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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 Goodpasture Syndrome. Among its related pathways are Cell adhesion_ECM remodeling and Degradation of the extracellular matrix. Gene Ontology (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

Additional gene information 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

GeneHancer (GH) Regulatory Elements for NID1 Gene

Promoters and enhancers for NID1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J236062 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 655.4 -0.8 -750 6.3 HDGF PKNOX1 FOXA2 MLX ARID4B DMAP1 ZNF2 IRF4 YY1 SLC30A9 NID1 GC01P236064 ARID4B ENSG00000273058 GGPS1 ENSG00000230325 HEATR1 RPS21P1 MTR LYST
GH01J236039 Enhancer 1.1 ENCODE dbSUPER 17.6 +25.1 25117 1.1 FOXA2 MLX ARID4B DMAP1 ETS1 YY1 NFKBIZ RXRA SP5 MXD4 NID1 ENSG00000252822 RNU5E-2P LOC105373212
GH01J236008 Enhancer 1 Ensembl ENCODE dbSUPER 16.2 +55.1 55105 2.2 JUN CEBPB EP300 ZBTB40 NR2F2 ZKSCAN1 SP1 MAFF JUND POLR2A NID1 ENSG00000252822 LOC105373212
GH01J236516 Enhancer 1.3 Ensembl ENCODE dbSUPER 12.4 -452.6 -452585 2.3 FOXA2 ZNF133 FEZF1 ZNF2 MCM3 SP5 MCM5 REST PPARG NFIL3 LGALS8 HEATR1 ENSG00000230325 ENSG00000273058 MTR NID1 RPL35P1 LDHAP2 GC01P236501
GH01J236017 Enhancer 0.9 Ensembl ENCODE 15.5 +45.1 45100 4.6 FOXA2 MAX RAD21 YY1 GATA3 EGR1 POLR2A HNF4G RXRA HLF NID1 ENSG00000252822 LYST LOC105373212
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NID1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NID1 gene promoter:
  • MEF-2A
  • aMEF-2
  • HNF-4alpha2
  • HNF-4alpha1
  • SRY
  • GATA-3
  • LCR-F1
  • HEN1
  • Pax-5

Genomic Locations for NID1 Gene

Genomic Locations for NID1 Gene
chr1:235,975,830-236,065,181
(GRCh38/hg38)
Size:
89,352 bases
Orientation:
Minus strand
chr1:236,139,130-236,228,481
(GRCh37/hg19)
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 isoforms=2935, Thr347, Thr339, Ser333, Ser327, isoforms=2311, and isoforms=2310
  • Modification sites at PhosphoSitePlus

Other Protein References for NID1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for NID1 Gene

Domains & Families for NID1 Gene

Gene Families for NID1 Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted secreted proteins

Suggested Antigen Peptide Sequences for NID1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

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

No data available for 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.

Phenotypes From GWAS Catalog for NID1 Gene

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 IEA,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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NID1

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:0005604 basement membrane IDA 22952693
GO:0005605 basal lamina IEA --
GO:0005615 extracellular space IEA --
GO:0031012 colocalizes_with extracellular matrix ISS 22261194
genes like me logo Genes that share ontologies with NID1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for NID1 Gene

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 IEA,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

(2) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(360) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for NID1 Gene

Nidogen 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NID1

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, 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(2.4)
  • Skin(2.2)
genes like me logo Genes that share expression patterns with NID1: view

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 33
  • 99.01 (n)
OneToOne
dog
(Canis familiaris)
Mammalia NID1 34 33
  • 86.79 (n)
OneToOne
cow
(Bos Taurus)
Mammalia NID1 34 33
  • 86.27 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Nid1 16 34 33
  • 83.56 (n)
rat
(Rattus norvegicus)
Mammalia Nid1 33
  • 83.04 (n)
oppossum
(Monodelphis domestica)
Mammalia NID1 34
  • 79 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia NID1 34
  • 61 (a)
OneToOne
chicken
(Gallus gallus)
Aves NID1 34 33
  • 67.96 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NID1 34
  • 57 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nid1 33
  • 63 (n)
zebrafish
(Danio rerio)
Actinopterygii nid1a 34 33
  • 57.65 (n)
OneToMany
NID1 (1 of 2) 34
  • 49 (a)
OneToMany
mgbb01h02 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9665 33
fruit fly
(Drosophila melanogaster)
Insecta Ndg 34
  • 26 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea nid-1 34
  • 22 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3675 34
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for NID1: view image

Paralogs for NID1 Gene

Paralogs for NID1 Gene

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

  • NID1_HUMAN
  • L8EC96_HUMAN
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 Variation AA Info Type
rs397515471 uncertain-significance, Variant of unknown significance 236,038,227(-) G/A coding_sequence_variant, stop_gained
rs730882225 likely-pathogenic, Focal epilepsy, Hemiparesis, Hydrocephalus 235,980,495(-) C/T splice_donor_variant
rs869312945 uncertain-significance, Inborn genetic diseases 236,029,648(-) G/A coding_sequence_variant, missense_variant
VAR_035835 A colorectal cancer sample p.Phe1036Ser
rs1064793217 likely-pathogenic, not provided 236,065,078(-) A/T initiator_codon_variant, missense_variant

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)

Additional Variant Information for NID1 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for NID1 Gene

MalaCards: The human disease database

(10) MalaCards diseases for NID1 Gene - From: HGMD, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
neuronal intestinal dysplasia
goodpasture syndrome
  • anti-glomerular basement membrane disease
pierson syndrome
  • microcoria-congenital nephrotic syndrome
keratopathy
laurence-moon syndrome
  • lnms
- elite association - COSMIC cancer census association via MalaCards
Search NID1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for 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 58
  2. Human nidogen: cDNA cloning, cellular expression, and mapping of the gene to chromosome Iq43. (PMID: 2471408) Olsen DR … Uitto J (American journal of human genetics 1989) 2 3 4 58
  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 (Human molecular genetics 2011) 3 44 58
  4. Nidogen 1 and 2 gene promoters are aberrantly methylated in human gastrointestinal cancer. (PMID: 17328794) Ulazzi L … Negrini M (Molecular cancer 2007) 3 22 58
  5. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 58

Products for NID1 Gene

Sources for NID1 Gene

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