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] See more...

Aliases for NID2 Gene

Aliases for NID2 Gene

  • Nidogen 2 2 3 5
  • Osteonidogen 2 3 4
  • Nidogen-2 3 4
  • NID-2 3 4

External Ids for NID2 Gene

Previous GeneCards Identifiers for NID2 Gene

  • GC14M049794
  • GC14M046267
  • GC14M050461
  • GC14M051541
  • GC14M052471
  • GC14M032632

Summaries for NID2 Gene

Entrez Gene Summary for NID2 Gene

  • 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]

GeneCards Summary for NID2 Gene

NID2 (Nidogen 2) is a Protein Coding gene. Diseases associated with NID2 include Clivus Chordoma. Among its related pathways are Degradation of the extracellular matrix and MET promotes cell motility. Gene Ontology (GO) annotations related to this gene include calcium ion binding and collagen binding. An important paralog of this gene is NID1.

UniProtKB/Swiss-Prot Summary for NID2 Gene

  • Cell adhesion glycoprotein which is widely distributed in basement membranes. Binds to collagens I and IV, to perlecan and to laminin 1. Does not bind fibulins. It probably has a role in cell-extracellular matrix interactions.

Gene Wiki entry for NID2 Gene

Additional gene information for NID2 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NID2 Gene

Genomics for NID2 Gene

GeneHancer (GH) Regulatory Elements for NID2 Gene

Promoters and enhancers for NID2 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
GH14J052067 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 504.8 +0.3 288 4.3 TCF12 ZIC2 ZBTB10 ZBTB26 SAP30 NFYB ZNF341 OSR2 NR2F2 CTCF NID2 LOC105378180 lnc-RTRAF-1 GNPNAT1 piR-48759-086
GH14J052075 Enhancer 1.3 FANTOM5 Ensembl ENCODE dbSUPER 12.3 -10.0 -10027 7.7 FOS TCF7 EP300 DEK BRCA1 CEBPB CHD2 JUN RCOR1 NR2F2 NID2 RF00994-321 lnc-RTRAF-1
GH14J052018 Enhancer 1.1 Ensembl ENCODE dbSUPER 10.1 +46.4 46398 9.5 FOS RELA EP300 FOXA2 BCL11A NR2F2 ZNF316 CEBPB MEF2B POLR2A RTRAF NID2 GNG2 piR-48759-086 lnc-NID2-5
GH14J052029 Enhancer 1.1 Ensembl ENCODE CraniofacialAtlas dbSUPER 9.7 +37.5 37530 5 RBM25 ZNF316 RCOR1 NR2F2 NFE2 MAFK FOS ZFP91 MAFG GATA2 piR-48759-086 PTGDR RTRAF NID2 GNPNAT1
GH14J052012 Enhancer 1 Ensembl ENCODE dbSUPER 10 +54.7 54731 4.2 CTCF MXI1 NR2F2 ZNF316 MAFF YY1 MAFK USF1 POLR2A RAD21 RTRAF PTGDR NID2 GNG2 GNPNAT1 lnc-NID2-5 piR-48759-086
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NID2 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NID2

Top Transcription factor binding sites by QIAGEN in the NID2 gene promoter:
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • Oct-B1
  • oct-B2
  • oct-B3
  • Pax-4a

Genomic Locations for NID2 Gene

Genomic Locations for NID2 Gene
chr14:52,004,802-52,069,231
(GRCh38/hg38)
Size:
64,430 bases
Orientation:
Minus strand
chr14:52,471,520-52,535,946
(GRCh37/hg19)
Size:
64,427 bases
Orientation:
Minus strand

Genomic View for NID2 Gene

Genes around NID2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NID2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NID2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NID2 Gene

Proteins for NID2 Gene

  • Protein details for NID2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q14112-NID2_HUMAN
    Recommended name:
    Nidogen-2
    Protein Accession:
    Q14112
    Secondary Accessions:
    • A8K6I7
    • B4DU19
    • O43710

    Protein attributes for NID2 Gene

    Size:
    1375 amino acids
    Molecular mass:
    151254 Da
    Quaternary structure:
    • Interacts with LAMA2 (By similarity). Interacts with COL13A1.
    SequenceCaution:
    • Sequence=BAA13087.1; Type=Frameshift; Evidence={ECO:0000305}; Sequence=BAA24112.1; Type=Frameshift; Evidence={ECO:0000305};

    Alternative splice isoforms for NID2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NID2 Gene

Post-translational modifications for NID2 Gene

  • Highly N- and O-glycosylated.
  • Glycosylation at Ser358, Ser359, Thr360, Thr365, Thr369, Ser370, Thr391, Ser393, Asn417, Ser448, Ser452, Thr455, Thr456, Ser459, Thr479, Asn658, Asn693, Asn703, and Asn1124
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect

Other Protein References for NID2 Gene

No data available for DME Specific Peptides for NID2 Gene

Domains & Families for NID2 Gene

Gene Families for NID2 Gene

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

Protein Domains for NID2 Gene

Blocks:
  • Aspartic acid and asparagine hydroxylation site
  • EGF-like calcium-binding
  • Thyroglobulin type-1
  • Low-density lipoprotein receptor, YWTD repeat
  • Nidogen, extracellular region
  • G2 nidogen and fibulin G2F
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for NID2 Gene

GenScript: Design optimal peptide antigens:
  • Osteonidogen (NID2_HUMAN)
  • NID2 protein (Q8IV28_HUMAN)
genes like me logo Genes that share domains with NID2: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for NID2 Gene

Function for NID2 Gene

Molecular function for NID2 Gene

UniProtKB/Swiss-Prot Function:
Cell adhesion glycoprotein which is widely distributed in basement membranes. Binds to collagens I and IV, to perlecan and to laminin 1. Does not bind fibulins. It probably has a role in cell-extracellular matrix interactions.

Phenotypes From GWAS Catalog for NID2 Gene

Gene Ontology (GO) - Molecular Function for NID2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005201 extracellular matrix structural constituent RCA 20551380
GO:0005509 calcium ion binding IEA --
GO:0005515 protein binding IPI 11956183
GO:0005518 collagen binding TAS 9733643
genes like me logo Genes that share ontologies with NID2: view
genes like me logo Genes that share phenotypes with NID2: view

Animal Model Products

CRISPR Products

miRNA for NID2 Gene

miRTarBase miRNAs that target NID2

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NID2

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NID2 Gene

Localization for NID2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NID2 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 NID2 gene
Compartment Confidence
plasma membrane 5
extracellular 5
cytoskeleton 2
mitochondrion 1
nucleus 1
endoplasmic reticulum 1
cytosol 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NID2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005604 basement membrane IDA,TAS 22952693
GO:0005886 plasma membrane IDA --
GO:0031012 extracellular matrix IEA --
GO:0062023 colocalizes_with collagen-containing extracellular matrix ISS 22261194
genes like me logo Genes that share ontologies with NID2: view

Pathways & Interactions for NID2 Gene

genes like me logo Genes that share pathways with NID2: view

Pathways by source for NID2 Gene

2 Reactome pathways for NID2 Gene

Gene Ontology (GO) - Biological Process for NID2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion TAS 9733643
GO:0007160 cell-matrix adhesion IEA --
GO:0030198 extracellular matrix organization TAS --
GO:0071711 basement membrane organization TAS 22952693
genes like me logo Genes that share ontologies with NID2: view

No data available for SIGNOR curated interactions for NID2 Gene

Drugs & Compounds for NID2 Gene

No Compound Related Data Available

Transcripts for NID2 Gene

mRNA/cDNA for NID2 Gene

1 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
8 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NID2

Alternative Splicing Database (ASD) splice patterns (SP) for NID2 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13a · 13b ^ 14a · 14b ^ 15a · 15b ^ 16a · 16b ^ 17a · 17b ^ 18 ^
SP1: - - - -
SP2:
SP3: - -
SP4:
SP5:
SP6:
SP7:

ExUns: 19a · 19b · 19c ^ 20a · 20b ^ 21a · 21b ^ 22
SP1: - -
SP2:
SP3:
SP4: - -
SP5: -
SP6:
SP7:

Relevant External Links for NID2 Gene

GeneLoc Exon Structure for
NID2

Expression for NID2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for NID2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for NID2 Gene

This gene is overexpressed in Adipocyte (21.0) and Urinary Bladder (7.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for NID2 Gene



Protein tissue co-expression partners for NID2 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NID2

SOURCE GeneReport for Unigene cluster for NID2 Gene:

Hs.369840

mRNA Expression by UniProt/SwissProt for NID2 Gene:

Q14112-NID2_HUMAN
Tissue specificity: Heart, placenta and bone. Less in pancreas, kidney and skeletal muscle.

Evidence on tissue expression from TISSUES for NID2 Gene

  • Liver(4.3)
  • Bone(4)
  • Heart(3.1)
  • Gall bladder(2.4)
  • Eye(2.3)
  • Intestine(2)
  • Muscle(2)
genes like me logo Genes that share expression patterns with NID2: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for NID2 Gene

Orthologs for NID2 Gene

This gene was present in the common ancestor of animals.

Orthologs for NID2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NID2 31 30
  • 99.35 (n)
OneToOne
dog
(Canis familiaris)
Mammalia NID2 31 30
  • 86.81 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Nid2 17 31 30
  • 82.76 (n)
cow
(Bos Taurus)
Mammalia NID2 31
  • 82 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Nid2 30
  • 81.9 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia NID2 31
  • 63 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia NID2 31
  • 60 (a)
OneToOne
chicken
(Gallus gallus)
Aves NID2 31 30
  • 67.29 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NID2 31
  • 65 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nid2 30
  • 58.46 (n)
Str.6011 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.8084 30
zebrafish
(Danio rerio)
Actinopterygii nid2a 31 30
  • 58.06 (n)
OneToMany
nid2b 31
  • 44 (a)
OneToMany
nid2 30
fruit fly
(Drosophila melanogaster)
Insecta Ndg 31
  • 27 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea nid-1 31
  • 23 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3675 31
  • 35 (a)
OneToMany
Species where no ortholog for NID2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • 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 NID2 Gene

ENSEMBL:
Gene Tree for NID2 (if available)
TreeFam:
Gene Tree for NID2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NID2: view image

Paralogs for NID2 Gene

Paralogs for NID2 Gene

(8) SIMAP similar genes for NID2 Gene using alignment to 4 proteins:

  • NID2_HUMAN
  • H0YJV3_HUMAN
  • L8EAL3_HUMAN
  • Q8IV28_HUMAN
genes like me logo Genes that share paralogs with NID2: view

Variants for NID2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NID2 Gene

SNP ID Clinical significance and condition Chr 14 pos Variation AA Info Type
714333 Benign: not provided 52,020,132(-) G/A SYNONYMOUS_VARIANT
714334 Benign: not provided 52,027,278(-) C/T MISSENSE_VARIANT
718101 Benign: not provided 52,010,917(-) A/G SYNONYMOUS_VARIANT
724770 Likely Benign: not provided 52,006,562(-) G/A MISSENSE_VARIANT,THREE_PRIME_UTR_VARIANT
725070 Likely Benign: not provided 52,042,913(-) G/C MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for NID2 Gene

Structural Variations from Database of Genomic Variants (DGV) for NID2 Gene

Variant ID Type Subtype PubMed ID
nsv1138301 CNV deletion 24896259
nsv85620 CNV insertion 16902084
nsv952842 CNV duplication 24416366

Variation tolerance for NID2 Gene

Residual Variation Intolerance Score: 99.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.98; 79.97% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NID2 Gene

Human Gene Mutation Database (HGMD)
NID2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NID2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NID2 Gene

Disorders for NID2 Gene

MalaCards: The human disease database

(1) MalaCards diseases for NID2 Gene - From: DISEASES

Disorder Aliases PubMed IDs
clivus chordoma
  • chordoma of clivus
- elite association - COSMIC cancer census association via MalaCards
Search NID2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for NID2

genes like me logo Genes that share disorders with NID2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NID2 Gene

Publications for NID2 Gene

  1. Nidogen-2: a new basement membrane protein with diverse binding properties. (PMID: 9733643) Kohfeldt E … Timpl R (Journal of molecular biology 1998) 2 3 4 54
  2. Framingham Heart Study genome-wide association: results for pulmonary function measures. (PMID: 17903307) Wilk JB … O'Connor GT (BMC medical genetics 2007) 3 41 54
  3. Nidogen 1 and 2 gene promoters are aberrantly methylated in human gastrointestinal cancer. (PMID: 17328794) Ulazzi L … Negrini M (Molecular cancer 2007) 3 23 54
  4. The type XIII collagen ectodomain is a 150-nm rod and capable of binding to fibronectin, nidogen-2, perlecan, and heparin. (PMID: 11956183) Tu H … Pihlajaniemi T (The Journal of biological chemistry 2002) 3 4 54
  5. Integrated bioinformatics analysis reveals novel key biomarkers and potential candidate small molecule drugs in gastric cancer. (PMID: 30975489) Wu Q … Zhou YL (Pathology, research and practice 2019) 3 54

Products for NID2 Gene

Sources for NID2 Gene