nid1a nidogen 1a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: nid1aprovided by ZNC
Official Full Name: nidogen 1aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-050302-58
See related: Ensembl:ENSDARG00000068710 AllianceGenome:ZFIN:ZDB-GENE-050302-58
Gene type: protein coding
RefSeq status: MODEL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: nid1; im:7055206; im:7142300; mg:bb01h02
Summary: Predicted to enable calcium ion binding activity. Predicted to act upstream of or within cell-matrix adhesion. Predicted to be located in basement membrane and extracellular region. Predicted to be active in plasma membrane. Is expressed in several structures, including digestive system; myoseptum; nervous system; optic fissure; and swim bladder. Orthologous to human NID1 (nidogen 1). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 13

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	13	NC_007124.7 (50067218..50139809, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	13	NC_007124.6 (49753659..49826565, complement)

Chromosome 13 - NC_007124.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Short body length phenotype is compensated by the upregulation of nidogen family members in a deleterious nid1a mutation of zebrafish
Title: Short body length phenotype is compensated by the upregulation of nidogen family members in a deleterious nid1a mutation of zebrafish.

Submit: New GeneRIF Correction

General gene information

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Markers

AI105788 (e-PCR)
- UniSTS:206850

fd54g11.x1 (e-PCR)
- UniSTS:195642

fb70g11.y1 (e-PCR)
- UniSTS:191037

Homology

NCBI Orthologs

Orthologs from OrthoDB

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables Wnt receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables Wnt-protein binding	IBA Inferred from Biological aspect of Ancestor more info
enables calcium ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in canonical Wnt signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cell adhesion	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cell-matrix adhesion	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in basement membrane	IEA Inferred from Electronic Annotation more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info
located_in membrane	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: nidogen-1

Names: nidogen 1

NCBI Reference Sequences (RefSeq)

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RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCz11 Primary Assembly

Genomic

NC_007124.7 Reference GRCz11 Primary Assembly

Range

50067218..50139809 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_686064.8 → XP_691156.5 nidogen-1 isoform X1

UniProtKB/TrEMBL

A0A8N7UUY5, F1RAG3

Related

ENSDARP00000090249.4, ENSDART00000099475.6

Conserved Domains (9) summary

smart00135
Location:942 → 983

LY; Low-density lipoprotein-receptor YWTD domain

smart00179
Location:644 → 686

EGF_CA; Calcium-binding EGF-like domain

cd00255
Location:373 → 594

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:920 → 957

Ldl_recept_b; Low-density lipoprotein receptor repeat class B

pfam00086
Location:781 → 848

Thyroglobulin_1; Thyroglobulin type-1 repeat

pfam08450
Location:903 → 1130

SGL; SMP-30/Gluconolaconase/LRE-like region

pfam12947
Location:739 → 772

EGF_3; EGF domain

pfam14670
Location:1140 → 1164

FXa_inhibition; Coagulation Factor Xa inhibitory site

cl02648
Location:103 → 250

NIDO; Nidogen-like

Reference GRCz11 ALT_DRER_TU_1

Genomic

NW_018394890.1 Reference GRCz11 ALT_DRER_TU_1

Range

249631..267619 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_021472743.1 → XP_021328418.1 nidogen-1 isoform X2

UniProtKB/TrEMBL

A0A8M9PN19

Conserved Domains (3) summary

smart00135
Location:24 → 65

LY; Low-density lipoprotein-receptor YWTD domain

pfam00058
Location:2 → 39

Ldl_recept_b; Low-density lipoprotein receptor repeat class B

pfam14670
Location:222 → 246

FXa_inhibition; Coagulation Factor Xa inhibitory site