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

Gene ID: 150223, updated on 2-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
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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)

Genotypes

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 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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