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YDJC Gene

protein-coding   GIFtS: 47
GCID: GC22M021982

YdjC Homolog (Bacterial)

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
YdjC Homolog (Bacterial)1 2
UPF0249 Protein YdjC Homolog2

External Ids:    HGNC: 271581   Entrez Gene: 1502232   Ensembl: ENSG000001611797   UniProtKB: A8MPS73   
ORGUL members:         

Export aliases for YDJC gene to outside databases

Previous GC identifers: GC22M020312 GC22M004940


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for YDJC Gene:
YDJC (YdjC homolog (bacterial)) is a protein-coding gene. GO annotations related to this gene include hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000022.10  NT_011520.13  NC_018933.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the YDJC gene promoter:
         Pax-5   Brachyury   E47   YY1   GATA-1   CREB   MEF-2A   SREBP-1a   deltaCREB   aMEF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidYDJC promoter sequence
   Search Chromatin IP Primers for YDJC

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat YDJC


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 22q11.21   Ensembl cytogenetic band:  22q11.21   HGNC cytogenetic band: 22q11.21

YDJC Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
YDJC gene location

GeneLoc information about chromosome 22         GeneLoc Exon Structure

GeneLoc location for GC22M021982:  view genomic region     (about GC identifiers)

Start:
21,982,378 bp from pter      End:
21,984,353 bp from pter
Size:
1,976 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: YDJC_HUMAN, A8MPS7 (See protein sequence)
Recommended Name: UPF0249 protein ydjC homolog  
Size: 323 amino acids; 34466 Da
Secondary accessions: Q2YDT4 Q4V9R7
Alternative splicing: 3 isoforms:  A8MPS7-1   A8MPS7-2   A8MPS7-3   (May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay)

Explore the universe of human proteins at neXtProt for YDJC: NX_A8MPS7

Explore proteomics data for YDJC at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys92
  • Modification sites at PhosphoSitePlus

  • See YDJC Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001017964.1  
    ENSEMBL proteins: 
     ENSP00000292778   ENSP00000402481   ENSP00000381847  

    YDJC Human Recombinant Protein Products:

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    antibodies-online proteins for YDJC (3 products) 

     
    antibodies-online peptides for YDJC

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    antibodies-online kits for YDJC (4 products) 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    3 InterPro protein domains:
     IPR006879 Uncharacterised_UPF0249/HpnK
     IPR002509 Polysac_deacetylase
     IPR011330 Glyco_hydro/deAcase_b/a-brl

    Graphical View of Domain Structure for InterPro Entry A8MPS7

    ProtoNet protein and cluster: A8MPS7

    UniProtKB/Swiss-Prot: YDJC_HUMAN, A8MPS7
    Similarity: Belongs to the UPF0249 family


    Find genes that share domains with YDJC           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016810hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds IEA--
         
    Find genes that share ontologies with YDJC           About GenesLikeMe


    Phenotypes:
         1 MGI phenotypic allele for Ydjc (no phenotypes)

    Find genes that share phenotypes with YDJC           About GenesLikeMe

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for YDJC

    miRNA
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    miRTarBase miRNAs that target YDJC:
    hsa-mir-28-3p (MIRT038947), hsa-mir-877-3p (MIRT036985), hsa-mir-193b-3p (MIRT041237), hsa-mir-615-3p (MIRT040030)

    Block miRNA regulation of human, mouse, rat YDJC using miScript Target Protectors
    2 qRT-PCR Assays for microRNAs that regulate YDJC:
    hsa-miR-1184 hsa-miR-593*
    SwitchGear 3'UTR luciferase reporter plasmidYDJC 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat YDJC

    Gene Editing
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol1
    extracellular1
    mitochondrion1
    nucleus1
    peroxisome1
    plasma membrane1

    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for YDJC
    Interactions:

        Search GeneGlobe Interaction Network for YDJC

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005975carbohydrate metabolic process IEA--

    Find genes that share ontologies with YDJC           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for YDJC



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for YDJC gene (2 alternative transcripts): 
    NM_001017965.1  NM_001017964.1  

    Unigene Cluster for YDJC:

    YdjC homolog (bacterial)
    Hs.355952  [show with all ESTs]
    Unigene Representative Sequence: BM906422
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000464015 ENST00000468686 ENST00000292778(uc002zvb.2 uc002zvd.2)
    ENST00000415762(uc002zvc.2) ENST00000473985 ENST00000482998 ENST00000398873

    miRNA
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    Block miRNA regulation of human, mouse, rat YDJC using miScript Target Protectors
    2 qRT-PCR Assays for microRNAs that regulate YDJC:
    hsa-miR-1184 hsa-miR-593*
    SwitchGear 3'UTR luciferase reporter plasmidYDJC 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for YDJC
    Predesigned siRNA for gene silencing in human, mouse, rat YDJC
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    GenScript: all cDNA clones in your preferred vector: YDJC (NM_001017964)
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    Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat YDJC
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for YDJC
    Search Pre-validated RT2 qPCR Primer Assays in human, mouse, rat YDJC
      QuantiTect SYBR Green Assays in human, mouse, rat YDJC
      QuantiFast Probe-based Assays in human, mouse, rat YDJC

    Additional mRNA sequence: 

    BC053663.1 BC057814.1 BC110075.1 BC110799.1 BC133043.1 BC133047.1 

    14 DOTS entries:

    DT.412232  DT.92462297  DT.101982274  DT.100821877  DT.97771308  DT.95133953  DT.100821875  DT.100821876 
    DT.75140188  DT.100692072  DT.100803936  DT.100833796  DT.95133954  DT.95133976 

    Selected AceView cDNA sequences (see all 199):

    AI656234 BM920756 BI907254 BM273054 BM273290 CR613432 CR618402 BX326782 
    BM273095 BM851387 CR600451 AI263048 BE791432 BU857339 BQ050386 BM761651 
    BU631753 CR597037 CR613078 CR590781 CR620409 AI083906 AI221458 AI471630 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for YDJC (see all 11)    About this scheme

    ExUns: 1a · 1b · 1c · 1d · 1e ^ 2a · 2b ^ 3 ^ 4a · 4b · 4c · 4d ^ 5a · 5b · 5c · 5d · 5e · 5f
    SP1:                                                                                                            
    SP2:                                      -                                                                     
    SP3:                                      -           -     -     -     -                                       
    SP4:                                -     -                                                                     
    SP5:                                                  -     -     -     -                                       


    ECgene alternative splicing isoforms for YDJC

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    YDJC expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TTGCAATGCA
    YDJC Expression
    About this image


    YDJC expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 2) fully expand
     
     Trophoblast (Extraembryonic Tissues)
             Mural Trophectoderm Cells Mural Trophectoderm
     
     Epiblast (Early Embryonic Tissues)
             Epiblast Cells Epiblast
    YDJC Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    YDJC Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.355952
        Custom PCR Arrays for YDJC
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for YDJC

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of chordates.

    Orthologs for YDJC gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ydjc1 , 5 YdjC homolog (bacterial)1, 5 84.03(n)1
    89.64(a)1
      16 (10.63 cM)5
    691011  NM_026940.41  NP_081216.11 
     171446215 
    chicken
    (Gallus gallus)
    Aves YDJC1 YdjC homolog (bacterial) 58.36(n)
    55.63(a)
      771088  XM_004945483.1  XP_004945540.1 
    lizard
    (Anolis carolinensis)
    Reptilia YDJC6
    YdjC homolog (bacterial)
    50(a)
    1 ↔ 1
    GL343282.1(1145954-1155672)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.334942 Xenopus laevis transcribed sequence with weak similarity more 72.25(n)    BJ627709.1 
    zebrafish
    (Danio rerio)
    Actinopterygii ydjc1 YdjC homolog (bacterial) 55.82(n)
    50.34(a)
      569036  NM_001082862.1  NP_001076331.1 


    ENSEMBL Gene Tree for YDJC (if available)
    TreeFam Gene Tree for YDJC (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for YDJC (see all 82)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 22 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1395680371,2
    --21981976(+) GCTGGC/GATTAC 1 -- ds50010--------
    rs59987331,2
    --21982011(+) taattC/Ttgtat 1 -- ds50010--------
    rs1849848311,2
    --21982053(+) TCAGAC/TTGGTC 1 -- ds50010--------
    rs18110691,2
    C,A,H--21982054(+) CAGACG/TGGTCT 1 -- ds50010--------
    rs1397701311,2
    --21982061(+) GTCTCA/GCACTC 1 -- ds50010--------
    rs8788251,2
    C,F,A,H--21982249(-) GCTGCA/GATTTT 1 -- ds5001103Minor allele frequency- G:0.47NA EA NS PA EU CA WA CSA 6462
    rs8618571,2
    C,F,A,H--21982340(+) TTTCTG/CTGAGG 1 -- ds5001109Minor allele frequency- C:0.45EA NA NS PA EU CA WA CSA 6837
    rs10468431,2
    F--21982432(-) TCACCA/CCTGGG 1 -- ut31 ese31Minor allele frequency- C:0.02MN 184
    rs1886572621,2
    --21982444(+) GGTGTG/TTGCAT 1 -- ut310--------
    rs1810133491,2
    --21982482(+) TGCGGA/GCCCTA 1 -- ut310--------

    HapMap Linkage Disequilibrium report for YDJC (21982378 - 21984353 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for YDJC:    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv4882n71CNV Loss21882294
    nsv516806CNV Loss19592680
    nsv914458CNV Loss21882294
    dgv4881n71CNV Loss21882294
    nsv7350OTHER Inversion18451855

    Human Gene Mutation Database (HGMD): YDJC
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing YDJC
    DNA2.0 Custom Variant and Variant Library Synthesis for YDJC

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    Find genes that share disorders with YDJC           About GenesLikeMe

    Genetic Association Database (GAD): YDJC

    Export disorders for YDJC gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for YDJC gene, integrated from 10 sources (see all 12):
    (articles sorted by number of sources associating them with YDJC)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci. (PubMed id 21383967)1, 4 Zhernakova A....Plenge R.M. (PLoS Genet. 2011)
    2. Multiple common variants for celiac disease influencing immune gene expression. (PubMed id 20190752)1, 4 Dubois P.C....van Heel D.A. (Nat. Genet. 2010)
    3. Crystal structure of the YdjC-family protein TTHB029 from Thermus thermophilus HB8: structural relationship with peptidoglycan N-acetylglucosamine deacetylase. (PubMed id 18177738)1, 3 Imagawa T....Tsuge H. (Biochem. Biophys. Res. Commun. 2008)
    4. Seventy-five genetic loci influencing the human red blood cell. (PubMed id 23222517)1 van der Harst P....Chambers J.C. (Nature 2012)
    5. Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (amp 2012)
    6. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. (PubMed id 23128233)1 Jostins L....Cho J.H. (Nature 2012)
    7. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)
    8. Global identification of modular cullin-RING ligase substrates. (PubMed id 21963094)1 Emanuele M.J....Elledge S.J. (Cell 2011)
    9. Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. (PubMed id 21102463)1 Franke A....Parkes M. (Nat. Genet. 2010)
    10. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 150223 HGNC: 27158 AceView: LOC150223 Ensembl:ENSG00000161179 euGenes: HUgn150223
    ECgene: YDJC H-InvDB: YDJC

    (According to HUGE)
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for YDJC Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for YDJC gene:
    Search GeneIP for patents involving YDJC

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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