NID1 nidogen 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NID1provided by HGNC
Official Full Name: nidogen 1provided by HGNC
Primary source: HGNC:HGNC:7821
See related: Ensembl:ENSG00000116962 MIM:131390; AllianceGenome:HGNC:7821
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
Summary: 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, Jul 2008]
Expression: Broad expression in placenta (RPKM 93.1), gall bladder (RPKM 48.2) and 20 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1q42.3

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (235975830..236065090, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (235372074..235461403, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (236139130..236228390, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Obesity impairs skeletal muscle repair through NID-1 mediated extracellular matrix remodeling by mesenchymal progenitors.
Title: Obesity impairs skeletal muscle repair through NID-1 mediated extracellular matrix remodeling by mesenchymal progenitors.
Human Cytomegalovirus Utilizes Multiple Viral Proteins to Regulate the Basement Membrane Protein Nidogen 1.
Title: Human Cytomegalovirus Utilizes Multiple Viral Proteins to Regulate the Basement Membrane Protein Nidogen 1.
Nidogen-1 could play a role in diabetic kidney disease development in type 2 diabetes: a genome-wide association meta-analysis.
Title: Nidogen-1 could play a role in diabetic kidney disease development in type 2 diabetes: a genome-wide association meta-analysis.
Loss of enteric neuronal Ndrg4 promotes colorectal cancer via increased release of Nid1 and Fbln2.
Title: Loss of enteric neuronal Ndrg4 promotes colorectal cancer via increased release of Nid1 and Fbln2.
Nidogen-1 expression is associated with overall survival and temozolomide sensitivity in low-grade glioma patients.
Title: Nidogen-1 expression is associated with overall survival and temozolomide sensitivity in low-grade glioma patients.
MicroRNA-1298-3p inhibits proliferation and invasion of glioma cells by downregulating Nidogen-1.
Title: MicroRNA-1298-3p inhibits proliferation and invasion of glioma cells by downregulating Nidogen-1.
Increased NID1 Expression among Breast Cancer Lung Metastatic Women; A Comparative Analysis between Naive and Treated Cases.
Title: Increased NID1 Expression among Breast Cancer Lung Metastatic Women; A Comparative Analysis between Naive and Treated Cases.
Results showed that NID1 level in oral cavity squamous cell carcinoma (OSCC) tissues was increased compared with adjacent noncancerous epithelium. Importantly, the elevated NID1 level was correlated with the advanced stages of OSCC, as well as the poor survival of OSCC patients.
Title: Proteomic Profiling of Paired Interstitial Fluids Reveals Dysregulated Pathways and Salivary NID1 as a Biomarker of Oral Cavity Squamous Cell Carcinoma.
Nidogen-1 Contributes to the Interaction Network Involved in Pro-B Cell Retention in the Peri-sinusoidal Hematopoietic Stem Cell Niche.
Title: Nidogen-1 Contributes to the Interaction Network Involved in Pro-B Cell Retention in the Peri-sinusoidal Hematopoietic Stem Cell Niche.
This case report provides further evidence that variants in NID1 may be clinically relevant for the development of a phenotype that is consistent with ADDWOC, and extends the phenotype of NID1-associated ADDWOC to include arachnoid cysts.
Title: NID1 variant associated with occipital cephaloceles in a family expressing a spectrum of phenotypes.

Submit: New GeneRIF Correction See all GeneRIFs (25)

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
Genome-wide association study identifies nidogen 1 (NID1) as a susceptibility locus to cutaneous nevi and melanoma risk. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AL009616 (e-PCR)
- UniSTS:13830

CTC-USP-BR001 (e-PCR)
- UniSTS:240951

NID_V232 (e-PCR)
- UniSTS:462911

NID_942.2 (e-PCR)
- UniSTS:462911

G20558 (e-PCR)
- UniSTS:24912

A005W43 (e-PCR)
- UniSTS:24913

SHGC-141812 (e-PCR)
- UniSTS:171091

RH122964 (e-PCR)
- UniSTS:135261

SHGC-76550 (e-PCR)
- UniSTS:67185

D1S2389 (e-PCR)
- UniSTS:31413

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables Wnt receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables Wnt-protein binding	IBA Inferred from Biological aspect of Ancestor more info
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables collagen binding	IDA Inferred from Direct Assay 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 laminin binding	IDA Inferred from Direct Assay more info	PubMed
enables laminin-1 binding	IEA Inferred from Electronic Annotation more info
enables proteoglycan 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 canonical Wnt signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell-matrix adhesion	IEA Inferred from Electronic Annotation more info
involved_in glomerular basement membrane development	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of cell adhesion	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of cell-substrate adhesion	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of integrin-mediated signaling pathway	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of muscle cell differentiation	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of basement membrane organization	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in basement membrane	IDA Inferred from Direct Assay more info	PubMed
located_in basement membrane	NAS Non-traceable Author Statement more info	PubMed
colocalizes_with collagen-containing extracellular matrix	HDA more info	PubMed
located_in collagen-containing extracellular matrix	HDA more info	PubMed
colocalizes_with collagen-containing extracellular matrix	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in extracellular exosome	HDA more info	PubMed
located_in extracellular region	TAS Traceable Author Statement more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
part_of protein complex involved in cell-matrix adhesion	NAS Non-traceable Author Statement more info	PubMed

General protein information

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Preferred Names: nidogen-1

Names: NID-1; enactin; entactin; epididymis secretory sperm binding protein

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.

Genomic

NG_033228.1 RefSeqGene

Range

5092..94352

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_002508.3 → NP_002499.2 nidogen-1 precursor

See identical proteins and their annotated locations for NP_002499.2

Status: REVIEWED

Source sequence(s)

AL122018, AL139161, BQ549657, CN267119, DA269707, M30269

Consensus CDS

CCDS1608.1

UniProtKB/Swiss-Prot

P14543, Q14942, Q59FL2, Q5TAF2, Q5TAF3, Q86XD7

UniProtKB/TrEMBL

A0A384MR25

Related

ENSP00000264187.6, ENST00000264187.7

Conserved Domains (8) summary

smart00135
Location:1014 → 1055

LY; Low-density lipoprotein-receptor YWTD domain

smart00179
Location:710 → 751

EGF_CA; Calcium-binding EGF-like domain

smart00539
Location:106 → 269

NIDO; Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins

cd00255
Location:429 → 660

nidG2; Nidogen, G2 domain; Nidogen is an important component of the basement membrane, an extracellular sheet-like matrix. Nidogen is a multifunctional protein that interacts with many other basement membrane proteins, like collagen, perlecan, lamin, and has a ...

pfam00058
Location:992 → 1029

Ldl_recept_b; Low-density lipoprotein receptor repeat class B

pfam00086
Location:849 → 919

Thyroglobulin_1; Thyroglobulin type-1 repeat

pfam12947
Location:811 → 839

EGF_3; EGF domain

pfam14670
Location:1212 → 1236

FXa_inhibition; Coagulation Factor Xa inhibitory site