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    Ydjc YdjC chitooligosaccharide deacetylase homolog [ Rattus norvegicus (Norway rat) ]

    Gene ID: 287938, updated on 13-Apr-2024

    Summary

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    Official Symbol
    Ydjcprovided by RGD
    Official Full Name
    YdjC chitooligosaccharide deacetylase homologprovided by RGD
    Primary source
    RGD:1359227
    See related
    Ensembl:ENSRNOG00000001861 AllianceGenome:RGD:1359227
    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 deacetylase activity. Predicted to be involved in carbohydrate metabolic process. Orthologous to human YDJC (YdjC chitooligosaccharide deacetylase homolog). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Testes (RPKM 48.0), Adrenal (RPKM 40.4) and 8 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Ydjc in Genome Data Viewer
    Location:
    11q23
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 11 NC_086029.1 (97338529..97348909, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 11 NC_051346.1 (83832177..83844691, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 11 NC_005110.4 (88089142..88094254, complement)

    Chromosome 11 - NC_086029.1Genomic Context describing neighboring genes Neighboring gene HIC ZBTB transcriptional repressor 2 Neighboring gene RIMS binding protein 3 Neighboring gene small nucleolar RNA SNORA51 Neighboring gene ubiquitin-conjugating enzyme E2L 3 Neighboring gene coiled-coil domain containing 116 Neighboring gene RIKEN cDNA 2610318N02 gene like Neighboring gene stromal cell-derived factor 2-like 1 Neighboring gene microRNA 301b

    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. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    2. 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 deacetylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in carbohydrate metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    carbohydrate deacetylase
    Names
    UPF0249 protein ydjC homolog
    YdjC homolog
    NP_001013885.2
    XP_038943996.1
    XP_038943998.1
    XP_038943999.1
    XP_038944000.1
    XP_063126393.1

    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_001013863.2 → NP_001013885.2  carbohydrate deacetylase

      See identical proteins and their annotated locations for NP_001013885.2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000011
      UniProtKB/TrEMBL
      A6JSM8
      Conserved Domains (1) summary
      cd10806
      Location:7 → 286
      YdjC_like_2; uncharacterized YdjC-like family proteins from eukaryotes

    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_086029.1 Reference GRCr8

      Range
      97338529..97348909 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063270323.1 → XP_063126393.1  carbohydrate deacetylase isoform X3

    2. XM_039088070.2 → XP_038943998.1  carbohydrate deacetylase isoform X2

      Conserved Domains (1) summary
      cd10806
      Location:7 → 262
      YdjC_like_2; uncharacterized YdjC-like family proteins from eukaryotes

    3. XM_039088072.2 → XP_038944000.1  carbohydrate deacetylase isoform X5

      UniProtKB/TrEMBL
      A0A8I5ZWK3, Q5RJN8
      Related
      ENSRNOP00000083127.1
      Conserved Domains (1) summary
      cl15692
      Location:20 → 198
      CE4_SF; Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily

    4. XM_039088071.2 → XP_038943999.1  carbohydrate deacetylase isoform X4

      UniProtKB/TrEMBL
      Q5RJN8
      Conserved Domains (1) summary
      cl15692
      Location:20 → 199
      CE4_SF; Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily

    5. XM_039088068.2 → XP_038943996.1  carbohydrate deacetylase isoform X1

      UniProtKB/TrEMBL
      G3V683
      Related
      ENSRNOP00000002542.4
      Conserved Domains (1) summary
      cd10806
      Location:7 → 287
      YdjC_like_2; uncharacterized YdjC-like family proteins from eukaryotes

    RNA

    1. XR_010055937.1 RNA Sequence

    2. XR_005490989.2 RNA Sequence

    3. XR_005490990.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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