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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

NGRN Gene

protein-coding   GIFtS: 49
GCID: GC15P090808

Neugrin, Neurite Outgrowth Associated

  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)
About This Section

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Neugrin, Neurite Outgrowth Associated1 2     DSC922
Mesenchymal Stem Cell Protein DSC922 3     neugrin2
Neurite Outgrowth-Associated Protein2 3     Neurite Outgrowth Associated Protein2
Spinal Cord-Derived Protein FI58G2 3     FI58G3

External Ids:    HGNC: 180771   Entrez Gene: 513352   Ensembl: ENSG000001827687   UniProtKB: Q9NPE23   
ORGUL members:         
NONCODE14:n408119      

Export aliases for NGRN gene to outside databases

Previous GC identifers: GC15P088596 GC15P088609 GC15P066920


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for NGRN Gene: 
NGRN (neugrin, neurite outgrowth associated) is a protein-coding gene, and is affiliated with the lncRNA class. Diseases associated with NGRN include differentiating neuroblastoma, and pancreatic ductal adenocarcinoma. GO annotations related to this gene include molecular_function.

UniProtKB/Swiss-Prot: NGRN_HUMAN, Q9NPE2
Function: May be involved in neuronal differentiation




(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000015.9  NC_018926.2  NT_010274.17  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the NGRN gene promoter:
         HOXA3   Brachyury   YY1   CREB   CP2   POU2F1   deltaCREB   c-Myb   NF-Y   CBF(2)   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidNGRN promoter sequence
   Search SABiosciences Chromatin IP Primers for NGRN

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat NGRN


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

Entrez Gene cytogenetic band: 15q26.1   Ensembl cytogenetic band:  15q26.1   HGNC cytogenetic band: 15q26.1

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

GeneLoc information about chromosome 15         GeneLoc Exon Structure

GeneLoc location for GC15P090808:  view genomic region     (about GC identifiers)

Start:
90,808,891 bp from pter      End:
90,816,463 bp from pter
Size:
7,573 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: NGRN_HUMAN, Q9NPE2 (See protein sequence)
Recommended Name: Neugrin precursor  
Size: 291 amino acids; 32408 Da
Subcellular location: Nucleus. Secreted (Potential)
Sequence caution: Sequence=AAF65447.1; Type=Erroneous translation; Note=Wrong choice of CDS; Sequence=AAG09725.1;
Type=Erroneous translation; Note=Wrong choice of CDS; Sequence=AAG09725.1; Type=Frameshift; Positions=47;
Sequence=AAH01682.1; Type=Erroneous translation; Note=Wrong choice of CDS; Sequence=AAH07222.1; Type=Erroneous
translation; Note=Wrong choice of CDS; Sequence=AAH09389.1; Type=Erroneous translation; Note=Wrong choice of CDS;
Sequence=AAH17192.1; Type=Erroneous translation; Note=Wrong choice of CDS; Sequence=BAB21533.1; Type=Erroneous
translation; Note=Wrong choice of CDS; Sequence=BAB21533.1; Type=Frameshift; Positions=47; Sequence=BAG35525.1;
Type=Erroneous translation; Note=Wrong choice of CDS; Sequence=BAG35525.1; Type=Miscellaneous discrepancy;
Note=N-terminus does not match isoform 2; Sequence=CAB96088.1; Type=Erroneous translation; Note=Wrong choice of
CDS; Sequence=CAD39160.1; Type=Erroneous translation; Note=Wrong choice of CDS;
Secondary accessions: B2R6M8 Q4V9L7 Q9HBL4
Alternative splicing: 2 isoforms:  Q9NPE2-2   Q9NPE2-3   (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 NGRN: NX_Q9NPE2

Explore proteomics data for NGRN at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9NPE2

  • NGRN Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    NGRN Protein Expression
    REFSEQ proteins: NP_001028260.2  
    ENSEMBL proteins: 
     ENSP00000368389  

    Human Recombinant Protein Products for NGRN: 
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    Cloud-Clone Corp. Proteins for NGRN 

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region IEA--
    GO:0005634nucleus NAS11118320

    NGRN for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    1 InterPro protein domain:
     IPR010487 Neugrin-related

    Graphical View of Domain Structure for InterPro Entry Q9NPE2

    ProtoNet protein and cluster: Q9NPE2

    UniProtKB/Swiss-Prot: NGRN_HUMAN, Q9NPE2
    Similarity: Belongs to the neugrin family


    NGRN 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,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: NGRN_HUMAN, Q9NPE2
    Function: May be involved in neuronal differentiation
    Induction: Highly up-regulated in neuroblastostoma cells by retinoic acid treatment inducing neurite outgrowth

         Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
         
    NGRN for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for NGRN:
     Increased HPV18 LCR reporter a 

         1 MGI mutant phenotype (inferred from 1 allele(MGI details for Ngrn):
     mortality/aging 

    NGRN for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for NGRN 
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    2 QIAGEN miScript miRNA Assays for microRNAs that regulate NGRN:
    hsa-miR-124* hsa-miR-4255
    SwitchGear 3'UTR luciferase reporter plasmidNGRN 3' UTR sequence
    Inhib. RNA
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    (Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for NGRN

    STRING Interaction Network Preview (showing 3 interactants - click image to see more details)

    5/247 Interacting proteins for NGRN (Q9NPE22, 3 ENSP000003683894) via UniProtKB, MINT, STRING, and/or I2D (see all 247)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ICT1Q141972, 3, ENSP000003015854MINT-8079030 I2D: score=1 STRING: ENSP00000301585
    E2F1Q010943I2D: score=1 
    AARS2Q5JTZ92MINT-8079030
    AASSQ9UDR52MINT-8079030
    ABCB7O750272MINT-8079030
    About this table

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0030182neuron differentiation NAS11118320

    NGRN for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for NGRN

    Search CenterWatch for drugs/clinical trials and news about NGRN

    (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,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for NGRN gene (2 alternative transcripts): 
    NM_016645.2  NM_001033088.1  

    Unigene Cluster for NGRN:

    Neugrin, neurite outgrowth associated
    Hs.135471  [show with all ESTs]
    Unigene Representative Sequence: AB029315
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000331497(uc002bpf.1 uc002bpg.1) ENST00000379095
    miRNA
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    2 QIAGEN miScript miRNA Assays for microRNAs that regulate NGRN:
    hsa-miR-124* hsa-miR-4255
    SwitchGear 3'UTR luciferase reporter plasmidNGRN 3' UTR sequence
    Inhib. RNA
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      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat NGRN

    Additional mRNA sequence: 

    AB029315.1 AF225423.1 AF242770.1 AK312641.1 AL355699.1 AL360142.1 AL834503.1 AY049780.1 
    BC001682.2 BC007222.1 BC009389.2 BC017192.2 BC019023.2 BC096824.1 NR_028052.1 

    24/25 DOTS entries (see all 25):

    DT.95200729  DT.100880913  DT.101985414  DT.449823  DT.91772111  DT.100880916  DT.100038836  DT.100880912 
    DT.100801763  DT.95362694  DT.100813545  DT.100880908  DT.100880910  DT.121026743  DT.100880906  DT.91772117 
    DT.100034260  DT.100679017  DT.100830045  DT.102833461  DT.121026730  DT.80100936  DT.91772122  DT.95200724 

    24/864 AceView cDNA sequences (see all 864):

    T34796 AA366240 BE796296 BU860056 W76636 T33617 BQ017037 AI143845 
    BQ016344 BU615938 BC019023 AA732665 BU069409 BQ229950 BE778329 AI332842 
    AV706815 CB994081 BQ613872 BE877412 BQ709788 AA642999 BE408151 CR600787 

    GeneLoc Exon Structure

    5/6 Alternative Splicing Database (ASD) splice patterns (SP) for NGRN (see all 6)    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9a · 9b ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14a · 14b · 14c ^ 15 ^ 16a · 16b · 16c
    SP1:                          -     -                       -     -                 -                       -     -     -                           
    SP2:                                                        -                                                                                       
    SP3:                                                                                                                                                
    SP4:                                                                                                                                                
    SP5:                                                                                                                                                


    ECgene alternative splicing isoforms for NGRN

    (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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

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


    See NGRN Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for NGRN

    SOURCE GeneReport for Unigene cluster: Hs.135471

    UniProtKB/Swiss-Prot: NGRN_HUMAN, Q9NPE2
    Tissue specificity: Expressed at high levels in heart, brain and skeletal muscle. In brain, mainly expressed in
    neurons rather than glial cells

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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)
    About This Section

    This gene was present in the common ancestor of chordates.

    Orthologs for NGRN gene from 2/6 species (see all 6)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ngrn1 , 5 neugrin, neurite outgrowth associated1, 5 79.31(n)1
    72.07(a)1
      7 (45.58 cM)5
    834851  NM_031375.41  NP_113552.31 
     802612155 
    zebrafish
    (Danio rerio)
    Actinopterygii si:ch211-199o1.51 si:ch211-199o1.5 48.69(n)
    41.2(a)
      569275  NM_001045253.1  NP_001038718.1 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for NGRN gene

    NGRN for paralogs           About GeneDecksing


    5 Pseudogenes.org Pseudogenes for NGRN
    PGOHUM00000247168 PGOHUM00000257064 PGOHUM00000250169 PGOHUM00000243243 PGOHUM00000260197


    (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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/130 SNPs in NGRN are shown (see all 130)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 15 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1453973711,2
    C--90811000(+) GGAATA/TTTTGT 2 -- int10--------
    rs1414775891,2
    --90811027(+) AGTAAC/GGTTGC 2 -- int10--------
    rs1437908181,2
    --90811073(+) ATATTA/GCTAAG 2 -- int10--------
    rs1468325831,2
    --90811105(+) CTATTC/TTTCAT 2 -- int10--------
    rs1406751841,2
    --90811175(+) CAAGAC/TTTTGT 2 -- int10--------
    rs1436899041,2
    C--90811233(+) TTTTCA/GTTTGT 2 -- int10--------
    rs351442991,2
    F--90811290(+) GAGTGC/TAGTGG 2 -- int11Minor allele frequency- T:0.25NA 8
    rs1839723911,2
    --90811476(+) GTGATC/GCACCC 2 -- int10--------
    rs169441041,2
    C,F,H--90811569(+) CAAACC/TTTCCA 2 -- int19Minor allele frequency- T:0.05NA NS EA CSA WA 680
    rs1885142541,2
    --90811591(+) ATCTCC/TCTTTA 2 -- int10--------

    HapMap Linkage Disequilibrium report for NGRN (90808891 - 90816463 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for NGRN:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv833087CNV Loss17160897
    dgv2435n71CNV Loss21882294
    esv2751541CNV Gain17911159
    essv11326CNV CNV17122850
    dgv776e1CNV Complex17122850

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    9 diseases for NGRN:    About MalaCards
    differentiating neuroblastoma    pancreatic ductal adenocarcinoma    neuroblastoma    nasopharyngitis
    lateral sclerosis    amyotrophic lateral sclerosis    adenocarcinoma    pancreatitis
    neuronitis


    NGRN for disorders           About GeneDecksing

    1 Novoseek inferred disease relationship for NGRN gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    inflammation 16.1 2 15477757 (1)


    Export disorders for NGRN 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)
    About This Section

    PubMed articles for NGRN gene, integrated from 9 sources (see all 14):
    (articles sorted by number of sources associating them with NGRN)
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    1. Two novel genes, human neugrin and mouse m-neugrin, are upregulated with neuronal differentiation in neuroblastoma cells. (PubMed id 11118320)1, 2, 3, 9 Ishigaki S.... Sobue G. (2000)
    2. A functional peptidyl-tRNA hydrolase, ICT1, has been recruited into the human mitochondrial ribosome. (PubMed id 20186120)1 Richter R....Chrzanowska-Lightowlers Z.M. (2010)
    3. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. (PubMed id 20068231)2 Olsen J.V....Mann M. (2010)
    4. Two-hybrid analysis identifies PSMD11, a non-ATPase s ubunit of the proteasome, as a novel interaction partner of AMP-activated prote in kinase. (PubMed id 19616115)1 Moreno D....Sanz P. (2009)
    5. A quantitative atlas of mitotic phosphorylation. (PubMed id 18669648)2 Dephoure N.... Gygi S.P. (2008)
    6. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (2007)
    7. Analysis of the DNA sequence and duplication history of human chromosome 15. (PubMed id 16572171)2 Zody M.C....Nusbaum C. (2006)
    8. 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. (2004)
    9. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (2004)
    10. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)

    (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)
    About This Section
    Entrez Gene: 51335 HGNC: 18077 AceView: NEUGRIN Ensembl:ENSG00000182768 euGenes: HUgn51335
    ECgene: NGRN H-InvDB: NGRN

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for NGRN Pharmacogenomics, SNPs, Pathways

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

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



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