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NID1 nidogen 1 [ Homo sapiens (human) ]

Gene ID: 4811, updated on 7-Dec-2018

Summary

Official Symbol
NID1provided by HGNC
Official Full Name
nidogen 1provided by HGNC
Primary source
HGNC:HGNC:7821
See related
Ensembl:ENSG00000116962 MIM:131390
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

Genomic context

See NID1 in Genome Data Viewer
Location:
1q42.3
Exon count:
20
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (235975830..236065181, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (236139130..236228481, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373215 Neighboring gene uncharacterized LOC105373212 Neighboring gene RNA, U6 small nuclear 968, pseudogene Neighboring gene meiotic recombination hotspot NID3 Neighboring gene meiotic recombination hotspot NID2 Neighboring gene meiotic recombination hotspot NID1 Neighboring gene MS32 minisatellite repeat instability region Neighboring gene aconitase 2, mitochondrial pseudogene

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association study identifies nidogen 1 (NID1) as a susceptibility locus to cutaneous nevi and melanoma risk.
NHGRI GWA Catalog

Pathways from BioSystems

  • Degradation of the extracellular matrix, organism-specific biosystem (from REACTOME)
    Degradation of the extracellular matrix, organism-specific biosystemMatrix metalloproteinases (MMPs), previously referred to as matrixins because of their role in degradation of the extracellular matrix (ECM), are zinc and calcium dependent proteases belonging to the...
  • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
    Extracellular matrix organization, organism-specific biosystemThe extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin and associated-microfibrils, fibronectin and laminins embedded...
  • Laminin interactions, organism-specific biosystem (from REACTOME)
    Laminin interactions, organism-specific biosystemLaminins are a large family of conserved, multidomain trimeric basement membrane proteins. There are many theoretical trimer combinations but only 18 have been described (Domogatskaya et al. 2012, Mi...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
collagen binding IDA
Inferred from Direct Assay
more info
PubMed 
extracellular matrix structural constituent HDA PubMed 
extracellular matrix structural constituent ISS
Inferred from Sequence or Structural Similarity
more info
 
laminin binding IDA
Inferred from Direct Assay
more info
PubMed 
laminin-1 binding IEA
Inferred from Electronic Annotation
more info
 
proteoglycan binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
basement membrane organization TAS
Traceable Author Statement
more info
PubMed 
cell-matrix adhesion IEA
Inferred from Electronic Annotation
more info
 
extracellular matrix organization TAS
Traceable Author Statement
more info
 
glomerular basement membrane development IEA
Inferred from Electronic Annotation
more info
 
positive regulation of cell-substrate adhesion IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
nidogen-1
Names
NID-1
enactin
entactin
epididymis secretory sperm binding protein

NCBI Reference Sequences (RefSeq)

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

  1. NG_033228.1 RefSeqGene

    Range
    5001..94352
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_002508.3NP_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
    Related
    ENSP00000264187.6, ENST00000264187.6
    Conserved Domains (8) summary
    smart00135
    Location:10141055
    LY; Low-density lipoprotein-receptor YWTD domain
    smart00179
    Location:710751
    EGF_CA; Calcium-binding EGF-like domain
    smart00539
    Location:106269
    NIDO; Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins
    cd00255
    Location:429660
    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:9921029
    Ldl_recept_b; Low-density lipoprotein receptor repeat class B
    pfam00086
    Location:849919
    Thyroglobulin_1; Thyroglobulin type-1 repeat
    pfam12947
    Location:811839
    EGF_3; EGF domain
    pfam14670
    Location:12121236
    FXa_inhibition; Coagulation Factor Xa inhibitory site

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    235975830..236065181 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011544195.3XP_011542497.1  nidogen-1 isoform X1

    Related
    ENSP00000355554.3, ENST00000366595.7
    Conserved Domains (7) summary
    smart00135
    Location:9721013
    LY; Low-density lipoprotein-receptor YWTD domain
    smart00539
    Location:106269
    NIDO; Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins
    cd00255
    Location:429660
    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:950987
    Ldl_recept_b; Low-density lipoprotein receptor repeat class B
    pfam00086
    Location:807877
    Thyroglobulin_1; Thyroglobulin type-1 repeat
    pfam12947
    Location:769797
    EGF_3; EGF domain
    pfam14670
    Location:11701200
    FXa_inhibition; Coagulation Factor Xa inhibitory site
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