Human Gene NID1 (ENST00000366595.7) from GENCODE V44
  Description: 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. (from UniProt P14543)
RefSeq Summary (NM_002508): 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].
Gencode Transcript: ENST00000366595.7
Gencode Gene: ENSG00000116962.15
Transcript (Including UTRs)
   Position: hg38 chr1:235,975,830-236,065,109 Size: 89,280 Total Exon Count: 17 Strand: -
Coding Region
   Position: hg38 chr1:235,977,867-236,065,079 Size: 87,213 Coding Exon Count: 17 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:235,975,830-236,065,109)mRNA (may differ from genome)Protein (1114 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGencodeGeneCardsHGNC
HPRDLynxMalacardsMGIneXtProtPubMed
ReactomeUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: NID1_HUMAN
DESCRIPTION: RecName: Full=Nidogen-1; Short=NID-1; AltName: Full=Entactin; Flags: Precursor;
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.
SUBUNIT: Interacts with FBLN1 and LGALS3BP (By similarity). Interacts with PLXDC1.
SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix, basement membrane.
PTM: N- and O-glycosylated.
SIMILARITY: Contains 6 EGF-like domains.
SIMILARITY: Contains 4 LDL-receptor class B repeats.
SIMILARITY: Contains 1 NIDO domain.
SIMILARITY: Contains 1 nidogen G2 beta-barrel domain.
SIMILARITY: Contains 1 thyroglobulin type-1 domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: NID1
Diseases sorted by gene-association score: neuronal intestinal dysplasia (17), goodpasture syndrome (11), keratopathy (8), laurence-moon syndrome (8), mucocutaneous leishmaniasis (7), bullous keratopathy (7), paralytic poliomyelitis (6), alport syndrome (5)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 116.59 RPKM in Cells - Cultured fibroblasts
Total median expression: 1636.40 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -10.5030-0.350 Picture PostScript Text
3' UTR -482.502037-0.237 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011042 - 6-blade_b-propeller_TolB-like
IPR000742 - EG-like_dom
IPR001881 - EGF-like_Ca-bd
IPR013032 - EGF-like_CS
IPR000152 - EGF-type_Asp/Asn_hydroxyl_site
IPR018097 - EGF_Ca-bd_CS
IPR024731 - EGF_dom_MSP1-like
IPR006605 - G2_nidogen/fibulin_G2F
IPR009017 - Green_fluorescent_prot-like
IPR000033 - LDLR_classB_rpt
IPR003886 - Nidogen_extracell_dom
IPR000716 - Thyroglobulin_1

Pfam Domains:
PF12947 - EGF domain
PF07645 - Calcium-binding EGF domain
PF07474 - G2F domain
PF00058 - Low-density lipoprotein receptor repeat class B
PF06119 - Nidogen-like
PF00086 - Thyroglobulin type-1 repeat

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1NDX - Model


ModBase Predicted Comparative 3D Structure on P14543
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005509 calcium ion binding
GO:0005518 collagen binding
GO:0043236 laminin binding
GO:0043237 laminin-1 binding
GO:0043394 proteoglycan binding
GO:0050840 extracellular matrix binding

Biological Process:
GO:0007155 cell adhesion
GO:0007160 cell-matrix adhesion
GO:0010811 positive regulation of cell-substrate adhesion
GO:0030198 extracellular matrix organization
GO:0032836 glomerular basement membrane development
GO:0071711 basement membrane organization

Cellular Component:
GO:0005576 extracellular region
GO:0005604 basement membrane
GO:0005605 basal lamina
GO:0031012 extracellular matrix
GO:0070062 extracellular exosome
GO:0071944 cell periphery


-  Descriptions from all associated GenBank mRNAs
  BC045606 - Homo sapiens nidogen 1, mRNA (cDNA clone MGC:33141 IMAGE:5271590), complete cds.
GQ891509 - Homo sapiens clone HEL-S-230 epididymis secretory sperm binding protein mRNA, complete cds.
LF384899 - JP 2014500723-A/192402: Polycomb-Associated Non-Coding RNAs.
MA620476 - JP 2018138019-A/192402: Polycomb-Associated Non-Coding RNAs.
M30269 - Human nidogen mRNA, complete cds.
AB209448 - Homo sapiens mRNA for nidogen (enactin) variant protein.
AK297234 - Homo sapiens cDNA FLJ51241 complete cds, highly similar to Nidogen-1 precursor.
CU692272 - Synthetic construct Homo sapiens gateway clone IMAGE:100021010 5' read NID1 mRNA.
LF330968 - JP 2014500723-A/138471: Polycomb-Associated Non-Coding RNAs.
MA566545 - JP 2018138019-A/138471: Polycomb-Associated Non-Coding RNAs.
LF330967 - JP 2014500723-A/138470: Polycomb-Associated Non-Coding RNAs.
MA566544 - JP 2018138019-A/138470: Polycomb-Associated Non-Coding RNAs.
LF330966 - JP 2014500723-A/138469: Polycomb-Associated Non-Coding RNAs.
MA566543 - JP 2018138019-A/138469: Polycomb-Associated Non-Coding RNAs.
LF330965 - JP 2014500723-A/138468: Polycomb-Associated Non-Coding RNAs.
MA566542 - JP 2018138019-A/138468: Polycomb-Associated Non-Coding RNAs.
M27445 - Homo sapiens nidogen (NID) mRNA, 3' end.
JD320337 - Sequence 301361 from Patent EP1572962.
JD473689 - Sequence 454713 from Patent EP1572962.
JD356156 - Sequence 337180 from Patent EP1572962.
JD166452 - Sequence 147476 from Patent EP1572962.
JD427139 - Sequence 408163 from Patent EP1572962.
LF330962 - JP 2014500723-A/138465: Polycomb-Associated Non-Coding RNAs.
MA566539 - JP 2018138019-A/138465: Polycomb-Associated Non-Coding RNAs.
JD183343 - Sequence 164367 from Patent EP1572962.
LF330961 - JP 2014500723-A/138464: Polycomb-Associated Non-Coding RNAs.
MA566538 - JP 2018138019-A/138464: Polycomb-Associated Non-Coding RNAs.
LF330959 - JP 2014500723-A/138462: Polycomb-Associated Non-Coding RNAs.
MA566536 - JP 2018138019-A/138462: Polycomb-Associated Non-Coding RNAs.
JD240907 - Sequence 221931 from Patent EP1572962.
LF330958 - JP 2014500723-A/138461: Polycomb-Associated Non-Coding RNAs.
MA566535 - JP 2018138019-A/138461: Polycomb-Associated Non-Coding RNAs.
JD321819 - Sequence 302843 from Patent EP1572962.
JD509313 - Sequence 490337 from Patent EP1572962.
LF330956 - JP 2014500723-A/138459: Polycomb-Associated Non-Coding RNAs.
MA566533 - JP 2018138019-A/138459: Polycomb-Associated Non-Coding RNAs.
JD061850 - Sequence 42874 from Patent EP1572962.
JD102475 - Sequence 83499 from Patent EP1572962.
JD042255 - Sequence 23279 from Patent EP1572962.
JD387365 - Sequence 368389 from Patent EP1572962.
JD439440 - Sequence 420464 from Patent EP1572962.
JD209917 - Sequence 190941 from Patent EP1572962.
LF330954 - JP 2014500723-A/138457: Polycomb-Associated Non-Coding RNAs.
MA566531 - JP 2018138019-A/138457: Polycomb-Associated Non-Coding RNAs.
JD434059 - Sequence 415083 from Patent EP1572962.
JD487392 - Sequence 468416 from Patent EP1572962.
LF330953 - JP 2014500723-A/138456: Polycomb-Associated Non-Coding RNAs.
MA566530 - JP 2018138019-A/138456: Polycomb-Associated Non-Coding RNAs.
LF330950 - JP 2014500723-A/138453: Polycomb-Associated Non-Coding RNAs.
MA566527 - JP 2018138019-A/138453: Polycomb-Associated Non-Coding RNAs.
LF330948 - JP 2014500723-A/138451: Polycomb-Associated Non-Coding RNAs.
MA566525 - JP 2018138019-A/138451: Polycomb-Associated Non-Coding RNAs.
LF330945 - JP 2014500723-A/138448: Polycomb-Associated Non-Coding RNAs.
MA566522 - JP 2018138019-A/138448: Polycomb-Associated Non-Coding RNAs.
LF330943 - JP 2014500723-A/138446: Polycomb-Associated Non-Coding RNAs.
MA566520 - JP 2018138019-A/138446: Polycomb-Associated Non-Coding RNAs.
LF330941 - JP 2014500723-A/138444: Polycomb-Associated Non-Coding RNAs.
MA566518 - JP 2018138019-A/138444: Polycomb-Associated Non-Coding RNAs.
LF330940 - JP 2014500723-A/138443: Polycomb-Associated Non-Coding RNAs.
MA566517 - JP 2018138019-A/138443: Polycomb-Associated Non-Coding RNAs.
LF330939 - JP 2014500723-A/138442: Polycomb-Associated Non-Coding RNAs.
MA566516 - JP 2018138019-A/138442: Polycomb-Associated Non-Coding RNAs.
LF330937 - JP 2014500723-A/138440: Polycomb-Associated Non-Coding RNAs.
MA566514 - JP 2018138019-A/138440: Polycomb-Associated Non-Coding RNAs.
LF330935 - JP 2014500723-A/138438: Polycomb-Associated Non-Coding RNAs.
MA566512 - JP 2018138019-A/138438: Polycomb-Associated Non-Coding RNAs.
LF330934 - JP 2014500723-A/138437: Polycomb-Associated Non-Coding RNAs.
MA566511 - JP 2018138019-A/138437: Polycomb-Associated Non-Coding RNAs.
LF330932 - JP 2014500723-A/138435: Polycomb-Associated Non-Coding RNAs.
MA566509 - JP 2018138019-A/138435: Polycomb-Associated Non-Coding RNAs.
LF330931 - JP 2014500723-A/138434: Polycomb-Associated Non-Coding RNAs.
MA566508 - JP 2018138019-A/138434: Polycomb-Associated Non-Coding RNAs.
LF330929 - JP 2014500723-A/138432: Polycomb-Associated Non-Coding RNAs.
MA566506 - JP 2018138019-A/138432: Polycomb-Associated Non-Coding RNAs.
LF330927 - JP 2014500723-A/138430: Polycomb-Associated Non-Coding RNAs.
MA566504 - JP 2018138019-A/138430: Polycomb-Associated Non-Coding RNAs.
LF330926 - JP 2014500723-A/138429: Polycomb-Associated Non-Coding RNAs.
MA566503 - JP 2018138019-A/138429: Polycomb-Associated Non-Coding RNAs.
LF330925 - JP 2014500723-A/138428: Polycomb-Associated Non-Coding RNAs.
MA566502 - JP 2018138019-A/138428: Polycomb-Associated Non-Coding RNAs.
LF330924 - JP 2014500723-A/138427: Polycomb-Associated Non-Coding RNAs.
MA566501 - JP 2018138019-A/138427: Polycomb-Associated Non-Coding RNAs.
LF330922 - JP 2014500723-A/138425: Polycomb-Associated Non-Coding RNAs.
MA566499 - JP 2018138019-A/138425: Polycomb-Associated Non-Coding RNAs.
LF330920 - JP 2014500723-A/138423: Polycomb-Associated Non-Coding RNAs.
MA566497 - JP 2018138019-A/138423: Polycomb-Associated Non-Coding RNAs.
LF330919 - JP 2014500723-A/138422: Polycomb-Associated Non-Coding RNAs.
MA566496 - JP 2018138019-A/138422: Polycomb-Associated Non-Coding RNAs.
LF330918 - JP 2014500723-A/138421: Polycomb-Associated Non-Coding RNAs.
MA566495 - JP 2018138019-A/138421: Polycomb-Associated Non-Coding RNAs.
LF330917 - JP 2014500723-A/138420: Polycomb-Associated Non-Coding RNAs.
MA566494 - JP 2018138019-A/138420: Polycomb-Associated Non-Coding RNAs.
LF330916 - JP 2014500723-A/138419: Polycomb-Associated Non-Coding RNAs.
MA566493 - JP 2018138019-A/138419: Polycomb-Associated Non-Coding RNAs.
LF330915 - JP 2014500723-A/138418: Polycomb-Associated Non-Coding RNAs.
MA566492 - JP 2018138019-A/138418: Polycomb-Associated Non-Coding RNAs.
BC012501 - Homo sapiens nidogen 1, mRNA (cDNA clone IMAGE:4513545), with apparent retained intron.
LF213302 - JP 2014500723-A/20805: Polycomb-Associated Non-Coding RNAs.
MA448879 - JP 2018138019-A/20805: Polycomb-Associated Non-Coding RNAs.
LF209685 - JP 2014500723-A/17188: Polycomb-Associated Non-Coding RNAs.
MA445262 - JP 2018138019-A/17188: Polycomb-Associated Non-Coding RNAs.
LF330900 - JP 2014500723-A/138403: Polycomb-Associated Non-Coding RNAs.
MA566477 - JP 2018138019-A/138403: Polycomb-Associated Non-Coding RNAs.
LF330909 - JP 2014500723-A/138412: Polycomb-Associated Non-Coding RNAs.
MA566486 - JP 2018138019-A/138412: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P14543 (Reactome details) participates in the following event(s):

R-HSA-1592270 NID1 degradation by MMP1, 9, 12, ELANE
R-HSA-2533965 NID1 degradation by MMP14, MMP15
R-HSA-2533970 NID1 degradation by MMP3, 7
R-HSA-3791319 NID1 degradation by MMP19
R-HSA-2327803 Laminins bind Nidogens 1, 2
R-HSA-2426450 Laminins:Nidogens binds collagen type IV networks
R-HSA-2426530 Laminins:Nidogens binds HSPG2
R-HSA-1474228 Degradation of the extracellular matrix
R-HSA-3000157 Laminin interactions
R-HSA-1474244 Extracellular matrix organization

-  Other Names for This Gene
  Alternate Gene Symbols: BC045606, ENST00000366595.1, ENST00000366595.2, ENST00000366595.3, ENST00000366595.4, ENST00000366595.5, ENST00000366595.6, NID, NID1_HUMAN, P14543, Q14942, Q59FL2, Q5TAF2, Q5TAF3, Q86XD7, uc009xgd.1, uc009xgd.2, uc009xgd.3, uc009xgd.4
UCSC ID: ENST00000366595.7
RefSeq Accession: NM_002508
Protein: P14543 (aka NID1_HUMAN)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.