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    NID2 nidogen 2 [ Homo sapiens (human) ]

    Gene ID: 22795, updated on 2-Nov-2024

    Summary

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    Official Symbol
    NID2provided by HGNC
    Official Full Name
    nidogen 2provided by HGNC
    Primary source
    HGNC:HGNC:13389
    See related
    Ensembl:ENSG00000087303 MIM:605399; AllianceGenome:HGNC:13389
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NID-2
    Summary
    This gene encodes a member of the nidogen family of basement membrane proteins. This protein is a cell-adhesion protein that binds collagens I and IV and laminin and may be involved in maintaining the structure of the basement membrane.[provided by RefSeq, Jun 2010]
    Expression
    Broad expression in placenta (RPKM 30.5), thyroid (RPKM 21.7) and 16 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See NID2 in Genome Data Viewer
    Location:
    14q22.1
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (52004809..52069059, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (46211853..46276147, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (52471527..52535777, complement)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene G protein subunit gamma 2 Neighboring gene uncharacterized LOC102723604 Neighboring gene uncharacterized LOC105370497 Neighboring gene Sharpr-MPRA regulatory region 5932 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8385 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:52480482-52481434 Neighboring gene RNA transcription, translation and transport factor Neighboring gene Sharpr-MPRA regulatory region 12958 Neighboring gene uncharacterized LOC105378180 Neighboring gene CAGE-defined high expression enhancer upstream of NID2 Neighboring gene long intergenic non-protein coding RNA 2319 Neighboring gene cytochrome c oxidase subunit 5A pseudogene 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Elevated levels of serum nidogen-2 in esophageal squamous cell carcinoma. Chai AWY, et al. Cancer Biomark, 2018 Feb 14. PMID 29278876
    2. Nidogen-2: a new serum biomarker for ovarian cancer. Kuk C, et al. Clin Biochem, 2010 Mar. PMID 19883638, Free PMC Article
    3. Nidogen-2: A new biomarker in colon cancer patients. Kiziltan R, et al. Ann Ital Chir, 2022. PMID 34593672
    4. Nidogen-2 Maintains the Contractile Phenotype of Vascular Smooth Muscle Cells and Prevents Neointima Formation via Bridging Jagged1-Notch3 Signaling. Mao C, et al. Circulation, 2021 Oct 12. PMID 34315224
    5. Epithelial basement membrane proteins perlecan and nidogen-2 are up-regulated in stromal cells after epithelial injury in human corneas. Torricelli AA, et al. Exp Eye Res, 2015 May. PMID 25797478, Free PMC Article

    See all (60) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Association of NID2 SNPs with Glioma Risk and Prognosis in the Chinese Population.
      Title: Association of NID2 SNPs with Glioma Risk and Prognosis in the Chinese Population.
    2. Nidogen-2: A new biomarker in colon cancer patients.
      Title: Nidogen-2: A new biomarker in colon cancer patients.
    3. Nidogen-2 Maintains the Contractile Phenotype of Vascular Smooth Muscle Cells and Prevents Neointima Formation via Bridging Jagged1-Notch3 Signaling.
      Title: Nidogen-2 Maintains the Contractile Phenotype of Vascular Smooth Muscle Cells and Prevents Neointima Formation via Bridging Jagged1-Notch3 Signaling.
    4. A pilot proteomic study with a prospective cohort suspected to develop preeclampsia.
      Title: A pilot proteomic study with a prospective cohort suspected to develop preeclampsia.
    5. Genome-Scale Analysis Identified NID2, SPARC, and MFAP2 as Prognosis Markers of Overall Survival in Gastric Cancer.
      Title: Genome-Scale Analysis Identified NID2, SPARC, and MFAP2 as Prognosis Markers of Overall Survival in Gastric Cancer.
    6. Silencing NID2 by DNA Hypermethylation Promotes Lung Cancer.
      Title: Silencing NID2 by DNA Hypermethylation Promotes Lung Cancer.
    7. Evaluation of NID2 promoter methylation for screening of Oral squamous cell carcinoma.
      Title: Evaluation of NID2 promoter methylation for screening of Oral squamous cell carcinoma.
    8. Our study demonstrates that up-regulated NID2 plays an important role in promoting the invasion and migration of gastric cancer cells and has a potential of being a novel biomarker for diagnosis, treatment and prognosis of gastric cancer in the future.
      Title: NID2 can serve as a potential prognosis prediction biomarker and promotes the invasion and migration of gastric cancer.
    9. Our results indicated that NID2, COL4A1 and COL4A2 could be the potential novel biomarkers for gastric cancer diagnosis prognosis and the promising therapeutic targets
      Title: Integrated bioinformatics analysis reveals novel key biomarkers and potential candidate small molecule drugs in gastric cancer.
    10. High NID2 methylation is associated with non-small cell lung cancer.
      Title: The more potential performance of nidogen 2 methylation by tissue or plasma DNA over brichoalveolar lavage DNA in diagnosis of nonsmall cell lung cancer.
    Submit: New GeneRIF Correction See all GeneRIFs (24)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    A genome-wide gene-environment interaction analysis for tobacco smoke and lung cancer susceptibility.
    EBI GWAS Catalog
    Framingham Heart Study genome-wide association: results for pulmonary function measures.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables collagen binding TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables extracellular matrix structural constituent ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables extracellular matrix structural constituent RCA
    inferred from Reviewed Computational Analysis
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in basement membrane organization TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in cell adhesion TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in cell-matrix adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in basement membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in basement membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    colocalizes_with collagen-containing extracellular matrix HDA PubMed 
    located_in collagen-containing extracellular matrix HDA PubMed 
    located_in extracellular exosome HDA PubMed 
    located_in extracellular region TAS
    Traceable Author Statement
    more info
    		  
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    nidogen-2
    Names
    osteonidogen

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_007361.4 → NP_031387.3  nidogen-2 precursor

      See identical proteins and their annotated locations for NP_031387.3

      Status: REVIEWED

      Source sequence(s)
      AJ223500, AL118557, BM719690, CA413165
      Consensus CDS
      CCDS9706.1
      UniProtKB/Swiss-Prot
      A8K6I7, B4DU19, O43710, Q14112
      UniProtKB/TrEMBL
      Q5CZI2
      Related
      ENSP00000216286.4, ENST00000216286.10
      Conserved Domains (6) summary
      smart00135
      Location:1221 → 1265
      LY; Low-density lipoprotein-receptor YWTD domain
      smart00179
      Location:801 → 843
      EGF_CA; Calcium-binding EGF-like domain
      smart00539
      Location:108 → 273
      NIDO; Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins
      smart00682
      Location:525 → 757
      G2F; G2 nidogen domain and fibulin
      cd00191
      Location:939 → 1005
      TY; Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases
      pfam12947
      Location:896 → 929
      EGF_3; EGF domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      52004809..52069059 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005267407.5 → XP_005267464.1  nidogen-2 isoform X3

      UniProtKB/TrEMBL
      Q5CZI2
      Conserved Domains (6) summary
      smart00135
      Location:1173 → 1217
      LY; Low-density lipoprotein-receptor YWTD domain
      smart00179
      Location:801 → 843
      EGF_CA; Calcium-binding EGF-like domain
      smart00539
      Location:108 → 273
      NIDO; Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins
      smart00682
      Location:525 → 757
      G2F; G2 nidogen domain and fibulin
      cd00191
      Location:891 → 957
      TY; Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases
      pfam12947
      Location:848 → 881
      EGF_3; EGF domain

    2. XM_005267406.5 → XP_005267463.1  nidogen-2 isoform X2

      Conserved Domains (6) summary
      smart00135
      Location:1200 → 1244
      LY; Low-density lipoprotein-receptor YWTD domain
      smart00179
      Location:828 → 870
      EGF_CA; Calcium-binding EGF-like domain
      smart00539
      Location:108 → 273
      NIDO; Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins
      smart00682
      Location:552 → 784
      G2F; G2 nidogen domain and fibulin
      cd00191
      Location:918 → 984
      TY; Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases
      pfam12947
      Location:875 → 908
      EGF_3; EGF domain

    3. XM_005267405.5 → XP_005267462.1  nidogen-2 isoform X1

      Conserved Domains (6) summary
      smart00135
      Location:1248 → 1292
      LY; Low-density lipoprotein-receptor YWTD domain
      smart00179
      Location:828 → 870
      EGF_CA; Calcium-binding EGF-like domain
      smart00539
      Location:108 → 273
      NIDO; Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins
      smart00682
      Location:552 → 784
      G2F; G2 nidogen domain and fibulin
      cd00191
      Location:966 → 1032
      TY; Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases
      pfam12947
      Location:923 → 956
      EGF_3; EGF domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      46211853..46276147 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054375571.1 → XP_054231546.1  nidogen-2 isoform X3

    2. XM_054375570.1 → XP_054231545.1  nidogen-2 isoform X2

    3. XM_054375569.1 → XP_054231544.1  nidogen-2 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q14112.3 GenPept UniProtKB/Swiss-Prot:Q14112

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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