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    Wdr59 WD repeat domain 59 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 690751, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Wdr59provided by RGD
    Official Full Name
    WD repeat domain 59provided by RGD
    Primary source
    RGD:1592213
    See related
    EnsemblRapid:ENSRNOG00000018967 AllianceGenome:RGD:1592213
    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
    Summary
    Predicted to enable signaling adaptor activity. Predicted to be involved in cellular response to amino acid starvation and positive regulation of TORC1 signaling. Predicted to be located in cytosol and lysosomal membrane. Predicted to be part of GATOR2 complex. Predicted to be active in vacuolar membrane. Orthologous to human WDR59 (WD repeat domain 59). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Adrenal (RPKM 63.4), Kidney (RPKM 48.0) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Wdr59 in Genome Data Viewer
    Location:
    19q12
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 19 NC_086037.1 (56321529..56393195, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 19 NC_051354.1 (39416432..39483773, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 19 NC_005118.4 (43651686..43714391, complement)

    Chromosome 19 - NC_086037.1Genomic Context describing neighboring genes Neighboring gene fatty acid 2-hydroxylase Neighboring gene small nucleolar RNA SNORA17 Neighboring gene 60S ribosomal protein L29-like Neighboring gene uncharacterized LOC120098630 Neighboring gene uncharacterized LOC134483371 Neighboring gene zinc and ring finger 1 Neighboring gene lactate dehydrogenase D

    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. Regulation of mTORC1 by amino acids. Bar-Peled L, et al. Trends Cell Biol, 2014 Jul. PMID 24698685, Free PMC Article
    2. A Tumor suppressor complex with GAP activity for the Rag GTPases that signal amino acid sufficiency to mTORC1. Bar-Peled L, et al. Science, 2013 May 31. PMID 23723238, Free PMC Article
    3. KICSTOR recruits GATOR1 to the lysosome and is necessary for nutrients to regulate mTORC1. Wolfson RL, et al. Nature, 2017 Mar 16. PMID 28199306, Free PMC Article
    4. 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 signaling adaptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in cellular response to amino acid starvation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cellular response to amino acid starvation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cellular response to nutrient levels ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of TORC1 signaling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of TORC1 signaling ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of GATOR2 complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of Seh1-associated complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in lysosomal membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in vacuolar membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    GATOR2 complex protein WDR59; similar to WD repeat domain 59
    Names
    GATOR complex protein WDR59
    WD repeat-containing protein 59

    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_001432043.1 → NP_001418972.1  similar to WD repeat domain 59 isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000019
      UniProtKB/TrEMBL
      D3ZGZ9

    2. NM_001432044.1 → NP_001418973.1  similar to WD repeat domain 59 isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000019
      UniProtKB/TrEMBL
      D3ZGZ9

    3. NM_001432045.1 → NP_001418974.1  similar to WD repeat domain 59 isoform 3

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000019
      UniProtKB/TrEMBL
      D3ZGZ9

    4. NM_001432046.1 → NP_001418975.1  similar to WD repeat domain 59 isoform 4

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000019
      UniProtKB/TrEMBL
      D3ZGZ9

    5. NM_001432047.1 → NP_001418976.1  similar to WD repeat domain 59 isoform 5

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000019
      UniProtKB/TrEMBL
      A0A8I6G9F8, D3ZGZ9

    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_086037.1 Reference GRCr8

      Range
      56321529..56393195 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063278659.1 → XP_063134729.1  GATOR2 complex protein WDR59 isoform X6

      UniProtKB/TrEMBL
      D3ZGZ9

    2. XM_039098254.2 → XP_038954182.1  GATOR2 complex protein WDR59 isoform X5

      UniProtKB/TrEMBL
      D3ZGZ9
      Conserved Domains (4) summary
      smart00591
      Location:394 → 494
      RWD; domain in RING finger and WD repeat containing proteins and DEXDc-like helicases subfamily related to the UBCc domain
      COG2319
      Location:34 → 314
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:62 → 103
      7WD40; WD40 repeat [structural motif]
      cd16692
      Location:941 → 987
      mRING-H2-C3H3C2_WDR59; Modified RING finger, H2 subclass (C3H3C2-type), found in WD repeat-containing protein 59 (WDR59) and similar proteins

    3. XM_039098253.2 → XP_038954181.1  GATOR2 complex protein WDR59 isoform X4

      UniProtKB/TrEMBL
      D3ZGZ9
      Conserved Domains (4) summary
      smart00591
      Location:394 → 494
      RWD; domain in RING finger and WD repeat containing proteins and DEXDc-like helicases subfamily related to the UBCc domain
      COG2319
      Location:34 → 314
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:62 → 103
      7WD40; WD40 repeat [structural motif]
      cd16692
      Location:944 → 990
      mRING-H2-C3H3C2_WDR59; Modified RING finger, H2 subclass (C3H3C2-type), found in WD repeat-containing protein 59 (WDR59) and similar proteins

    4. XM_063278660.1 → XP_063134730.1  GATOR2 complex protein WDR59 isoform X8

    5. XM_039098250.2 → XP_038954178.1  GATOR2 complex protein WDR59 isoform X1

      Related
      ENSRNOP00000082422.2, ENSRNOT00000112568.2
      Conserved Domains (4) summary
      smart00591
      Location:401 → 501
      RWD; domain in RING finger and WD repeat containing proteins and DEXDc-like helicases subfamily related to the UBCc domain
      COG2319
      Location:34 → 314
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:62 → 103
      7WD40; WD40 repeat [structural motif]
      cd16692
      Location:951 → 997
      mRING-H2-C3H3C2_WDR59; Modified RING finger, H2 subclass (C3H3C2-type), found in WD repeat-containing protein 59 (WDR59) and similar proteins

    6. XM_039098262.2 → XP_038954190.1  GATOR2 complex protein WDR59 isoform X12

      UniProtKB/TrEMBL
      D3ZGZ9
      Conserved Domains (4) summary
      smart00591
      Location:394 → 494
      RWD; domain in RING finger and WD repeat containing proteins and DEXDc-like helicases subfamily related to the UBCc domain
      COG2319
      Location:34 → 314
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:62 → 103
      7WD40; WD40 repeat [structural motif]
      cd16692
      Location:921 → 967
      mRING-H2-C3H3C2_WDR59; Modified RING finger, H2 subclass (C3H3C2-type), found in WD repeat-containing protein 59 (WDR59) and similar proteins

    7. XM_039098257.2 → XP_038954185.1  GATOR2 complex protein WDR59 isoform X11

      UniProtKB/TrEMBL
      D3ZGZ9
      Conserved Domains (4) summary
      smart00591
      Location:394 → 494
      RWD; domain in RING finger and WD repeat containing proteins and DEXDc-like helicases subfamily related to the UBCc domain
      COG2319
      Location:34 → 314
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:62 → 103
      7WD40; WD40 repeat [structural motif]
      cd16692
      Location:922 → 968
      mRING-H2-C3H3C2_WDR59; Modified RING finger, H2 subclass (C3H3C2-type), found in WD repeat-containing protein 59 (WDR59) and similar proteins

    8. XM_039098256.2 → XP_038954184.1  GATOR2 complex protein WDR59 isoform X10

      UniProtKB/TrEMBL
      D3ZGZ9
      Conserved Domains (4) summary
      smart00591
      Location:394 → 494
      RWD; domain in RING finger and WD repeat containing proteins and DEXDc-like helicases subfamily related to the UBCc domain
      COG2319
      Location:34 → 314
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:62 → 103
      7WD40; WD40 repeat [structural motif]
      cd16692
      Location:925 → 971
      mRING-H2-C3H3C2_WDR59; Modified RING finger, H2 subclass (C3H3C2-type), found in WD repeat-containing protein 59 (WDR59) and similar proteins

    9. XM_063278661.1 → XP_063134731.1  GATOR2 complex protein WDR59 isoform X9

    10. XM_039098255.2 → XP_038954183.1  GATOR2 complex protein WDR59 isoform X7

      Conserved Domains (4) summary
      smart00591
      Location:401 → 501
      RWD; domain in RING finger and WD repeat containing proteins and DEXDc-like helicases subfamily related to the UBCc domain
      COG2319
      Location:34 → 314
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:62 → 103
      7WD40; WD40 repeat [structural motif]
      cd16692
      Location:932 → 978
      mRING-H2-C3H3C2_WDR59; Modified RING finger, H2 subclass (C3H3C2-type), found in WD repeat-containing protein 59 (WDR59) and similar proteins

    11. XM_039098252.2 → XP_038954180.1  GATOR2 complex protein WDR59 isoform X3

      UniProtKB/TrEMBL
      D3ZGZ9
      Conserved Domains (4) summary
      smart00591
      Location:401 → 501
      RWD; domain in RING finger and WD repeat containing proteins and DEXDc-like helicases subfamily related to the UBCc domain
      COG2319
      Location:34 → 314
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:62 → 103
      7WD40; WD40 repeat [structural motif]
      cd16692
      Location:947 → 993
      mRING-H2-C3H3C2_WDR59; Modified RING finger, H2 subclass (C3H3C2-type), found in WD repeat-containing protein 59 (WDR59) and similar proteins

    12. XM_039098251.2 → XP_038954179.1  GATOR2 complex protein WDR59 isoform X2

      Conserved Domains (4) summary
      smart00591
      Location:401 → 501
      RWD; domain in RING finger and WD repeat containing proteins and DEXDc-like helicases subfamily related to the UBCc domain
      COG2319
      Location:34 → 314
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:62 → 103
      7WD40; WD40 repeat [structural motif]
      cd16692
      Location:948 → 994
      mRING-H2-C3H3C2_WDR59; Modified RING finger, H2 subclass (C3H3C2-type), found in WD repeat-containing protein 59 (WDR59) and similar proteins

    13. XM_039098258.2 → XP_038954186.1  GATOR2 complex protein WDR59 isoform X13

      UniProtKB/TrEMBL
      D3ZGZ9
      Related
      ENSRNOP00000039886.6, ENSRNOT00000047179.8
      Conserved Domains (3) summary
      smart00591
      Location:401 → 501
      RWD; domain in RING finger and WD repeat containing proteins and DEXDc-like helicases subfamily related to the UBCc domain
      sd00039
      Location:62 → 103
      7WD40; WD40 repeat [structural motif]
      cl29593
      Location:100 → 343
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    14. XM_063278663.1 → XP_063134733.1  GATOR2 complex protein WDR59 isoform X16

    15. XM_039098259.2 → XP_038954187.1  GATOR2 complex protein WDR59 isoform X15

      Conserved Domains (3) summary
      smart00591
      Location:401 → 501
      RWD; domain in RING finger and WD repeat containing proteins and DEXDc-like helicases subfamily related to the UBCc domain
      sd00039
      Location:62 → 103
      7WD40; WD40 repeat [structural motif]
      cl29593
      Location:100 → 343
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    16. XM_063278662.1 → XP_063134732.1  GATOR2 complex protein WDR59 isoform X14

    17. XM_039098260.2 → XP_038954188.1  GATOR2 complex protein WDR59 isoform X17

      Conserved Domains (3) summary
      smart00591
      Location:401 → 501
      RWD; domain in RING finger and WD repeat containing proteins and DEXDc-like helicases subfamily related to the UBCc domain
      sd00039
      Location:62 → 103
      7WD40; WD40 repeat [structural motif]
      cl29593
      Location:100 → 343
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    Nucleotide Protein Strain
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