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    YDJC YdjC chitooligosaccharide deacetylase homolog [ Homo sapiens (human) ]

    Gene ID: 150223, updated on 14-Nov-2024

    Summary

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    Official Symbol
    YDJCprovided by HGNC
    Official Full Name
    YdjC chitooligosaccharide deacetylase homologprovided by HGNC
    Primary source
    HGNC:HGNC:27158
    See related
    Ensembl:ENSG00000161179 MIM:619770; AllianceGenome:HGNC:27158
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Predicted to enable deacetylase activity and magnesium ion binding activity. Predicted to be involved in carbohydrate metabolic process. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in kidney (RPKM 4.9), colon (RPKM 4.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See YDJC in Genome Data Viewer
    Location:
    22q11.21
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (21628089..21630022, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (22041573..22043506, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (21982378..21984311, complement)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene RN7SK pseudogene 221 Neighboring gene RIMS binding protein 3C Neighboring gene ReSE screen-validated silencer GRCh37_chr22:21908512-21908665 Neighboring gene Sharpr-MPRA regulatory region 10827 Neighboring gene ubiquitin conjugating enzyme E2 L3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:21914232-21914792 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:21920997-21921184 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13507 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13508 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18698 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13509 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:21945023-21945836 Neighboring gene VISTA enhancer hs2026 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:21977501-21978034 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:21979673-21979941 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:21982145-21982752 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13510 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13511 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:21986781-21987280 Neighboring gene coiled-coil domain containing 116 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13512 Neighboring gene stromal cell derived factor 2 like 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Crystal structure of the YdjC-family protein TTHB029 from Thermus thermophilus HB8: structural relationship with peptidoglycan N-acetylglucosamine deacetylase. Imagawa T, et al. Biochem Biophys Res Commun, 2008 Mar 14. PMID 18177738
    2. YDJC Induces Epithelial-Mesenchymal Transition via Escaping from Interaction with CDC16 through Ubiquitination of PP2A. Kim EJ, et al. J Oncol, 2019. PMID 31485224, Free PMC Article
    3. Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci. Zhernakova A, et al. PLoS Genet, 2011 Feb. PMID 21383967, Free PMC Article
    4. Multiple common variants for celiac disease influencing immune gene expression. Dubois PC, et al. Nat Genet, 2010 Apr. PMID 20190752, Free PMC Article
    5. Seventy-five genetic loci influencing the human red blood cell. van der Harst P, et al. Nature, 2012 Dec 20. PMID 23222517, Free PMC Article

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genetics of rheumatoid arthritis contributes to biology and drug discovery.
    EBI GWAS Catalog
    Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
    EBI GWAS Catalog
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci.
    EBI GWAS Catalog
    Multiple common variants for celiac disease influencing immune gene expression.
    EBI GWAS Catalog
    Seventy-five genetic loci influencing the human red blood cell.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC133160

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables deacetylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables magnesium ion binding ISS
    Inferred from Sequence or Structural Similarity
    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_001017964.1
    NP_001358279.1

    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_001017964.2 → NP_001017964.1  carbohydrate deacetylase isoform 1

      See identical proteins and their annotated locations for NP_001017964.1

      Status: VALIDATED

      Source sequence(s)
      BC057814, BI597711, BQ050386
      Consensus CDS
      CCDS33613.1
      UniProtKB/Swiss-Prot
      A8MPS7, Q2YDT4, Q4V9R7
      Related
      ENSP00000292778.6, ENST00000292778.11
      Conserved Domains (1) summary
      cd10806
      Location:7 → 286
      YdjC_like_2; uncharacterized YdjC-like family proteins from eukaryotes

    2. NM_001371350.1 → NP_001358279.1  carbohydrate deacetylase isoform 2

      Status: VALIDATED

      Source sequence(s)
      BC096754, BC110075, BC110799
      Consensus CDS
      CCDS93126.1
      Related
      ENSP00000381847.3, ENST00000398873.4
      Conserved Domains (1) summary
      cl15692
      Location:7 → 142
      CE4_SF; Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily

    RNA

    1. NR_163922.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      BC110799, BC133043
      Related
      ENST00000415762.6

    2. NR_163923.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      BC057814, BC096754, BC110799, BM048037

    3. NR_163924.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      BC057814, BC096754, BC110799, BG105883
      Related
      ENST00000473985.1

    4. NR_163925.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      BC096754, BC110075, BC110799, BI199854

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      21628089..21630022 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      22041573..22043506 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001017965.1: Suppressed sequence

      Description
      NM_001017965.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A8MPS7.1 GenPept UniProtKB/Swiss-Prot:A8MPS7

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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