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NID1 Gene

protein-coding   GIFtS: 56

GC01M234205
nidogen 1
(Previous name: nidogen (enactin) )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbol: NID)
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
About This Section

Aliases
Entactin 3
NID 2, 3
NID-1 3
OTTHUMP00000037970 2
enactin 1, 2
entactin 2
Descriptions
nidogen (enactin) 1
nidogen 1 2
External Ids
HGNC: 78211
Entrez Gene: 48112
UniProtKB: P145433
Ensembl: ENSG000001169627
Search outside databases for aliases for NID1 gene

Previous GC identifer: GC01M232466

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

EntrezGene summary for NID1:
This gene encodes a member of the nidogen family of basement membrane glycoproteins. The protein
interacts with several other components of basement membranes, and may play a role in cell
interactions with the extracellular matrix. [provided by RefSeq]

UniProtKB/Swiss-Prot: NID1_HUMAN, P14543
Function: Sulfated glycoprotein widely distributed in basement membranes and tightly associated
with laminin. Also binds to collagen IV and perlecan. It probably has a role in cell-extracellular
matrix interactions

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the NID1 gene  

Entrez Gene cytogenetic band: 1q43   Ensembl cytogenetic band:  1q42.3   HGNC cytogenetic band: 1q43

NID1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M234205:     (about GC identifiers)

Start:
234,205,753 bp from pter
End:
234,295,104 bp from pter
Size:
89,352 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000001.9  NT_004836.17  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
About This Section

UniProtKB/Swiss-Prot: NID1_HUMAN, P14543 (See protein sequence)
Recommended Name: Nidogen-1 precursor  
Size: 1247 amino acids; 136453 Da
Subunit: Interacts with FBLN1 and LGALS3BP (By similarity)
Subcellular location: Secreted, extracellular space, extracellular matrix, basement membrane
PDB structures from and Proteopedia :
1NDX (3D)    
Secondary accessions: Q14942 Q59FL2 Q5TAF2 Q5TAF3 Q86XD7
Alternative splicing: 2 isoforms:  P14543-1   P14543-2   

Post-translational modifications:

  • N- and O-glycosylated1


  • REFSEQ proteins: NP_002499.2  

    ENSEMBL proteins: 
    ENSP00000264187 ENSP00000355554 


    Human Recombinant Proteins 
    Browse Drug Discovery Central at Invitrogen for human recombinant proteins
    Browse Purified and Recombinant Proteins at Millipore
    Browse Human Recombinant Proteins at Sigma-Aldrich  
    R&D Systems Recombinant & Natural Proteins for NID1 (Nidogen-1/Entactin)
    Browse recombinant and purified proteins available from Enzo Life Sciences
    Recombinant Proteins from Abcam (Entactin)
    Human Recombinant Proteins from Abnova (NID1)
                    Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

    3 Gene Ontology (GO) cellular component terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576 extracellular region IEA--
    GO:0005604 basement membrane IEA--
    GO:0016020 membrane IEA--
    About this table

    Antibodies for NID1: 
    Browse Antibodies Central at Invitrogen
    Millipore Mono- and Polyclonal Antibodies for the study of NID1
    Sigma-Aldrich Antibodies for NID1
    R&D Systems Antibodies for NID1 (Nidogen-1/Entactin)
    Antibodies from Abcam (Entactin), each with their AbpromiseSM
    Monoclonal and Polyclonal Antibodies from Abnova (NID1)
    Novus Biologicals Antibodies for NID1

    Assays for NID1: 
    Browse Invitrogen for biochemical assays
    Browse Kits and Assays available from Millipore
    R&D Systems ELISAs for NID1 (Nidogen-1/Entactin)         (see all)
    Browse biochemical assays available from Enzo Life Sciences

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    5/13 InterPro domains/families (see all 13 ):
     IPR000033 LDLR
     IPR003886 NIDO
     IPR001881 EGF_Ca_bd
     IPR000742 EGF_3
     IPR000716 Thyroglobulin_1


       GeneDecks  NID1 for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry P14543

    ProtoNet protein and cluster: P14543

    5/6 Blocks protein families (see all 6 ):
    IPB000033 Low-density lipoprotein receptor
    IPB000152 Aspartic acid and asparagine hydroxylation site
    IPB000716 Thyroglobulin type-1
    IPB001881 EGF-like calcium-binding
    IPB003886 Nidogen


    UniProtKB/Swiss-Prot: NID1_HUMAN, P14543
    Similarity: Contains 6 EGF-like domains
    Similarity: Contains 4 LDL-receptor class B repeats
    Similarity: Contains 1 NIDO domain
    Similarity: Contains 1 nidogen G2 beta-barrel domain
    Similarity: Contains 1 thyroglobulin type-1 domain

    (According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
    shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
    RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (NID1)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (NID1)
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_002508

                  Applied Biosystems Silencer® siRNAs for NID1

                  Sigma-Aldrich siRNA for NID1  
                         Sigma-Aldrich shRNA Panels and shRNA for NID1  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Clones:Invitrogen Clones for NID1
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_002508
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_002508
                                     untagged cDNA clones in CMV expression vector (see all 2): BC012501 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_002508

    UniProtKB/Swiss-Prot: NID1_HUMAN, P14543
    Function: Sulfated glycoprotein widely distributed in basement membranes and tightly associated
    with laminin. Also binds to collagen IV and perlecan. It probably has a role in cell-extracellular
    matrix interactions

    7 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Nid1):

    behavior/neurologicalcellularmusclenervous system
    othervision/eye

    2 Gene Ontology (GO) molecular function terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005509 calcium ion binding IEA--
    GO:0005515 protein binding IEA--
    About this table

    (Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
    Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section


    2 Millipore Pathways for NID1
     Cell adhesion ECM remodeling
     Metalloproteases in connective tissue degradation

       GeneDecks  NID1 for the pathways selected above  
    About GeneDecksing


    5/30 Interacting proteins for NID1 (ENSP000002641873 P145432) via UniProtKB, MINT, and/or STRING (see all 30 )
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SKILP127572MINT-61679
    FN1ENSP000003235343STRING (score=.97)
    FBLN1ENSP000002627233STRING (score=.968)
    COL4A1ENSP000003649733STRING (score=.967)
    FBLN2ENSP000002957613STRING (score=.929)
    About this table

    4 Gene Ontology (GO) biological process terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007155 cell adhesion IEA--
    GO:0007160 cell-matrix adhesion IEA--
    GO:0008218 bioluminescence IEA--
    GO:0018298 protein-chromophore linkage IEA--
    About this table
    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
    About This Section

    Browse drugs & compounds from Enzo Life Sciences
    Browse Small Molecules at Sigma-Aldrich

    Browse Tocris compounds for NID1
    8 Novoseek chemical compound relationships for NID1 gene
    Compound   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    matrigel 62.25 9 10671375 (3), 1694169 (1), 16322790 (1), 9196442 (1) (see all 7)
    heparan sulfate 47.39 6 16322790 (2), 9257191 (1), 9115292 (1), 11530869 (1) (see all 5)
    thioflavin t 43.61 2 11376898 (1)
    fibrinogen 34.83 22 1680863 (3), 8433553 (3), 16322790 (2), 8307776 (2) (see all 7)
    chondroitin sulfate 31.84 3 16322790 (1), 9088920 (1), 1388118 (1)
    dithiothreitol 11.82 1 8764158 (1)
    calcium 0.00 5 2191952 (3), 2119632 (1)
    zinc 0.00 1 8636109 (1)
    About this table


    (GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView,
    non coding RNAs according to RNAdb,
    ESTs according to GeneTide,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from Invitrogen, Millipore, and/or Abnova,
    siRNAs from Applied Biosystems, Sigma-Aldrich,
    shRNA from Sigma-Aldrich, OriGene,
    Tagged/untagged cDNA clones from OriGene,
    Expression Assays from Applied Biosystems)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (NID1)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (NID1)
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_002508

                  Sigma-Aldrich siRNA for NID1  
                         Sigma-Aldrich shRNA Panels and shRNA for NID1  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_002508  

    REFSEQ mRNAs for NID1 gene: 

    NM_002508.2   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_002508  

                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_002508
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_002508
                                     untagged cDNA clones in CMV expression vector (see all 2): BC012501 

    Additional cDNA sequence: 

    AB209448.1 AK091903.1 AK297234.1 BC045606.1 CR590230.1 CR609449.1 CR611614.1 M27445.1 
    M30269.1 

    5 DOTS entries:

    DT.95242319  DT.91711901  DT.91824076  DT.95077663  DT.95164677 

    24/360 AceView cDNA sequences (see all 360 ):

    BX281509 T47984 W70299 BM985308 AA303089 CD615010 CD615001 AA733037 
    AI139518 BM995513 BM974594 CF530096 BQ002869 AI336371 CR609449 BQ581313 
    AA045312 R58194 BE018553 AW069455 CA444631 D56097 AW338118 AI311537 

    highest scoring ESTs for NID1:

    M30269 AL710094 AL710104 BC045606 BG289659 CB988156 AA001935 AA044764 AA045312 AA045418 

    Unigene Cluster for NID1:

    Nidogen 1
    Hs.356624  [show with all ESTs]
    Unigene Representative Sequence: NM_002508


    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for NID1

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16a · 16b ^ 17 ^ 18 ^ 19 ^ 20a · 20b · 20c
    SP1:                                                                                                                                          
    SP2:                                                                                            -                                             
    SP3:                                                        -     -     -                                                                     

    About this scheme

    ECgene alternative splicing isoforms for NID1

    2 Ensembl transcripts including schematic representations:
    ENST00000264187  ENST00000366595  
    (Experimental results according to 1GeneNote and GNF BioGPS,
    probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
    Expression Assays from Applied Biosystems )
    About This Section

    NID1 expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for NID1

    1 / 2 / 3

    6 probe-sets matching NID1 gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
    35366_at2, 3 U95-A 1 1.00 1.00 1.00 1.00 M30269 1.00 1.00 1.00 1

    202007_at2, 3 U133-A 1 1.00 1.00 -- -- BF940043 0.60 1.00 0.82 1

    202008_s_at2, 3 U133-A 1 1.00 1.00 -- -- NM_002508 0.60 1.00 0.82 1

    202007_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

    202008_s_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

    1561082_at*2 U133Plus2 NULL 0.00 0.00 -- -- -- -- -- -- --
    GeneDecks  NID1 for binary patterns associated with the probe-sets selected above  
    About GeneDecksing
    About this table    
    Data from (Publications) and GNF BioGPS
        About these images
    About these images

    CGAP SAGE TAG: ATTTTGTATG

    SOURCE GeneReport for Unigene cluster: Hs.356624

    Expression variation in blood from EXPOLDB for NID1

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
    About This Section


    Orthologs for NID1 gene from 5/9 species (see all 9 )
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    NID11   -- nidogen 1 86.79(n)
    88.02(a)
    488958  XM_546076.2  XP_546076.2 
    chimpanzee
    (Pan troglodytes)
    NID11   -- nidogen 1 99.01(n)
    99.12(a)
    469718  XM_001156001.1  XP_001156001.1 
    cow
    (Bos taurus)
    NID11   -- nidogen 1 86.27(n)
    86.78(a)
    534319  XM_614049.3  XP_614049.2 
    rat
    (Rattus norvegicus)
    Nid11   -- nidogen 1 83.37(n)
    85.38(a)
    25494  XM_213954.4  XP_213954.4 
    mouse
    (Mus musculus)
    Nid11, 5 13 (7.00 cM)5
    nidogen 11, 5 83.65(n)1
    85.37(a)1
    180731  NM_010917.11  NP_035047.11 
     AK0416335  AK0848765  (see all 21)
    About this table        Species with no ortholog for NID1

    ENSEMBL Gene Tree for NID1
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

    Paralogs for NID1 gene
    SORL12  NID22  

    (According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
    About This Section


    10/697 NCBI SNPs in NID1 are shown (see all 697 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 210)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 1 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    rs107331331,2
    A,C,F,H234275396(+) TTCAAC/TTGATT 1 V/I mis112Minor allele frequency- N:0.00EA NA EU WA 1050
    rs32131901,2
    A,C,F,H234207797(-) CGAACA/GGAAAT 1 Q/R mis118Minor allele frequency- N:0.00CSAM EA EU WA NA 3246
    rs120935421,2
    A,C,F,H234295970(+) CGTTAC/ATTTGG 1 -- ng31 tfbs38Minor allele frequency- A:0.04EU EA WA 838
    rs10482531,2
    A,C,F,H234206889(-) CTGCTG/TGCACT 1 -- ut3111Minor allele frequency- T:0.42EA MN NA EU WA 2236
    rs37385311,2
    C,F,H234241950(+) CTTGGC/ATGGCA 1 H/Q mis1 ese312Minor allele frequency- A:0.14EU EA WA 1220
    rs168331831,2
    C,F,H234272063(+) CCAGAC/TGAGTG 1 R/H mis1 ese312Minor allele frequency- T:0.02NA EU EA WA 1038
    rs10483161,2
    A,C,F234206440(-) AAGGAA/GTCGAG 1 -- ut31 ese36Minor allele frequency- N:0.00EA MN NA 1886
    rs168331541,2
    C,F,H234268152(+) TCTGGC/TGGGAA 1 R/H mis1 ese37Minor allele frequency- T:0.00NA EU EA WA 548
    rs168330601,2
    C,F,H234220829(+) CGCCTT/CTGCTT 1 E/K mis112Minor allele frequency- C:0.01NA EU EA WA 1058
    --
    rs8731,2
    A,C,F234207362(-) TGAGCT/CGGGGC 1 -- ut31 ese35Minor allele frequency- C:0.42EA MN NA 1794
    About this table

    HapMap Linkage Disequilibrium images for NID1 (up to first 250kb)

    (in which this Gene is Involved, According to OMIM, UniProtKB, Novoseek, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
    About This Section

    OMIM: 131390

    10/16 Novoseek disease relationships for NID1 gene (see all 16 )

    Disease   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    glomerulonephritis 38.94 4 2067216 (1), 2119467 (1)
    carcinoma adenoid cystic 27.51 1 1315206 (1)
    choriocarcinoma 23.25 2 8433553 (1)
    prostate carcinoma 20.60 4 1527019 (2), 7823596 (1)
    nephritis 18.42 1 2119467 (1)
    renal disease 14.81 2 10571774 (1), 2067216 (1)
    liver fibrosis 11.80 1 11264572 (1)
    adenocarcinoma 5.83 1 1315206 (1)
    cancer 1.90 2 17328794 (1)
    tumors 0.82 4 2334137 (1), 7823596 (1), 15949695 (1), 1419059 (1)
    About this table

    (Possibly Related Articles in Doctor's Guide)
    About This Section

      --

    (in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
    About This Section

    10/146 PubMed articles for NID1 gene (see all 146 ):
    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section

     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)
    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, and/or H-InvDB)
    About This Section

    Entrez Gene: 4811 HGNC: 7821 AceView: NID Ensembl:ENSG00000116962 euGenes: HUgn4811
    ECgene: NID1 H-InvDB: NID1
    (According to HUGE)
    About This Section

      --
    (According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section

      --
    (Available from WIS Yeda, Salk, Tufts)
    About This Section

      --
    (Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
    Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
    Enzo Life Sciences, and/or Tocris Bioscience)
    About This Section



    Products for NID1:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



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     Predesigned and custom siRNAs for NID1 Antibodies for NID1
     Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
     Lentivirus-delivered shRNAs for NID1 Browse small molecules at Sigma-Aldrich
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