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

Gene ID: 287938, updated on 27-Nov-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
EnsemblRapid: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, Nov 2024]
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
    ENSRNOP00000070207.1, ENSRNOT00000078394.3
    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, ENSRNOT00000002542.8
    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

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