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Aliases for NID1 Gene

Aliases for NID1 Gene

  • Nidogen 1 2 3 5
  • Entactin 3 4
  • NID-1 3 4
  • NID 3 4
  • Nidogen (Enactin) 2
  • Nidogen-1 3
  • Enactin 3

External Ids for NID1 Gene

Previous HGNC Symbols for NID1 Gene

  • NID

Previous GeneCards Identifiers for NID1 Gene

  • GC01M232466
  • GC01M234205
  • GC01M236139
  • GC01M206590

Summaries for NID1 Gene

Entrez Gene Summary for NID1 Gene

  • 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]

GeneCards Summary for NID1 Gene

NID1 (Nidogen 1) is a Protein Coding gene. Diseases associated with NID1 include Neuronal Intestinal Dysplasia and Keratopathy. Among its related pathways are Degradation of the extracellular matrix and MET promotes cell motility. GO annotations related to this gene include calcium ion binding and laminin binding. An important paralog of this gene is NID2.

UniProtKB/Swiss-Prot for NID1 Gene

  • Sulfated glycoprotein widely distributed in basement membranes and tightly associated with laminin. Also binds to collagen IV and perlecan. It probably has a role in cell-extracellular matrix interactions.

Gene Wiki entry for NID1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NID1 Gene

Genomics for NID1 Gene

Regulatory Elements for NID1 Gene

Enhancers for NID1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01G236039 1.2 ENCODE dbSUPER 17.7 +25.1 25117 1.1 FOXA2 MLX ARID4B DMAP1 YY1 SP5 MXD4 MIER2 PPARG KAT8 NID1 ENSG00000252822 RNU5E-2P LOC105373212
GH01G236008 1.2 Ensembl ENCODE dbSUPER 16.2 +55.1 55106 2.2 CTCF JUN CEBPB EP300 ZBTB40 NR2F2 ZKSCAN1 JUND PRDM6 ZNF366 NID1 ENSG00000252822 LOC105373212
GH01G235983 1.6 FANTOM5 Ensembl ENCODE dbSUPER 11.2 +80.6 80604 3.1 KLF1 JUN RAD21 ZIC2 ZBTB48 GATA2 POLR2A SCRT2 FOS MAFK ENSG00000252822 NID1 RNU5E-2P GNG4 ENSG00000229291 GPR137B LOC105373212
GH01G236017 1 Ensembl ENCODE 15.5 +45.1 45101 4.6 MAX ZBTB40 RAD21 YY1 POLR2A HNF4G FOS HLF ZBED1 FOXA1 NID1 ENSG00000252822 LYST LOC105373212
GH01G236014 0.8 FANTOM5 ENCODE 16.8 +49.2 49217 2.6 ESRRA ZNF362 SCRT2 ZNF384 NR2F2 NID1 ENSG00000252822 LYST LOC105373212
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around NID1 on UCSC Golden Path with GeneCards custom track

Promoters for NID1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000022339 680 1800 HDGF MLX ARID4B DMAP1 ZNF2 YY1 SLC30A9 ZNF263 SP3 SP5

Genomic Location for NID1 Gene

Chromosome:
1
Start:
235,975,830 bp from pter
End:
236,065,181 bp from pter
Size:
89,352 bases
Orientation:
Minus strand

Genomic View for NID1 Gene

Genes around NID1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NID1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NID1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NID1 Gene

Proteins for NID1 Gene

  • Protein details for NID1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P14543-NID1_HUMAN
    Recommended name:
    Nidogen-1
    Protein Accession:
    P14543
    Secondary Accessions:
    • Q14942
    • Q59FL2
    • Q5TAF2
    • Q5TAF3
    • Q86XD7

    Protein attributes for NID1 Gene

    Size:
    1247 amino acids
    Molecular mass:
    136377 Da
    Quaternary structure:
    • Interacts with FBLN1 and LGALS3BP (By similarity). Interacts with PLXDC1.

    Three dimensional structures from OCA and Proteopedia for NID1 Gene

    Alternative splice isoforms for NID1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NID1 Gene

Post-translational modifications for NID1 Gene

  • N- and O-glycosylated.
  • Glycosylation at posLast=310310, Thr311, posLast=327327, posLast=333333, posLast=339339, posLast=347347, and Thr935
  • Modification sites at PhosphoSitePlus

Other Protein References for NID1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • R&D Systems Antibodies for NID1 (Nidogen-1/Entactin)

No data available for DME Specific Peptides for NID1 Gene

Domains & Families for NID1 Gene

No data available for Gene Families and UniProtKB/Swiss-Prot for NID1 Gene

Function for NID1 Gene

Molecular function for NID1 Gene

UniProtKB/Swiss-Prot Function:
Sulfated glycoprotein widely distributed in basement membranes and tightly associated with laminin. Also binds to collagen IV and perlecan. It probably has a role in cell-extracellular matrix interactions.

Gene Ontology (GO) - Molecular Function for NID1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
GO:0005518 collagen binding IDA 22952693
GO:0043236 laminin binding IDA 22952693
GO:0043237 laminin-1 binding IEA --
GO:0043394 proteoglycan binding IPI 22952693
genes like me logo Genes that share ontologies with NID1: view
genes like me logo Genes that share phenotypes with NID1: view

Animal Models for NID1 Gene

MGI Knock Outs for NID1:

Animal Model Products

  • Taconic Biosciences Mouse Models for NID1

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for NID1

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for NID1 Gene

Localization for NID1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NID1 Gene

Secreted, extracellular space, extracellular matrix, basement membrane.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for NID1 gene
Compartment Confidence
extracellular 5
plasma membrane 3
cytoskeleton 1
mitochondrion 1
nucleus 1
cytosol 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for NID1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005578 proteinaceous extracellular matrix IEA --
GO:0005604 basement membrane IDA 22952693
GO:0005605 basal lamina IEA --
GO:0005615 extracellular space IEA --
genes like me logo Genes that share ontologies with NID1: view

Pathways & Interactions for NID1 Gene

genes like me logo Genes that share pathways with NID1: view

Pathways by source for NID1 Gene

1 GeneGo (Thomson Reuters) pathway for NID1 Gene

Gene Ontology (GO) - Biological Process for NID1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA --
GO:0007160 cell-matrix adhesion IEA --
GO:0010811 positive regulation of cell-substrate adhesion IEA --
GO:0022617 extracellular matrix disassembly TAS --
GO:0030198 extracellular matrix organization TAS --
genes like me logo Genes that share ontologies with NID1: view

No data available for SIGNOR curated interactions for NID1 Gene

Drugs & Compounds for NID1 Gene

(7) Drugs for NID1 Gene - From: DrugBank and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Urokinase Approved, Investigational, Withdrawn Pharma Target 0

(7) Additional Compounds for NID1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with NID1: view

Transcripts for NID1 Gene

mRNA/cDNA for NID1 Gene

Unigene Clusters for NID1 Gene

Nidogen 1:
Representative Sequences:

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for NID1

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for NID1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16a · 16b ^ 17 ^ 18 ^ 19 ^ 20a · 20b · 20c
SP1:
SP2: -
SP3: - - -

Relevant External Links for NID1 Gene

GeneLoc Exon Structure for
NID1
ECgene alternative splicing isoforms for
NID1

Expression for NID1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NID1 Gene

Protein differential expression in normal tissues from HIPED for NID1 Gene

This gene is overexpressed in Adipocyte (13.7), Urinary Bladder (8.7), and Gallbladder (8.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for NID1 Gene



Protein tissue co-expression partners for NID1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of NID1 Gene:

NID1

SOURCE GeneReport for Unigene cluster for NID1 Gene:

Hs.356624

Evidence on tissue expression from TISSUES for NID1 Gene

  • Nervous system(4.7)
  • Liver(4.5)
  • Pancreas(4.2)
  • Heart(3.5)
  • Lung(3.1)
  • Kidney(3)
  • Eye(2.7)
  • Intestine(2.7)
  • Blood(2.6)
  • Gall bladder(2.6)
  • Muscle(2.3)
  • Skin(2.2)
genes like me logo Genes that share expression patterns with NID1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for NID1 Gene

Orthologs for NID1 Gene

This gene was present in the common ancestor of animals.

Orthologs for NID1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NID1 34 35
  • 99.01 (n)
dog
(Canis familiaris)
Mammalia NID1 34 35
  • 86.79 (n)
cow
(Bos Taurus)
Mammalia NID1 34 35
  • 86.27 (n)
mouse
(Mus musculus)
Mammalia Nid1 34 16 35
  • 83.56 (n)
rat
(Rattus norvegicus)
Mammalia Nid1 34
  • 83.04 (n)
oppossum
(Monodelphis domestica)
Mammalia NID1 35
  • 79 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia NID1 35
  • 61 (a)
OneToOne
chicken
(Gallus gallus)
Aves NID1 34 35
  • 67.96 (n)
lizard
(Anolis carolinensis)
Reptilia NID1 35
  • 57 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nid1 34
  • 63 (n)
zebrafish
(Danio rerio)
Actinopterygii nid1a 34 35
  • 57.65 (n)
NID1 (1 of 2) 35
  • 49 (a)
OneToMany
mgbb01h02 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9665 34
fruit fly
(Drosophila melanogaster)
Insecta Ndg 35
  • 26 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea nid-1 35
  • 22 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3675 35
  • 44 (a)
OneToMany
Species where no ortholog for NID1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for NID1 Gene

ENSEMBL:
Gene Tree for NID1 (if available)
TreeFam:
Gene Tree for NID1 (if available)

Paralogs for NID1 Gene

Paralogs for NID1 Gene

(2) SIMAP similar genes for NID1 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with NID1: view

Variants for NID1 Gene

Sequence variations from dbSNP and Humsavar for NID1 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
VAR_035835 A colorectal cancer sample
rs730882225 Likely pathogenic 235,980,495(-) TGCAG(A/G)TGATG splice-donor-variant
rs147665041 Uncertain significance 235,993,850(+) TCGTG(C/G)TGGCA reference, missense
rs397515471 Uncertain significance 236,038,227(-) CCCGC(C/T)AGACG reference, stop-gained
rs869312945 Uncertain significance 236,029,648(-) CCTGA(C/T)CATCG reference, missense

Structural Variations from Database of Genomic Variants (DGV) for NID1 Gene

Variant ID Type Subtype PubMed ID
esv2725363 CNV deletion 23290073
esv2725374 CNV deletion 23290073
esv3589203 CNV loss 21293372
esv3589204 CNV gain 21293372
esv9322 CNV gain 19470904
nsv1005877 CNV gain 25217958
nsv1012436 CNV loss 25217958
nsv1121448 CNV deletion 24896259
nsv509679 CNV insertion 20534489
nsv549394 CNV gain 21841781
nsv832958 CNV loss 17160897
nsv953997 CNV deletion 24416366

Variation tolerance for NID1 Gene

Residual Variation Intolerance Score: 89.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 14.25; 96.24% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for NID1 Gene

Human Gene Mutation Database (HGMD)
NID1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NID1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NID1 Gene

Disorders for NID1 Gene

MalaCards: The human disease database

(8) MalaCards diseases for NID1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
neuronal intestinal dysplasia
keratopathy
goodpasture syndrome
  • anti-glomerular basement membrane disease
mucocutaneous leishmaniasis
  • american cutaneous leishmaniasis
laurence-moon syndrome
  • laurence-moon-biedl syndrome
- elite association - COSMIC cancer census association via MalaCards
Search NID1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for NID1

Genetic Association Database (GAD)
NID1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
NID1
genes like me logo Genes that share disorders with NID1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NID1 Gene

Publications for NID1 Gene

  1. Genomic sequences and structural organization of the human nidogen gene (NID). (PMID: 7557988) Zimmermann K. … Nischt R. (Genomics 1995) 2 3 4 22 64
  2. Human nidogen: cDNA cloning, cellular expression, and mapping of the gene to chromosome 1q43. (PMID: 2471408) Olsen D.R. … Uitto J. (Am. J. Hum. Genet. 1989) 2 3 4 64
  3. Genome-wide association study identifies nidogen 1 (NID1) as a susceptibility locus to cutaneous nevi and melanoma risk. (PMID: 21478494) Nan H. … Han J. (Hum. Mol. Genet. 2011) 3 46 64
  4. Nidogen 1 and 2 gene promoters are aberrantly methylated in human gastrointestinal cancer. (PMID: 17328794) Ulazzi L. … Negrini M. (Mol. Cancer 2007) 3 22 64
  5. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory S.G. … Bentley D.R. (Nature 2006) 3 4 64

Products for NID1 Gene

Sources for NID1 Gene

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