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NUDT16L1 Gene

protein-coding   GIFtS: 50
GCID: GC16P004743

Nudix (Nucleoside Diphosphate Linked Moiety X)-Type Motif...

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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
Nudix (Nucleoside Diphosphate Linked Moiety X)-Type Motif 16-Like 11 2
SDOS2 3
NUDT16-Like Protein 12 3
Protein Syndesmos2

External Ids:    HGNC: 281541   Entrez Gene: 843092   Ensembl: ENSG000001681017   UniProtKB: Q9BRJ73   

Export aliases for NUDT16L1 gene to outside databases

Previous GC identifer: GC16P004684


(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 NUDT16L1 Gene:
NUDT16L1 (nudix (nucleoside diphosphate linked moiety X)-type motif 16-like 1) is a protein-coding gene. GO annotations related to this gene include m7G(5')pppN diphosphatase activity and protein homodimerization activity. An important paralog of this gene is NUDT16.

UniProtKB/Swiss-Prot: SDOS_HUMAN, Q9BRJ7
Function: Probable adapter protein, which may link syndecan-4 (SDC4) and paxilin (TGFB1I1 and PXN) receptors (By
similarity). Does not play a role in U8 snoRNA decapping activity. Binds U8 snoRNA




(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_000016.9  NT_010393.17  NC_018927.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the NUDT16L1 gene promoter:
         HFH-3   GCNF   NRSF form 1   HNF-3beta   NRSF form 2   GATA-1   FOXI1   GCNF-1   ARP-1   GCNF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidNUDT16L1 promoter sequence
   Search Chromatin IP Primers for NUDT16L1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat NUDT16L1


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

Entrez Gene cytogenetic band: 16p13.3   Ensembl cytogenetic band:  16p13.3   HGNC cytogenetic band: 16p13.3

NUDT16L1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NUDT16L1 gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16P004743:  view genomic region     (about GC identifiers)

Start:
4,743,694 bp from pter      End:
4,745,860 bp from pter
Size:
2,167 bases      Orientation:
plus 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: SDOS_HUMAN, Q9BRJ7 (See protein sequence)
Recommended Name: Protein syndesmos  
Size: 211 amino acids; 23338 Da
Subunit: Interacts with the cytoplasmic part of SDC4. Interacts with TGFB1I1 and PXN (By similarity)
Miscellaneous: Although strongly related to the nudix NUDT16 protein, it lacks the Nudix box and is therefore not
related to the rest of the family. Gene organization and evolutionary distribution suggest that syndesmos
NUDT16L1 probably originated as a gene duplication event of the more ancient U8 snoRNA-decapping enzyme NUDT16
Caution: Similar to U8 snoRNA-decapping enzyme NUDT16 but lacks a number of residues which are necessary for
activity
1 PDB 3D structure from and Proteopedia for NUDT16L1:
3KVH (3D)    
Secondary accessions: Q8NAI2
Alternative splicing: 2 isoforms:  Q9BRJ7-1   Q9BRJ7-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for NUDT16L1: NX_Q9BRJ7

Explore proteomics data for NUDT16L1 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See NUDT16L1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001180381.1  NP_115725.1  

    ENSEMBL proteins: 
     ENSP00000306670   ENSP00000466854   ENSP00000468346   ENSP00000458144   ENSP00000464821  

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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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    HGNC Gene Families:
    NUDT: Nudix motif containing

    1 InterPro protein domain:
     IPR015797 NUDIX_hydrolase_dom-like

    Graphical View of Domain Structure for InterPro Entry Q9BRJ7

    ProtoNet protein and cluster: Q9BRJ7

    1 Blocks protein domain: IPB000086 NUDIX hydrolase


    Find genes that share domains with NUDT16L1           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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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SDOS_HUMAN, Q9BRJ7
    Function: Probable adapter protein, which may link syndecan-4 (SDC4) and paxilin (TGFB1I1 and PXN) receptors (By
    similarity). Does not play a role in U8 snoRNA decapping activity. Binds U8 snoRNA

         Gene Ontology (GO): 5 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016787hydrolase activity ----
    GO:0030515snoRNA binding IDA18820299
    GO:0042803NOT protein homodimerization activity IDA18820299
    GO:0044822poly(A) RNA binding IDA--
    GO:0050072NOT m7G(5')pppN diphosphatase activity ISS--
         
    Find genes that share ontologies with NUDT16L1           About GenesLikeMe


    Animal Models:
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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
    SDOS_HUMAN, Q9BRJ7: Cytoplasm (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol2
    nucleus2
    peroxisome2
    mitochondrion1
    plasma membrane1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737cytoplasm IEA--

    Find genes that share ontologies with NUDT16L1           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 NUDT16L1 About    
    See pathways by source

    SuperPathContained pathways About
    1Syndecan-4-mediated signaling events
    Syndecan-4-mediated signaling events
    2Proteoglycans in cancer
    Proteoglycans in cancer


    Find genes that share SuperPaths with NUDT16L1           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 BioSystems Pathway for NUDT16L1
        Syndecan-4-mediated signaling events



    1 Kegg Pathway  (Kegg details for NUDT16L1):
        Proteoglycans in cancer

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for NUDT16L1
    Interactions:

        Search GeneGlobe Interaction Network for NUDT16L1

    STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

    Selected Interacting proteins for NUDT16L1 (Q9BRJ72, 3 ENSP000003066704) via UniProtKB, MINT, STRING, and/or I2D (see all 66)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    GABARAPO951663I2D: score=1 
    BAG2O958162MINT-8415355
    BAG6P463792MINT-8415355
    CCDC8Q9H0W52MINT-8415355
    CCT2P783712MINT-8415355
    About this table

    (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 NUDT16L1 (SDOS)



    (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 NUDT16L1 gene (2 alternative transcripts): 
    NM_001193452.1  NM_032349.3  

    Unigene Cluster for NUDT16L1:

    Nudix (nucleoside diphosphate linked moiety X)-type motif 16-like 1
    Hs.513315  [show with all ESTs]
    Unigene Representative Sequence: NM_001193452
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000304301 ENST00000586252 ENST00000586536 ENST00000405142(uc002cxf.2 uc021tci.1 uc002cxe.3)
    ENST00000590460
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      QuantiTect SYBR Green Assays in human, mouse, rat NUDT16L1
      QuantiFast Probe-based Assays in human, mouse, rat NUDT16L1

    Additional mRNA sequence: 

    AK315456.1 BC006223.2 

    6 DOTS entries:

    DT.444812  DT.100785063  DT.97844798  DT.100785060  DT.97823814  DT.100696681 

    Selected AceView cDNA sequences (see all 221):

    BI757129 BE048047 AI418038 NM_032349 BU175005 BI823073 BI060781 BM846916 
    AI278587 BQ012020 AI220804 CA447669 BX353043 BI914842 BF058583 AI826981 
    CB529708 AW615702 AI220749 CA312905 BM857012 BQ575948 BQ772856 BQ058429 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for NUDT16L1    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4a · 4b
    SP1:                                          
    SP2:                          -               
    SP3:                                          


    ECgene alternative splicing isoforms for NUDT16L1

    (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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    NUDT16L1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ATGCCCGAGG
    NUDT16L1 Expression
    About this image

    NUDT16L1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    NUDT16L1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.513315
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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 NUDT16L1 gene from Selected species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Nudt16l11 , 5 nudix (nucleoside diphosphate linked moiety X)-type more1, 5 85.47(n)1
    95.73(a)1
      16 (2.48 cM)5
    669111  NM_025839.31  NP_080115.11 
     49391115 
    chicken
    (Gallus gallus)
    Aves NUDT16L11 nudix (nucleoside diphosphate linked moiety X)-type more 79.9(n)
    79.9(a)
      395557  NM_204780.1  NP_990111.1 
    zebrafish
    (Danio rerio)
    Actinopterygii zgc:1037596
    FP015790.36
    Uncharacterized protein
    38(a)
    30(a)
    many ↔ many
    many ↔ many
    23(18873234-18878286) ENSDARG00000019503
    23(19097926-19098733) ENSDARG00000090001


    ENSEMBL Gene Tree for NUDT16L1 (if available)
    TreeFam Gene Tree for NUDT16L1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for NUDT16L1 gene
    NUDT162  
    1 SIMAP similar gene for NUDT16L1 using alignment to 5 protein entries:     SDOS_HUMAN (see all proteins):
    NUDT16

    Find genes that share paralogs with NUDT16L1           About GenesLikeMe



    (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 NUDT16L1 (see all 134)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 16 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs735214391,2
    C,F--4741740(+) GCACCC/TTGCGG 2 -- us2k12Minor allele frequency- T:0.03WA 120
    rs1144927671,2
    C,F--4741750(+) GCTGGC/TGTGTG 2 -- us2k11Minor allele frequency- T:0.03WA 118
    rs1916063251,2
    C--4741768(+) GACGGC/TGGGAG 2 -- us2k10--------
    rs1165264851,2
    C,F--4741777(+) AGCAGG/TTCTAG 2 -- us2k11Minor allele frequency- T:0.04WA 118
    rs1440447941,2
    --4741831(+) CCTCTC/GCACAG 2 -- us2k10--------
    rs1120471811,2
    C,F--4741836(+) GCACAG/ACCCCC 2 -- us2k12Minor allele frequency- A:0.04WA 120
    rs1464147691,2
    --4741841(+) GCCCCC/TGCTCC 2 -- us2k10--------
    rs767012391,2
    C,F--4741923(+) TTTGCG/ATGCAG 2 -- us2k11Minor allele frequency- A:0.05EA 120
    rs1408187131,2
    --4741943(+) CCACCA/GTGGCC 2 -- us2k10--------
    rs1438865981,2
    --4741962(+) AAGACC/TGTGAG 2 -- us2k10--------

    HapMap Linkage Disequilibrium report for NUDT16L1 (4743694 - 4745860 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 7 variations for NUDT16L1:    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv2587n71CNV Loss21882294
    nsv905248CNV Loss21882294
    dgv2590n71CNV Loss21882294
    nsv905243CNV Loss21882294
    dgv2589n71CNV Loss21882294
    nsv905249CNV Loss21882294
    dgv2588n71CNV Loss21882294

    Site Specific Mutation Identification with PCR Assays
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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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      --

    (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 NUDT16L1 gene, integrated from 10 sources (see all 21):
    (articles sorted by number of sources associating them with NUDT16L1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Evolutionary conservation supports ancient origin for Nudt16, a nuclear-localized, RNA-binding, RNA-decapping enzyme. (PubMed id 18820299)1, 2 Taylor M.J. and Peculis B.A. (Nucleic Acids Res. 2008)
    2. 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)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    4. Syndesmos, a syndecan-4 cytoplasmic domain interactor, binds to the focal adhesion adaptor proteins paxillin and Hic-5. (PubMed id 11805099)1, 3 Denhez F....Goetinck P.F. (J. Biol. Chem. 2002)
    5. 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)
    6. 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)
    7. 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)
    8. 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)
    9. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)
    10. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (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: 84309 HGNC: 28154 AceView: SDOS Ensembl:ENSG00000168101 euGenes: HUgn84309
    ECgene: NUDT16L1 Kegg: 84309 H-InvDB: NUDT16L1

    (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 NUDT16L1 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 NUDT16L1 gene:
    Search GeneIP for patents involving NUDT16L1

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



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