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NOMO3 Gene

protein-coding   GIFtS: 42
GCID: GC16P016326

NODAL Modulator 3

  See related diseases
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
NODAL Modulator 31 2
PM5 Protein 32 3
Nomo2
PM5 Protein, Middle Copy2

External Ids:    HGNC: 252421   Entrez Gene: 4080502   Ensembl: ENSG000001032267   OMIM: 6091595   UniProtKB: P698493   

Export aliases for NOMO3 gene to outside databases

Previous GC identifers: GC16P014835 GC16P016233 GC16U900522


(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 NOMO3 Gene:
This gene encodes a protein originally thought to be related to the collagenase gene family. This gene is one of
three highly similar genes in a duplicated region on the short arm of chromosome 16. These three genes encode
closely related proteins that may have the same function. The protein encoded by one of these genes has been
identified as part of a protein complex that participates in the Nodal signaling pathway during vertebrate
development. Mutations in ABCC6, which is located nearby, rather than mutations in this gene are associated with
pseudoxanthoma elasticum. (provided by RefSeq, Jul 2008)

GeneCards Summary for NOMO3 Gene:
NOMO3 (NODAL modulator 3) is a protein-coding gene. Diseases associated with NOMO3 include pseudoxanthoma elasticum, and malaria. GO annotations related to this gene include carbohydrate binding. An important paralog of this gene is NOMO2.

UniProtKB/Swiss-Prot: NOMO3_HUMAN, P69849
Function: May antagonize Nodal signaling (By similarity)




(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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Regulatory elements:
   Regulatory transcription factor binding sites in the NOMO3 gene promoter:
         GR   Elk-1   AML1a   Sp1   Lmo2   GATA-1   c-Ets-1   GR-alpha   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for NOMO3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat NOMO3


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

Entrez Gene cytogenetic band: 16p13   Ensembl cytogenetic band:  16p13.11   HGNC cytogenetic band: 16p13

NOMO3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NOMO3 gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16P016326:  view genomic region     (about GC identifiers)

Start:
16,326,352 bp from pter      End:
16,388,668 bp from pter
Size:
62,317 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., 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: NOMO3_HUMAN, P69849 (See protein sequence)
Recommended Name: Nodal modulator 3 precursor  
Size: 1222 amino acids; 134134 Da
Caution: There are 3 copies of the NOMO gene on chromosome 16p12-p13: NOMO1 (AC Q5JPE7), NOMO2 (AC Q5JPE7) and
NOMO3. All 3 are extremely similar, which makes their individual characterization difficult. Thus, most
experiments probably do not discriminate between the different members. The results reported in other entries may
therefore apply for this protein

Explore the universe of human proteins at neXtProt for NOMO3: NX_P69849

Explore proteomics data for NOMO3 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys134, Lys138, Lys159, Lys170, Lys175, Lys193, Lys356, Lys630, Lys770, Lys927,
                                 Lys1019, Lys1079
  • Glycosylation2 at Asn50, Asn218, Asn369, Asn618
  • Modification sites at PhosphoSitePlus

  • See NOMO3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001004067.1  
    ENSEMBL proteins: 
     ENSP00000382274   ENSP00000461721   ENSP00000263012   ENSP00000458267   ENSP00000458821  
     ENSP00000461870   ENSP00000459996   ENSP00000443768  

    NOMO3 Human Recombinant Protein Products:

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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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    4 InterPro protein domains:
     IPR008969 CarboxyPept-like_regulatory
     IPR013783 Ig-like_fold
     IPR013784 Carb-bd-like_fold
     IPR014766 CarboxyPept_regulatory_dom

    Graphical View of Domain Structure for InterPro Entry P69849

    ProtoNet protein and cluster: P69849

    1 Blocks protein domain: IPB008454 Cna B-type


    NOMO3 for domains           About GeneDecksing


    (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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: NOMO3_HUMAN, P69849
    Function: May antagonize Nodal signaling (By similarity)

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
    GO:0030246carbohydrate binding IEA--
         
    NOMO3 for ontologies           About GeneDecksing


    Animal Models:
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    miRTarBase miRNAs that target NOMO3:
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    Block miRNA regulation of human, mouse, rat NOMO3 using miScript Target Protectors
    8 qRT-PCR Assays for microRNAs that regulate NOMO3:
    hsa-miR-4291 hsa-miR-922 hsa-miR-342-3p hsa-miR-33a hsa-miR-214 hsa-miR-542-3p hsa-miR-33b hsa-miR-761
    SwitchGear 3'UTR luciferase reporter plasmidNOMO3 3' UTR sequence
    Inhib. RNA
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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
    NOMO3_HUMAN, P69849: Membrane; Single-pass type I membrane protein (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular2
    plasma membrane2
    endoplasmic reticulum1
    golgi apparatus1
    peroxisome1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005575cellular_component ND--
    GO:0016021integral component of membrane IEA--

    NOMO3 for ontologies           About GeneDecksing


    (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 NOMO3
    Interactions:

        Search GeneGlobe Interaction Network for NOMO3

    STRING Interaction Network Preview (showing 5 interactants - click image to see 23)

    Selected Interacting proteins for NOMO3 (P698492, 3 ENSP000003822744) via UniProtKB, MINT, STRING, and/or I2D (see all 23)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    UBQLN4Q9NRR52, 3, ENSP000003572924MINT-2879707 I2D: score=3 STRING: ENSP00000357292
    NCLNQ969V33, ENSP000002461174I2D: score=1 STRING: ENSP00000246117
    RYKP349253, ENSP000002960844I2D: score=1 STRING: ENSP00000296084
    CADENSP000002647054STRING: ENSP00000264705
    UBCENSP000003448184STRING: ENSP00000344818
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008150biological_process ND--

    NOMO3 for ontologies           About GeneDecksing



    (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 NOMO3



    (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, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for NOMO3 gene: 
    NM_001004067.3  

    18 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000399336(uc002dep.3 uc010bvp.2 uc002deq.3) ENST00000576589
    ENST00000263012 ENST00000575225 ENST00000572830 ENST00000570519 ENST00000576427
    ENST00000576269 ENST00000576460 ENST00000572033 ENST00000574894 ENST00000574157
    ENST00000572932 ENST00000573635 ENST00000571167 ENST00000570732 ENST00000570346
    ENST00000538468
    miRNA
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    8 qRT-PCR Assays for microRNAs that regulate NOMO3:
    hsa-miR-4291 hsa-miR-922 hsa-miR-342-3p hsa-miR-33a hsa-miR-214 hsa-miR-542-3p hsa-miR-33b hsa-miR-761
    SwitchGear 3'UTR luciferase reporter plasmidNOMO3 3' UTR sequence
    Inhib. RNA
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    Primer
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      QuantiTect SYBR Green Assays in human, mouse, rat NOMO3
      QuantiFast Probe-based Assays in human, mouse, rat NOMO3

    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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    NOMO3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GCGGGGTACC
    NOMO3 Expression
    About this image

    NOMO3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    NOMO3 Protein Expression
        Custom PCR Arrays for NOMO3
    Primer
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for NOMO3

    (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 eukaryotes.

    Orthologs for NOMO3 gene from Selected species (see all 16)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Nomo11 nodal modulator 1 86.37(n)
    93.28(a)
      211548  NM_153057.4  NP_694697.3 
    chicken
    (Gallus gallus)
    Aves PM51 pM5 protein 77.23(n)
    87.14(a)
      416602  XM_004945285.1  XP_004945342.1 
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    86(a)
    1 → many
    GL343580.1(301242-312387)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia nomo31 NODAL modulator 3 72.13(n)
    79.9(a)
      100158535  NM_001127971.1  NP_001121443.1 
    zebrafish
    (Danio rerio)
    Actinopterygii nomo1 nodal modulator 66.69(n)
    70.85(a)
      446115  XM_002662315.2  XP_002662361.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG13711 CG1371 46.05(n)
    34.28(a)
      36053  NM_136707.2  NP_610551.1 
    worm
    (Caenorhabditis elegans)
    Secernentea nra-41 nra-4 43.06(n)
    27.77(a)
      3565008  NM_070966.3  NP_503367.1 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT3G623601 AT3G62360 45.03(n)
    34.26(a)
      825409  NM_116101.3  NP_191795.1 
    rice
    (Oryza sativa)
    Liliopsida Os01g03006001 Os01g0300600 45.37(n)
    39.65(a)
      4325779  NM_001049353.1  NP_001042818.2 


    ENSEMBL Gene Tree for NOMO3 (if available)
    TreeFam Gene Tree for NOMO3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for NOMO3 gene
    NOMO21 2  NOMO11 2  
    3 SIMAP similar genes for NOMO3 using alignment to 9 protein entries:     NOMO3_HUMAN (see all proteins):
    DKFZp547A1913    NOMO1    NOMO2

    NOMO3 for paralogs           About GeneDecksing



    (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 NOMO3 (see all 296)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 16 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1496034791,2
    --16325013(+) CTCATA/GATTAT 1 -- us2k10--------
    rs2010127121,2
    C--16325930(+) GTGTG-/GT/TG 
            
    CGTGT
    1 -- us2k10--------
    rs1409949401,2
    --16326030(+) TCCACC/TCACCT 1 -- us2k10--------
    rs1446484771,2
    C--16326171(+) CCAACA/GAAATC 1 -- us2k10--------
    rs1478732651,2
    C--16326364(+) TGTGAA/CCGTGG 1 -- us2k10--------
    rs2016819041,2
    C--16327885(+) CTTTAA/GCAAGC 1 -- int10--------
    rs99354951,2
    C--16328533(+) GttcaT/Ctgagt 1 -- int11Minor allele frequency- C:0.00NA 2
    rs99229141,2
    C--16328557(+) CTGAGC/TCCCGG 1 -- int10--------
    rs99355841,2
    C--16328634(+) tactcT/Ccatga 1 -- int11Minor allele frequency- C:0.00NA 2
    rs1408353701,2
    --16328720(+) CAATCA/CGCAGG 1 -- int10--------

    HapMap Linkage Disequilibrium report for NOMO3 (16326352 - 16388668 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for NOMO3 (see all 17):    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv435664CNV Deletion17901297
    esv2714015CNV Deletion23290073
    nsv509599CNV Insertion20534489
    nsv9362CNV Loss18304495
    nsv428319CNV Loss18775914
    nsv9363CNV Loss18304495
    dgv2616n71CNV Gain21882294
    nsv905424CNV Gain21882294
    nsv457428CNV Gain19166990
    nsv905415CNV Gain21882294

    Site Specific Mutation Identification with PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing NOMO3
    DNA2.0 Custom Variant and Variant Library Synthesis for NOMO3

    (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: 609159    OMIM disorders: --

    4 diseases for NOMO3:    
    About MalaCards
    pseudoxanthoma elasticum    malaria    ataxia    prostatitis


    NOMO3 for disorders           About GeneDecksing


    Export disorders for NOMO3 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 NOMO3 gene, integrated from 10 sources (see all 23):
    (articles sorted by number of sources associating them with NOMO3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The sequence and analysis of duplication-rich human chromosome 16. (PubMed id 15616553)1, 2 Martin J.... Pennacchio L.A. (Nature 2004)
    2. Nicalin and its binding partner Nomo are novel Nodal signaling antagonists. (PubMed id 15257293)1, 3 Haffner C.... Haass C. (EMBO J. 2004)
    3. Genome duplications and other features in 12 Mb of DNA sequence from human chromosome 16p and 16q. (PubMed id 10493829)1, 2 Loftus B.J.... Adams M.D. (Genomics 1999)
    4. Charting the landscape of tandem BRCT domain-mediated protein interactions. (PubMed id 22990118)1 Woods N.T....Monteiro A.N. (Sci Signal 2012)
    5. 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)
    6. 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)
    7. Proteomic identification of common SCF ubiquitin ligase FBXO6-interacting glycoproteins in three kinds of cells. (PubMed id 22268729)1 Liu B....Wang L.S. (J. Proteome Res. 2012)
    8. 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)
    9. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
    10. Mindbomb 1, an E3 ubiquitin ligase, forms a complex with RYK to activate Wnt/I^-catenin signaling. (PubMed id 21875946)1 Berndt J.D....Moon R.T. (J. Cell 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: 408050 HGNC: 25242 Ensembl:ENSG00000103226 euGenes: HUgn408050 ECgene: NOMO3
    H-InvDB: NOMO3

    (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 NOMO3 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 NOMO3 gene:
    Search GeneIP for patents involving NOMO3

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



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