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NUDCD1 Gene

protein-coding   GIFtS: 49
GCID: GC08M110323

NudC Domain Containing 1

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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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Aliases
NudC Domain Containing 11 2
CML662 3 5
Chronic Myelogenous Leukemia Tumor Antigen 662 3
Tumor Antigen CML662 3
OVA662
NudC Domain-Containing Protein 12

External Ids:    HGNC: 243061   Entrez Gene: 849552   Ensembl: ENSG000001205267   OMIM: 6061095   UniProtKB: Q96RS63   

Export aliases for NUDCD1 gene to outside databases

Previous GC identifer: GC08M105575


(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 NUDCD1 Gene:
NUDCD1 (NudC domain containing 1) is a protein-coding gene.


(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_000008.10  NT_008046.17  NC_018919.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the NUDCD1 gene promoter:
         HOXA9B   HOXA9   ISGF-3   Sp1   Nkx6-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidNUDCD1 promoter sequence
   Search Chromatin IP Primers for NUDCD1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat NUDCD1


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

Entrez Gene cytogenetic band: 8q23   Ensembl cytogenetic band:  8q23.1   HGNC cytogenetic band: 8q23

NUDCD1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NUDCD1 gene location

GeneLoc information about chromosome 8         GeneLoc Exon Structure

GeneLoc location for GC08M110323:  view genomic region     (about GC identifiers)

Start:
110,253,148 bp from pter      End:
110,346,614 bp from pter
Size:
93,467 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., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: NUDC1_HUMAN, Q96RS6 (See protein sequence)
Recommended Name: NudC domain-containing protein 1  
Size: 583 amino acids; 66756 Da
Miscellaneous: Isoform 1 is the dominant immunogenic isoform and is capable of eliciting a humoral response in
individuals with a variety of solid tumors. Expression of isoform 1 in a wide variety of malignancies as well as
the presence of an immunogenic epitope suggest that it may be a suitable target for antigen-specific
immunotherapy
Secondary accessions: B4DVX6 Q4G130 Q8NDQ5 Q8NG18 Q96SI4 Q9BVR5
Alternative splicing: 3 isoforms:  Q96RS6-1   Q96RS6-2   Q96RS6-3   (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 NUDCD1: NX_Q96RS6

Explore proteomics data for NUDCD1 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See NUDCD1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001121683.1  NP_116258.2  

    ENSEMBL proteins: 
     ENSP00000239690   ENSP00000410707   ENSP00000430095   ENSP00000430859  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    2 InterPro protein domains:
     IPR008978 HSP20-like_chaperone
     IPR007052 CS_dom

    Graphical View of Domain Structure for InterPro Entry Q96RS6

    ProtoNet protein and cluster: Q96RS6

    UniProtKB/Swiss-Prot: NUDC1_HUMAN, Q96RS6
    Similarity: Contains 1 CS domain


    Find genes that share domains with NUDCD1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, 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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    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for NUDCD1
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    hsa-miR-3163 hsa-miR-2110 hsa-miR-200a hsa-miR-216b hsa-miR-181a-2* hsa-miR-4282 hsa-miR-141 hsa-miR-144
    SwitchGear 3'UTR luciferase reporter plasmidNUDCD1 3' UTR sequence
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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 UniProtKB/Swiss-Prot
    NUDC1_HUMAN, Q96RS6: Isoform 1: Cytoplasm. Nucleus
    NUDC1_HUMAN, Q96RS6: Isoform 2: Cytoplasm
    NUDC1_HUMAN, Q96RS6: Isoform 3: Cytoplasm. Nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol3

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005737cytoplasm IDA--

    Find genes that share ontologies with NUDCD1           About GenesLikeMe


    (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 NUDCD1
    Interactions:

        Search GeneGlobe Interaction Network for NUDCD1

    STRING Interaction Network Preview (showing 5 interactants - click image to see more details)

    5 Interacting proteins for NUDCD1 (Q96RS63 ENSP000002396904) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    USP36Q9P2753, ENSP000003105904I2D: score=2 STRING: ENSP00000310590
    JMJD6ENSP000003940854STRING: ENSP00000394085
    HMGCS1ENSP000003227064STRING: ENSP00000322706
    HMGCS2ENSP000003584144STRING: ENSP00000358414
    UBCENSP000003448184STRING: ENSP00000344818
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0002376immune system process IEA--

    Find genes that share ontologies with NUDCD1           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 NUDCD1 (NUDC1)



    (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 NUDCD1 gene (2 alternative transcripts): 
    NM_001128211.1  NM_032869.3  

    Unigene Cluster for NUDCD1:

    NudC domain containing 1
    Hs.380291  [show with all ESTs]
    Unigene Representative Sequence: NM_032869
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000239690(uc003yna.3 uc003ynb.4 uc010mcl.3) ENST00000427660(uc010mcm.1)
    ENST00000519607 ENST00000521439
    miRNA
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    hsa-miR-3163 hsa-miR-2110 hsa-miR-200a hsa-miR-216b hsa-miR-181a-2* hsa-miR-4282 hsa-miR-141 hsa-miR-144
    SwitchGear 3'UTR luciferase reporter plasmidNUDCD1 3' UTR sequence
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    Additional mRNA sequence: 

    AF283301.1 AF283302.1 AF521133.1 AK027897.1 AK301278.1 AK307663.1 AK311583.1 AK315006.1 
    AL832317.1 BC000967.2 BC031258.1 BC043406.1 

    8 DOTS entries:

    DT.101972324  DT.451680  DT.95079998  DT.95171777  DT.100782694  DT.317452  DT.121470153  DT.100782695 

    Selected AceView cDNA sequences (see all 153):

    AW768739 BF589164 AI921332 BM828661 BM787819 BM551230 AI057256 AA766486 
    AI075763 AL538437 CA448077 AI587089 BM790249 CR603601 CR613260 CB121102 
    AW471074 AI184878 AA569843 AA352036 CA428565 AA166785 BM911883 BQ232743 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for NUDCD1    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12
    SP1:              -                                                               
    SP2:              -           -                                                   
    SP3:                          -                                                   


    ECgene alternative splicing isoforms for NUDCD1

    (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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    NUDCD1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TTTTATATGA
    NUDCD1 Expression
    About this image


    NUDCD1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     
     Skeletal Muscle (Muscoskeletal System)    fully expand to see all 2 entries
             Mononuclear Myocytes Hyoid Arch Muscles
    NUDCD1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    NUDCD1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.380291

    UniProtKB/Swiss-Prot: NUDC1_HUMAN, Q96RS6
    Tissue specificity: Isoform 1 is specifically expressed in leukemias and a variety of solid tumor cell lines and
    is also detected in testis and heart. Isoform 2 is predominantly expressed in testis and weakly expressed in
    tumor cells

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    (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 animals.

    Orthologs for NUDCD1 gene from Selected species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Nudcd11 , 5 NudC domain containing 11, 5 89.18(n)1
    90.33(a)1
      15 (16.91 cM)5
    674291  NM_001113554.11  NP_001107026.11 
     443752275 
    chicken
    (Gallus gallus)
    Aves NUDCD11 NudC domain containing 1 75.19(n)
    75.64(a)
      428379  XM_004940000.1  XP_004940057.1 
    lizard
    (Anolis carolinensis)
    Reptilia NUDCD16
    NudC domain containing 1
    72(a)
    1 ↔ 1
    4(10771874-10825943)
    African clawed frog
    (Xenopus laevis)
    Amphibia cml66-prov2 chronic myelogenous leukemia tumor antigen 66 78.56(n)    BC056062.1 
    zebrafish
    (Danio rerio)
    Actinopterygii wufc11c022 Transcribed sequence with weak similarity to protein more 73.29(n)    BI979267.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG103471 CG10347 40.66(n)
    27.84(a)
      32141  NM_132527.2  NP_572755.1 
    worm
    (Caenorhabditis elegans)
    Secernentea C44E4.51 C44E4.5 42.34(n)
    27.41(a)
      172067  NM_059005.5  NP_491406.2 


    ENSEMBL Gene Tree for NUDCD1 (if available)
    TreeFam Gene Tree for NUDCD1 (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 NUDCD1 (see all 1782)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 8 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs761796931,2
    C,F--110252736(+) TTCCTG/CTGTAA 2 -- int12Minor allele frequency- C:0.18NA 122
    rs792083521,2
    C,F--110252868(+) TCTTTT/CTTCTA 2 -- int12Minor allele frequency- C:0.18NA 122
    rs1380934951,2
    --110252925(+) CCAAGC/GTTCTA 2 -- int10--------
    rs794515001,2
    F--110253065(+) TATCCT/CTAATA 2 -- int11Minor allele frequency- C:0.25NA 8
    rs1827604951,2
    --110253146(+) CTTAAC/TATGCA 2 -- spd10--------
    rs767543641,2
    C,F--110253241(+) AGGTAC/TTATAT 2 -- ut312Minor allele frequency- T:0.34CSA WA 119
    rs1417982551,2
    --110253302(+) AACATC/TGTTTA 2 -- ut310--------
    rs1501342781,2
    C--110253396(+) ACATGC/TGACAA 2 -- ut310--------
    rs779614441,2
    C,F--110253498(+) CAATAT/CATACA 2 -- ut311Minor allele frequency- C:0.04WA 118
    rs605845791,2
    C--110253558(+) TTCCCT/CAAGAG 2 -- ut312Minor allele frequency- C:0.05WA 120

    HapMap Linkage Disequilibrium report for NUDCD1 (110253148 - 110346614 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 6 variations for NUDCD1:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv6346CNV Insertion18451855
    dgv7845n71CNV Loss21882294
    nsv515589CNV Loss19592680
    dgv7844n71CNV Loss21882294
    nsv891272CNV Loss21882294
    dgv7843n71CNV Loss21882294

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing NUDCD1
    DNA2.0 Custom Variant and Variant Library Synthesis for NUDCD1

    (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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    OMIM gene information: 606109    OMIM disorders: --


    Find genes that share disorders with NUDCD1           About GenesLikeMe

    Genetic Association Database (GAD): NUDCD1

    Export disorders for NUDCD1 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 NUDCD1 gene, integrated from 10 sources (see all 20):
    (articles sorted by number of sources associating them with NUDCD1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. CML66, a broadly immunogenic tumor antigen, elicits a humoral immune response associated with remission of chronic myelogenous leukemia. (PubMed id 11416219)1, 2, 3 Yang X.-F.... Ritz J. (Proc. Natl. Acad. Sci. U.S.A. 2001)
    2. A novel mechanism of alternative promoter and splicing regulates the epitope generation of tumor antigen CML66-L. (PubMed id 14688378)1, 2 Yan Y.... Yang X.-F. (J. Immunol. 2004)
    3. Quantitative study of the interactome of PKCIP involved in the EGF-induced tumor cell chemotaxis. (PubMed id 23402259)1 Chen R....Zhang N. (J. Proteome Res. 2013)
    4. The HECT type ubiquitin ligase NEDL2 is degraded by anaphase-promoting complex/cyclosome (APC/C)-Cdh1, and its tight regulation maintains the metaphase to anaphase transition. (PubMed id 24163370)1 Lu L....Zhang L. (J. Biol. Chem. 2013)
    5. Systematic analysis of protein pools, isoforms, and modifications affecting turnover and subcellular localization. (PubMed id 22002106)2 Ahmad Y.... Lamond A.I. (Mol. Cell. Proteomics 2012)
    6. A high-throughput approach for measuring temporal changes in the interactome. (PubMed id 22863883)1 Kristensen A.R....Foster L.J. (Nat. Methods 2012)
    7. N-terminal acetylome analyses and functional insights of the N- terminal acetyltransferase NatB. (PubMed id 22814378)2 Van Damme P....Aldabe R. (Proc. Natl. Acad. Sci. U.S.A. 2012)
    8. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)
    9. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
    10. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (amp 2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 84955 HGNC: 24306 AceView: CML66 Ensembl:ENSG00000120526 euGenes: HUgn84955
    ECgene: NUDCD1 H-InvDB: NUDCD1

    (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 NUDCD1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for NUDCD1 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for NUDCD1 gene:
    Search GeneIP for patents involving NUDCD1

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



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