NID2 nidogen 2 [Homo sapiens (human)] - Gene

Summary

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
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

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_000014.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Nidogen-2: A new biomarker in colon cancer patients.
Title: Nidogen-2: A new biomarker in colon cancer patients.
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.
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.
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.
Silencing NID2 by DNA Hypermethylation Promotes Lung Cancer.
Title: Silencing NID2 by DNA Hypermethylation Promotes Lung Cancer.
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.
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.
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.
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.
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

Go to the top of the page Help

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 EBI GWAS CatalogPubMed
Framingham Heart Study genome-wide association: results for pulmonary function measures. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

D14S713E (e-PCR)
- UniSTS:151586

D14S836 (e-PCR)
- UniSTS:21835

SHGC-132026 (e-PCR)
- UniSTS:170608

NID2_9269 (e-PCR)
- UniSTS:468094

HUM0S17C09 (e-PCR)
- UniSTS:5265

D14S1201 (e-PCR)
- UniSTS:78514

D14S1197 (e-PCR)
- UniSTS:37317

D14S1018 (e-PCR), detects polymorphism
- UniSTS:46307

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 more info	PubMed
located_in collagen-containing extracellular matrix	HDA more info	PubMed
located_in extracellular exosome	HDA more info	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

Go to the top of the page Help

Preferred Names: nidogen-2

Names: osteonidogen

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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)

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

NC_000014.9 Reference GRCh38.p14 Primary Assembly

Range

52004809..52069059 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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