
      PPR; PPR repeat [structural motif]
      pfam02141
      Location:327 → 512
      DENN; DENN (AEX-3) domain
      pfam10240
      Location:51 → 205
      DUF2464; Protein of unknown function (DUF2464)
      pfam13041
      Location:847 → 888
      PPR_2; PPR repeat family

    4. NM_001307455.3 → NP_001294384.1  DENN domain type RAB GEF [Caenorhabditis elegans]

      See identical proteins and their annotated locations for NP_001294384.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      U4PRB3
      Conserved Domains (6) summary
      smart00801
      Location:580 → 654
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:199 → 286
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      sd00004
      Location:837 → 866
      PPR; PPR repeat [structural motif]
      pfam02141
      Location:327 → 512
      DENN; DENN (AEX-3) domain
      pfam10240
      Location:51 → 205
      DUF2464; Protein of unknown function (DUF2464)
      pfam13041
      Location:836 → 877
      PPR_2; PPR repeat family

    5. NM_001307458.3 → NP_001294387.1  DENN domain type RAB GEF [Caenorhabditis elegans]

      See identical proteins and their annotated locations for NP_001294387.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      U4PBM1
      Conserved Domains (6) summary
      smart00801
      Location:582 → 656
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:199 → 286
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      sd00004
      Location:852 → 881
      PPR; PPR repeat [structural motif]
      pfam02141
      Location:329 → 514
      DENN; DENN (AEX-3) domain
      pfam10240
      Location:51 → 205
      DUF2464; Protein of unknown function (DUF2464)
      pfam13041
      Location:851 → 892
      PPR_2; PPR repeat family

    6. NM_001307462.3 → NP_001294391.1  DENN domain type RAB GEF [Caenorhabditis elegans]

      See identical proteins and their annotated locations for NP_001294391.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      U4PB94
      Conserved Domains (6) summary
      smart00801
      Location:582 → 656
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:199 → 286
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      sd00004
      Location:850 → 879
      PPR; PPR repeat [structural motif]
      pfam02141
      Location:329 → 514
      DENN; DENN (AEX-3) domain
      pfam10240
      Location:51 → 205
      DUF2464; Protein of unknown function (DUF2464)
      pfam13041
      Location:849 → 890
      PPR_2; PPR repeat family

    7. NM_001307460.4 → NP_001294389.1  DENN domain type RAB GEF [Caenorhabditis elegans]

      See identical proteins and their annotated locations for NP_001294389.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      U4PRB8
      Conserved Domains (6) summary
      smart00801
      Location:582 → 656
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:199 → 286
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      sd00004
      Location:837 → 866
      PPR; PPR repeat [structural motif]
      pfam02141
      Location:329 → 514
      DENN; DENN (AEX-3) domain
      pfam10240
      Location:51 → 205
      DUF2464; Protein of unknown function (DUF2464)
      pfam13041
      Location:836 → 877
      PPR_2; PPR repeat family

    8. NM_001307457.3 → NP_001294386.1  DENN domain type RAB GEF [Caenorhabditis elegans]

      See identical proteins and their annotated locations for NP_001294386.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      U4PB89
      Conserved Domains (6) summary
      smart00801
      Location:580 → 654
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:199 → 286
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      sd00004
      Location:850 → 879
      PPR; PPR repeat [structural motif]
      pfam02141
      Location:327 → 512
      DENN; DENN (AEX-3) domain
      pfam10240
      Location:51 → 205
      DUF2464; Protein of unknown function (DUF2464)
      pfam13041
      Location:849 → 890
      PPR_2; PPR repeat family
    Nucleotide Protein
    Heading Accession and Version

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