Nid2 nidogen 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Nid2provided by RGD
Official Full Name: nidogen 2provided by RGD
Primary source: RGD:1311685
See related: EnsemblRapid:ENSRNOG00000000341 AllianceGenome:RGD:1311685
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: NID-2
Summary: Predicted to enable calcium ion binding activity. Predicted to be involved in cell-matrix adhesion. Located in cell surface. Orthologous to human NID2 (nidogen 2). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Kidney (RPKM 226.2), Muscle (RPKM 81.9) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 15p16

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	15	NC_086033.1 (4507224..4562949, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	15	NC_051350.1 (4458082..4513808, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	15	NC_005114.4 (4893999..4951893, complement)

Chromosome 15 - NC_086033.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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 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?

Results indicate that nidogen-2 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.

Submit: New GeneRIF Correction

General gene information

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Markers

BQ204566 (e-PCR)
- UniSTS:261141

AA945900 (e-PCR)
- UniSTS:250474

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cell-matrix adhesion	IBA Inferred from Biological aspect of Ancestor more info
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

Component	Evidence Code	Pubs
is_active_in basement membrane	IBA Inferred from Biological aspect of Ancestor more info
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 surface	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular matrix	ISO Inferred from Sequence Orthology more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: nidogen-2

Names: nidogen 2 (osteonidogen)

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_001012005.2 → NP_001012005.2 nidogen-2 precursor

See identical proteins and their annotated locations for NP_001012005.2

Status: PROVISIONAL

Source sequence(s)

BC169012

UniProtKB/Swiss-Prot

B5DFC9, Q5M812

UniProtKB/TrEMBL

A0A0G2K3C8

Related

ENSRNOP00000072586.3, ENSRNOT00000082196.3

Conserved Domains (7) summary

smart00135
Location:1199 → 1241

LY; Low-density lipoprotein-receptor YWTD domain

smart00179
Location:908 → 945

EGF_CA; Calcium-binding EGF-like domain

smart00539
Location:108 → 274

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

cd00191
Location:1040 → 1105

TY; Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases

cd00255
Location:543 → 767

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 ...

pfam07645
Location:817 → 858

EGF_CA; Calcium-binding EGF domain

pfam12947
Location:779 → 815

EGF_3; EGF domain