NID2 (nidogen 2)

Gene

• Entrez ID: 22795
• Gene name: Nidogen 2
• Gene symbol: NID2
• Synonyms (NCBI Gene): NID-2
• Chromosome: 14
• Chromosome location: 14q22.1
• Summary: 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

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT022756	hsa-miR-124-3p	Microarray	18668037
MIRT052404	hsa-let-7a-5p	CLASH	23622248
MIRT041174	hsa-miR-181d-5p	CLASH	23622248
MIRT1184851	hsa-miR-33a	CLIP-seq
MIRT1184852	hsa-miR-33b	CLIP-seq
MIRT1184853	hsa-miR-4277	CLIP-seq
MIRT1184854	hsa-miR-544	CLIP-seq
MIRT2053603	hsa-miR-1182	CLIP-seq
MIRT2053604	hsa-miR-1208	CLIP-seq
MIRT2053605	hsa-miR-1264	CLIP-seq
MIRT2053606	hsa-miR-2116	CLIP-seq
MIRT2053607	hsa-miR-2909	CLIP-seq
MIRT2053608	hsa-miR-4677-5p	CLIP-seq
MIRT2431604	hsa-miR-2467-3p	CLIP-seq
MIRT2431605	hsa-miR-3678-3p	CLIP-seq
MIRT2431606	hsa-miR-4257	CLIP-seq
MIRT2431607	hsa-miR-548c-3p	CLIP-seq
MIRT2455177	hsa-miR-1252	CLIP-seq
MIRT2455178	hsa-miR-218	CLIP-seq
MIRT2455179	hsa-miR-3159	CLIP-seq
MIRT2455180	hsa-miR-3187-3p	CLIP-seq
MIRT2455181	hsa-miR-4435	CLIP-seq
MIRT2455182	hsa-miR-4470	CLIP-seq
MIRT2455183	hsa-miR-4701-5p	CLIP-seq
MIRT2455184	hsa-miR-4717-3p	CLIP-seq
MIRT2455185	hsa-miR-4761-5p	CLIP-seq
MIRT2455186	hsa-miR-4775	CLIP-seq
MIRT2455187	hsa-miR-548s	CLIP-seq
MIRT2455188	hsa-miR-578	CLIP-seq
MIRT2455189	hsa-miR-588	CLIP-seq
MIRT2455190	hsa-miR-636	CLIP-seq
MIRT2455191	hsa-miR-651	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005201	Function	Extracellular matrix structural constituent	ISS
GO:0005201	Function	Extracellular matrix structural constituent	RCA	20551380, 27068509, 27559042, 28327460, 28675934
GO:0005509	Function	Calcium ion binding	IEA
GO:0005515	Function	Protein binding	IPI	11956183
GO:0005518	Function	Collagen binding	IEA
GO:0005518	Function	Collagen binding	TAS	9733643
GO:0005576	Component	Extracellular region	IEA
GO:0005576	Component	Extracellular region	TAS
GO:0005604	Component	Basement membrane	IBA
GO:0005604	Component	Basement membrane	IDA	22952693
GO:0005604	Component	Basement membrane	IEA
GO:0005604	Component	Basement membrane	TAS	9733643
GO:0005615	Component	Extracellular space	IBA
GO:0005886	Component	Plasma membrane	IDA
GO:0007155	Process	Cell adhesion	IEA
GO:0007155	Process	Cell adhesion	TAS	9733643
GO:0007160	Process	Cell-matrix adhesion	IBA
GO:0007160	Process	Cell-matrix adhesion	IEA
GO:0007160	Process	Cell-matrix adhesion	IEA
GO:0031012	Component	Extracellular matrix	HDA	20551380
GO:0031012	Component	Extracellular matrix	HDA	23658023, 27068509, 27559042, 28327460, 28675934
GO:0031012	Component	Extracellular matrix	IEA
GO:0070062	Component	Extracellular exosome	HDA	23533145
GO:0071711	Process	Basement membrane organization	IEA
GO:0071711	Process	Basement membrane organization	TAS	22952693

Other IDs

• MIM: 605399
• HGNC: 13389
• e!Ensembl: ENSG00000087303

Protein

• UniProt ID: Q14112
• Protein name: Nidogen-2 (NID-2) (Osteonidogen)
• Protein 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.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF06119	NIDO	179 → 272	Nidogen-like	Family
  PF07474	G2F	527 → 713	G2F domain	Domain
  PF12947	EGF_3	896 → 929	EGF domain	Domain
  PF00086	Thyroglobulin_1	940 → 1005	Thyroglobulin type-1 repeat	Domain
  PF00086	Thyroglobulin_1	1019 → 1084	Thyroglobulin type-1 repeat	Domain
  PF00058	Ldl_recept_b	1198 → 1238	Low-density lipoprotein receptor repeat class B	Repeat
  PF00058	Ldl_recept_b	1241 → 1283	Low-density lipoprotein receptor repeat class B	Repeat

• Tissue specificity: TISSUE SPECIFICITY: Detected in placenta (at protein level) (PubMed:32337544). Heart and bone. Less in pancreas, kidney and skeletal muscle. {ECO:0000269|PubMed:32337544}.
• Sequence:

  MEGDRVAGRPVLSSLPVLLLLPLLMLRAAALHPDELFPHGESWGDQLLQEGDDESSAVVK
  LANPLHFYEARFSNLYVGTNGIISTQDFPRETQYVDYDFPTDFPAIAPFLADIDTSHGRG
  RVLYREDTSPAVLGLAARYVRAGFPRSARFTPTHAFLATWEQVGAYEEVKRGALPSGELN
  TFQAVLASDGSDSYALFLYPANGLQFLGTRPKESYNVQLQLPARVGFCRGEADDLKSEGP
  YFSLTSTEQSVKNLYQLSNLGIPGVWAFHIGSTSPLDNVRPAAVGDLSAAHSSVPLGRSF
  SHATALESDYNEDNLDYYDVNEEEAEYLPGEPEEALNGHSSIDVSFQSKVDTKPLEESST
  LDPHTKEGTSLGEVGGPDLKGQVEPWDERETRSPAPPEVDRDSLAPSWETPPPYPENGSI
  QPYPDGGPVPSEMDVPPAHPEEEIVLRSYPASGHTTPLSRGTYEVGLEDNIGSNTEVFTY
  NAANKETCEHNHRQCSRHAFCTDYATGFCCHCQSKFYGNGKHCLPEGAPHRVNGKVSGHL
  HVGHTPVHFTDVDLHAYIVGNDGRAYTAISHIPQPAAQALLPLTPIGGLFGWLFALEKPG
  SENGFSLAGAAFTHDMEVTFYPGEETVRITQTAEGLDPENYLSIKTNIQGQVPYVSANFT
  AHISPYKELYHYSDSTVTSTSSRDYSLTFGAINQTWSYRIHQNITYQVCRHAPRHPSFPT
  TQQLNVDRVFALYNDEERVLRFAVTNQIGPVKEDSDPTPGNPCYDGSHMCDTTARCHPGT
  GVDYTCECASGYQGDGRNCVDENECATGFHRCGPNSVCINLPGSYRCECRSGYEFADDRH
  TCILITPPANPCEDGSHTCAPAGQARCVHHGGSTFSCACLPGYAGDGHQCTDVDECSENR
  CHPAATCYNTPGSFSCRCQPGYYGDGFQCIPDSTSSLTPCEQQQRHAQAQYAYPGARFHI
  PQCDEQGNFLPLQCHGSTGFCWCVDPDGHEVPGTQTPPGSTPPHCGPSPEPTQRPPTICE
  RWRENLLEHYGGTPRDDQYVPQCDDLGHFIPLQCHGKSDFCWCVDKDGREVQGTRSQPGT
  TPACIPTVAPPMVRPTPRPDVTPPSVGTFLLYTQGQQIGYLPLNGTRLQKDAAKTLLSLH
  GSIIVGIDYDCRERMVYWTDVAGRTISRAGLELGAEPETIVNSGLISPEGLAIDHIRRTM
  YWTDSVLDKIESALLDGSERKVLFYTDLVNPRAIAVDPIRGNLYWTDWNREAPKIETSSL
  DGENRRILINTDIGLPNGLTFDPFSKLLCWADAGTKKLECTLPDGTGRRVIQNNLKYPFS
  IVSYADHFYHTDWRRDGVVSVNKHSGQFTDEYLPEQRSHLYGITAVYPYCPTGRK

• Sequence length: 1375

Pathways

KEGG:

Cytoskeleton in muscle cells

Reactome:

Laminin interactions

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
BENIGN NEOPLASM	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLORECTAL CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CRANIOFACIAL MICROSOMIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEARING LOSS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LIVER CIRRHOSIS, EXPERIMENTAL	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SENSORINEURAL HEARING LOSS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Alzheimer Disease	Alzheimer disease	Pubtator	35627223	Associate	★☆☆☆☆ Found in Text Mining only
Amyotrophic Lateral Sclerosis	Amyotrophic lateral sclerosis	Pubtator	36768220	Associate	★☆☆☆☆ Found in Text Mining only
Bladder Neoplasm	Bladder Neoplasm	BEFREE	19674832, 23083854, 23682613, 26027762, 28106542		★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	23681936		★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	33500458	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma of bladder	Bladder carcinoma	BEFREE	19674832, 23083854, 23682613, 26027762, 28106542		★☆☆☆☆ Found in Text Mining only
Carcinoma of lung	Lung carcinoma	BEFREE	30826972		★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	24980822	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma, Ovarian Epithelial	Ovarian Epithelial carcinoma	BEFREE	29131023, 29278876		★☆☆☆☆ Found in Text Mining only
Cholesteatoma	Cholesteatoma	Pubtator	25093596	Associate	★☆☆☆☆ Found in Text Mining only
Colonic Diseases	Colonic disease	Pubtator	17328794	Associate	★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	35247911	Associate	★☆☆☆☆ Found in Text Mining only
Endometrial Neoplasms	Endometrial neoplasm	Pubtator	27874289	Associate	★☆☆☆☆ Found in Text Mining only
Endometriosis	Endometriosis	Pubtator	36232817	Associate	★☆☆☆☆ Found in Text Mining only
Gastrointestinal Neoplasms	Gastrointestinal Neoplasms	BEFREE	17328794		★☆☆☆☆ Found in Text Mining only
Gastrointestinal Neoplasms	Gastrointestinal neoplasm	Pubtator	17328794	Associate	★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	40332526	Associate	★☆☆☆☆ Found in Text Mining only
Goldenhar Syndrome	Goldenhar Syndrome	GWASCAT_DG	26853712		★☆☆☆☆ Found in Text Mining only
Idiopathic Pulmonary Fibrosis	Pulmonary Fibrosis	BEFREE	31426504		★☆☆☆☆ Found in Text Mining only
Idiopathic Pulmonary Fibrosis	Idiopathic pulmonary fibrosis	Pubtator	31426504	Associate	★☆☆☆☆ Found in Text Mining only
Leukemia Myeloid Acute	Myeloid leukemia	Pubtator	24493670	Associate	★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	21815147, 29278876		★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Lung neoplasms	Pubtator	31526458	Associate	★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	UNIPROT_DG			★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of lung	Lung Cancer	BEFREE	30826972		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of ovary	Ovarian cancer	BEFREE	29131023, 29278876		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	BEFREE	17328794, 30975489, 31362888		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of urinary bladder	Urinary bladder cancer	BEFREE	19674832, 23083854, 23682613, 26027762, 28106542		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	17328794, 31362888		★☆☆☆☆ Found in Text Mining only
Myositis Inclusion Body	Myositis	Pubtator	21672074	Associate	★☆☆☆☆ Found in Text Mining only
Nasopharyngeal carcinoma	Nasopharyngeal Carcinoma	BEFREE	27793011		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	21815147, 23681936, 23682613		★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	29970687		★☆☆☆☆ Found in Text Mining only
Osteoarthritis	Osteoarthritis	Pubtator	18438862	Associate	★☆☆☆☆ Found in Text Mining only
Osteoarthritis Knee	Osteoarthritis	Pubtator	18438862	Associate	★☆☆☆☆ Found in Text Mining only
Osteoporosis	Osteoporosis	Pubtator	32999266	Associate	★☆☆☆☆ Found in Text Mining only
ovarian neoplasm	Ovarian neoplasm	BEFREE	29131023, 29278876		★☆☆☆☆ Found in Text Mining only
Pemphigoid Bullous	Bullous pemphigoid	Pubtator	17637825	Associate	★☆☆☆☆ Found in Text Mining only
Scleroderma	Scleroderma	BEFREE	29760157		★☆☆☆☆ Found in Text Mining only
Scleroderma Diffuse	Scleroderma	Pubtator	29760157	Associate	★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma of esophagus	Esophagus Neoplasm	BEFREE	27793011, 29278876		★☆☆☆☆ Found in Text Mining only
Squamous Cell Carcinoma of Head and Neck	Squamous cell carcinoma	Pubtator	21558411, 32171289	Associate	★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma of mouth	Oral cavity carcinoma	BEFREE	21558411		★☆☆☆☆ Found in Text Mining only
Stomach Carcinoma	Stomach Carcinoma	BEFREE	30975489, 31362888		★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	17328794, 33758160	Associate	★☆☆☆☆ Found in Text Mining only
Systemic Scleroderma	Scleroderma	BEFREE	29760157		★☆☆☆☆ Found in Text Mining only
Urinary Bladder Neoplasms	Urinary bladder neoplasms	Pubtator	28106542, 29854012	Associate	★☆☆☆☆ Found in Text Mining only
Urothelial Carcinoma	Urothelial Carcinoma	BEFREE	24360662, 28106542		★☆☆☆☆ Found in Text Mining only