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NDNL2 Gene

protein-coding   GIFtS: 51
GCID: GC15M029560

Necdin-Like 2

  See NDNL2-related disease
at  

(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
Necdin-Like 21 2     NSE32
MAGEG12 3 5     NSMCE32
Hepatocellular Carcinoma-Associated Protein 42 3     Hepatocellular Carcinoma-Associated Protein HCA42
Necdin-Like Protein 22 3     Melanoma Antigen, Family G, 12
HCA42 3     Melanoma-Associated Antigen G12
MAGE-G1 Antigen2 3     Necdin-Like Gene 22
MAGEL32     

External Ids:    HGNC: 76771   Entrez Gene: 561602   Ensembl: ENSG000001851157   OMIM: 6082435   UniProtKB: Q96MG73   

Export aliases for NDNL2 gene to outside databases

Previous GC identifers: GC00U990785 GC15U900046 GC15M027276 GC15M027347 GC15M007218


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for NDNL2 Gene:
The protein encoded by this gene is part of the SMC5-6 chromatin reorganizing complex and is a member of the MAGE
superfamily. This is an intronless gene. (provided by RefSeq, May 2011)

GeneCards Summary for NDNL2 Gene:
NDNL2 (necdin-like 2) is a protein-coding gene. Diseases associated with NDNL2 include hepatocellular carcinoma. An important paralog of this gene is MAGEC2.

UniProtKB/Swiss-Prot: MAGG1_HUMAN, Q96MG7
Function: Component of the SMC5-SMC6 complex, a complex involved in repair of DNA double-strand breaks by
homologous recombination. The complex may promote sister chromatid homologous recombination by recruiting the
SMC1-SMC3 cohesin complex to double-strand breaks. The complex is required for telomere maintenance via
recombination in ALT (alternative lengthening of telomeres) cell lines and mediates sumoylation of shelterin
complex (telosome) components which is proposed to lead to shelterin complex disassembly in ALT-associated PML
bodies (APBs). In vitro enhances ubiquitin ligase activity of NSMCE1. Proposed to act through recruitment and/or
stabilization of the Ubl-conjugating enzyme (E2) at the E3:substrate complex. May be a growth suppressor that
facilitates the entry of the cell into cell cycle arrest




(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_000015.9  NC_018926.2  NT_010194.18  NT_187660.1  
Regulatory elements:
   Regulatory transcription factor binding sites in the NDNL2 gene promoter:
         LHX3b/Lhx3b   p53   SREBP-1c   CUTL1   SREBP-1b   GATA-2   SREBP-1a   POU2F1   POU2F1a   LHX3a/Lhx3a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidNDNL2 promoter sequence
   Search Chromatin IP Primers for NDNL2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat NDNL2


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

Entrez Gene cytogenetic band: 15q13.1   Ensembl cytogenetic band:  15q13.1   HGNC cytogenetic band: 15q13.1

NDNL2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NDNL2 gene location

GeneLoc information about chromosome 15         GeneLoc Exon Structure

GeneLoc location for GC15M029560:  view genomic region     (about GC identifiers)

Start:
29,560,353 bp from pter      End:
29,562,033 bp from pter
Size:
1,681 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: MAGG1_HUMAN, Q96MG7 (See protein sequence)
Recommended Name: Melanoma-associated antigen G1  
Size: 304 amino acids; 34308 Da
Subunit: Component of the SMC5-SMC6 complex which consists at least of SMC5, SMC6, NSMCE2, NSMCE1, NSMCE4A or EID3
and NDNL2. NSMCE1, NSMCE4A or EID3 and NDNL2 probably form a subcomplex that bridges the head domains of the
SMC5:SMC6 heterodimer. Interacts with PJA1. Binds the C-terminus of E2F1 and NGFR (By similarity)
Sequence caution: Sequence=BAB84964.1; Type=Frameshift; Positions=290;
1 PDB 3D structure from and Proteopedia for NDNL2:
3NW0 (3D)    
Secondary accessions: Q8IW16 Q8TEI6 Q9H214

Explore the universe of human proteins at neXtProt for NDNL2: NX_Q96MG7

Explore proteomics data for NDNL2 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys113, Lys128, Lys141
  • Modification sites at PhosphoSitePlus

  • See NDNL2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_619649.1  
    ENSEMBL proteins: 
     ENSP00000330694  

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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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    1 InterPro protein domain:
     IPR002190 MAGE

    Graphical View of Domain Structure for InterPro Entry Q96MG7

    ProtoNet protein and cluster: Q96MG7

    1 Blocks protein domain: IPB002190 MAGE protein

    UniProtKB/Swiss-Prot: MAGG1_HUMAN, Q96MG7
    Similarity: Contains 1 MAGE domain


    Find genes that share domains with NDNL2           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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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: MAGG1_HUMAN, Q96MG7
    Function: Component of the SMC5-SMC6 complex, a complex involved in repair of DNA double-strand breaks by
    homologous recombination. The complex may promote sister chromatid homologous recombination by recruiting the
    SMC1-SMC3 cohesin complex to double-strand breaks. The complex is required for telomere maintenance via
    recombination in ALT (alternative lengthening of telomeres) cell lines and mediates sumoylation of shelterin
    complex (telosome) components which is proposed to lead to shelterin complex disassembly in ALT-associated PML
    bodies (APBs). In vitro enhances ubiquitin ligase activity of NSMCE1. Proposed to act through recruitment and/or
    stabilization of the Ubl-conjugating enzyme (E2) at the E3:substrate complex. May be a growth suppressor that
    facilitates the entry of the cell into cell cycle arrest

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI18086888
         
    Find genes that share ontologies with NDNL2           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for NDNL2

    miRNA
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    hsa-mir-25-3p (MIRT050199), hsa-mir-30c-5p (MIRT047835)

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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
    MAGG1_HUMAN, Q96MG7: Cytoplasm (By similarity). Nucleus. Chromosome, telomere (Probable)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol2
    cytoskeleton1
    mitochondrion1
    peroxisome1
    plasma membrane1

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000781chromosome, telomeric region IEA--
    GO:0005634nucleus IEA--
    GO:0005737cytoplasm IEA--
    GO:0030915Smc5-Smc6 complex IDA18086888

    Find genes that share ontologies with NDNL2           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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    SuperPaths for NDNL2 About    
    See pathways by source

    SuperPathContained pathways About
    1p75(NTR)-mediated signaling
    p75(NTR)-mediated signaling


    1 BioSystems Pathway for NDNL2
        p75(NTR)-mediated signaling



        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for NDNL2
    Interactions:

        GeneGlobe Interaction Network for NDNL2

    STRING Interaction Network Preview (showing 5 interactants - click image to see 12)

    Selected Interacting proteins for NDNL2 (Q96MG71, 3 ENSP000003306944) via UniProtKB, MINT, STRING, and/or I2D (see all 13)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    E2F1Q010943, ENSP000003455714I2D: score=4 STRING: ENSP00000345571
    NGFRP081383, ENSP000001722294I2D: score=3 STRING: ENSP00000172229
    NSMCE1Q8WV221, ENSP000003550774EBI-2557356,EBI-2557372 STRING: ENSP00000355077
    NSMCE4AQ9NXX61, ENSP000003580194EBI-2557356,EBI-2557393 STRING: ENSP00000358019
    PJA1Q8NG271, ENSP000003550144EBI-2557356,EBI-714606 STRING: ENSP00000355014
    About this table

    Gene Ontology (GO): 5 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006281DNA repair IEA--
    GO:0006310DNA recombination IEA--
    GO:0006355regulation of transcription, DNA-templated IEA--
    GO:0031398positive regulation of protein ubiquitination IDA--
    GO:0040008regulation of growth IEA--

    Find genes that share ontologies with NDNL2           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 NDNL2 (MAGG1)



    (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 NDNL2 gene: 
    NM_138704.3  

    Unigene Cluster for NDNL2:

    Necdin-like 2
    Hs.94011  [show with all ESTs]
    Unigene Representative Sequence: AK074138
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000332303(uc001zco.3)
    miRNA
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      QuantiFast Probe-based Assays in human, mouse, rat NDNL2

    Additional mRNA sequence: 

    AF490510.1 AK056957.1 AK074138.1 BC035458.1 BC041166.1 BC053999.1 

    5 DOTS entries:

    DT.455987  DT.100776249  DT.92423061  DT.100034618  DT.92423059 

    Selected AceView cDNA sequences (see all 131):

    BU623901 BG575782 N48857 W04542 NM_138704 AW473739 BI518502 BC053999 
    BI759688 BQ772383 AA767569 BI759246 BM684358 CR603768 AA319151 BX102340 
    CR605030 AK056957 BC035458 AI224106 BE909407 CD742857 AK074138 AI185023 

    GeneLoc Exon Structure


    (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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    NDNL2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GTTCCAAGCA
    NDNL2 Expression
    About this image

    NDNL2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    NDNL2 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.94011

    UniProtKB/Swiss-Prot: MAGG1_HUMAN, Q96MG7
    Tissue specificity: Ubiquitous

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    In Situ
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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 chordates.

    Orthologs for NDNL2 gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ndnl21 , 5 necdin-like 21, 5 80.34(n)1
    83.09(a)1
      7 (34.77 cM)5
    666471  NM_023239.41  NP_075728.11 
     648670525 
    chicken
    (Gallus gallus)
    Aves NDNL21 necdin-like 2 62.52(n)
    52.07(a)
      100125831  NM_001105064.1  NP_001098534.1 
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    50(a)
    1 → many
    1(205667349-205679701)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia ndnl21 necdin-like 2 60.09(n)
    55.61(a)
      549684  NM_001016930.2  NP_001016930.1 
    zebrafish
    (Danio rerio)
    Actinopterygii ndnl26
    necdin-like 2
    45(a)
    1 → many
    23(13012414-13025121) ENSDARG00000058212


    ENSEMBL Gene Tree for NDNL2 (if available)
    TreeFam Gene Tree for NDNL2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for NDNL2 gene
    MAGEC22  MAGEA9B2  MAGEB52  MAGEB162  MAGEB12  MAGEB42  MAGEC12  MAGED42  
    MAGEA82  MAGED22  MAGEA122  MAGEA92  MAGEB172  MAGEB102  MAGEA62  MAGED12  
    MAGEA22  MAGEA32  MAGEB22  NDN2  MAGEB32  MAGED4B2  MAGEA42  MAGEA12  
    MAGEA102  MAGEB182  MAGEA2B2  MAGEB62  MAGEL22  TRO2  MAGEA112  MAGEF12  
    Selected SIMAP similar genes for NDNL2 using alignment to 1 protein entry:     MAGG1_HUMAN(see all similar genes):
    MAGEH1    MAGEB16    MAGED1    MAGEF1    TRO    MAGEA11
    MAGEC1    MAGE-B1    MAGEA10    MAGEB1    MAGED2    MAGEE1
    MAGEE2    MAGEA9B    MAGEC2    MAGEA9    MAGEB17    MAGEB18

    Find genes that share paralogs with NDNL2           About GenesLikeMe


    2 Pseudogenes.org Pseudogenes for NDNL2
    PGOHUM00000241390 PGOHUM00000241840


    (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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    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for NDNL2:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2751526CNV Loss17911159
    nsv522597CNV Loss19592680
    nsv903747CNV Gain21882294
    nsv527255CNV Gain19592680
    nsv515660CNV Gain19592680

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    (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: 608243    OMIM disorders: --

    1 disease for NDNL2:    
    About MalaCards
    hepatocellular carcinoma

    1 disease from the University of Copenhagen DISEASES database for NDNL2:
    Prader-Willi syndrome

    Find genes that share disorders with NDNL2           About GenesLikeMe

    Genetic Association Database (GAD): NDNL2

    Export disorders for NDNL2 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 NDNL2 gene, integrated from 10 sources (see all 21):
    (articles sorted by number of sources associating them with NDNL2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification of the proteins, including MAGEG1, that make up the human SMC5-6 protein complex. (PubMed id 18086888)1, 2, 3 Taylor E.M.... Lehmann A.R. (Mol. Cell. Biol. 2008)
    2. Interactions between the Nse3 and Nse4 components of the SMC5-6 complex identify evolutionarily conserved interactions between MAGE and EID Families. (PubMed id 21364888)1, 2 Hudson J.J....Palecek J. (PLoS ONE 2011)
    3. MAGE-RING protein complexes comprise a family of E3 ubiquitin ligases. (PubMed id 20864041)1, 2 Doyle J.M.... Potts P.R. (Mol. Cell 2010)
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    6. A necdin/MAGE-like gene in the chromosome 15 autism susceptibility region: expression, imprinting, and mapping of the human and mouse orthologues. (PubMed id 11782285)1, 2 Chibuk T.K.... Wevrick R. (BMC Genet. 2001)
    7. Necdin-related MAGE proteins differentially interact with the E2F1 transcription factor and the p75 neurotrophin receptor. (PubMed id 14593116)1, 9 Kuwako K....Yoshikawa K. (J. Biol. Chem. 2004)
    8. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
    9. Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. (PubMed id 23000965)1 Povlsen L.K....Choudhary C. (Nat. Cell Biol. 2012)
    10. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 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: 56160 HGNC: 7677 AceView: NDNL2 Ensembl:ENSG00000185115 euGenes: HUgn56160
    ECgene: NDNL2 H-InvDB: NDNL2

    (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 NDNL2 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for NDNL2 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 NDNL2 gene:
    Search GeneIP for patents involving NDNL2

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



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