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NID2 nidogen 2 [ Homo sapiens (human) ]

Gene ID: 22795, updated on 23-Nov-2023

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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (52004809..52069059, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (46211853..46276147, complement)
105.20220307 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
  • 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. Nidogen-2: A new biomarker in colon cancer patients. Kiziltan R, et al. Ann Ital Chir, 2022. PMID 34593672
  2. 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
  3. Evaluation of NID2 promoter methylation for screening of Oral squamous cell carcinoma. Srisuttee R, et al. BMC Cancer, 2020 Mar 14. PMID 32171289, Free PMC Article
  4. NID2 can serve as a potential prognosis prediction biomarker and promotes the invasion and migration of gastric cancer. Yu ZH, et al. Pathol Res Pract, 2019 Oct. PMID 31362888
  5. Silencing NID2 by DNA Hypermethylation Promotes Lung Cancer. Wang J, et al. Pathol Oncol Res, 2020 Apr. PMID 30826972

See all (59) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Nidogen-2: A new biomarker in colon cancer patients.
    Title: Nidogen-2: A new biomarker in colon cancer patients.
  2. 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.
  3. 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.
  4. 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.
  5. Silencing NID2 by DNA Hypermethylation Promotes Lung Cancer.
    Title: Silencing NID2 by DNA Hypermethylation Promotes Lung Cancer.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. the serum NID2 levels show significant elevation in the ESCC patients and those with relatively high serum NID2 levels ( 32.6 mu mu g/L) are significantly associated with poor survival outcome compared with those with very low serum NID2 levels (< < 20.0 mu mu g/L).
    Title: Elevated levels of serum nidogen-2 in esophageal squamous cell carcinoma.
Submit: New GeneRIF Correction See all GeneRIFs (23)

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_2023_10

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

    UniProtKB/TrEMBL
    Q5CZI2

  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

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