Nid1 nidogen 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Nid1provided by RGD
Official Full Name: nidogen 1provided by RGD
Primary source: RGD:3178
See related: EnsemblRapid:ENSRNOG00000002461 AllianceGenome:RGD:3178
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Nid
Summary: Predicted to enable collagen binding activity; laminin-1 binding activity; and proteoglycan binding activity. Predicted to act upstream of or within cell-matrix adhesion; glomerular basement membrane development; and positive regulation of cell-substrate adhesion. Predicted to be located in basement membrane. Orthologous to human NID1 (nidogen 1). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Heart (RPKM 456.4), Kidney (RPKM 434.0) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 17q12.3

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	17	NC_086035.1 (93069013..93142416)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	17	NC_051352.1 (86085133..86158272)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	17	NC_005116.4 (90553161..90627133, complement)

Chromosome 17 - NC_086035.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The purpose of the present study was to determine the acute response of nidogen immunoreactivity (Nd-ir) in blood vessels of the spinal cord following a dorsal hemisection.
Title: Acute changes of nidogen immunoreactivity in the basal lamina of the spinal cord vessels following dorsal hemisection without correlative changes of nidogen gene expression.
Altogether, these results indicate that nidogen has a prosurvival and promigratory activity on Schwann cells in the peripheral nerve.
Title: Nidogen is a prosurvival and promigratory factor for adult Schwann cells.
Rsults indicate that rat nidogen-1 could play an important role during embryogenesis, decidualization, and implantation in the endometrium of uterus.
Title: Expression of nidogens in rat uterus and embryo during decidualization and implantation.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Nid1 (e-PCR), detects polymorphism
- UniSTS:144018

Nid1 (e-PCR), detects polymorphism
- UniSTS:144020

L17324 (e-PCR)
- UniSTS:124877

AU026588 (e-PCR)
- UniSTS:114134

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables collagen binding	IEA Inferred from Electronic Annotation more info
enables collagen binding	ISO Inferred from Sequence Orthology more info
enables extracellular matrix binding	ISO Inferred from Sequence Orthology more info
enables laminin binding	ISO Inferred from Sequence Orthology more info
enables laminin-1 binding	IEA Inferred from Electronic Annotation more info
enables laminin-1 binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables proteoglycan binding	IEA Inferred from Electronic Annotation more info
enables proteoglycan binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in cell-matrix adhesion	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cell-matrix adhesion	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within extracellular matrix organization	ISO Inferred from Sequence Orthology more info
involved_in glomerular basement membrane development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within glomerular basement membrane development	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell-substrate adhesion	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of cell-substrate adhesion	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in basement membrane	IEA Inferred from Electronic Annotation more info
located_in basement membrane	ISO Inferred from Sequence Orthology more info
located_in cell periphery	ISO Inferred from Sequence Orthology more info
located_in extracellular matrix	ISO Inferred from Sequence Orthology more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: nidogen-1

Names: NID-1; entactin; nidogen (entactin)

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001398520.2 → NP_001385449.1 nidogen-1 precursor

Status: VALIDATED

Source sequence(s)

JAXUCZ010000017

UniProtKB/TrEMBL

F1LM84

Related

ENSRNOP00000003349.6, ENSRNOT00000003349.9

Conserved Domains (8) summary

smart00135
Location:1013 → 1054

LY; Low-density lipoprotein-receptor YWTD domain

smart00179
Location:709 → 750

EGF_CA; Calcium-binding EGF-like domain

smart00539
Location:106 → 269

NIDO; Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins

cd00255
Location:428 → 659

nidG2; Nidogen, G2 domain; Nidogen is an important component of the basement membrane, an extracellular sheet-like matrix. Nidogen is a multifunctional protein that interacts with many other basement membrane proteins, like collagen, perlecan, lamin, and has a ...

pfam00058
Location:991 → 1028

Ldl_recept_b; Low-density lipoprotein receptor repeat class B

pfam00086
Location:848 → 918

Thyroglobulin_1; Thyroglobulin type-1 repeat

pfam12947
Location:810 → 838

EGF_3; EGF domain

pfam14670
Location:1211 → 1235

FXa_inhibition; Coagulation Factor Xa inhibitory site