U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    nid1a nidogen 1a [ Danio rerio (zebrafish) ]

    Gene ID: 562690, updated on 9-Dec-2024

    Summary

    Go to the top of the page Help
    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 Wnt receptor activity and Wnt-protein binding activity. Predicted to be involved in canonical Wnt signaling pathway. 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, Dec 2024]
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See nid1a in Genome Data Viewer
    Location:
    chromosome: 13
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 13 NC_007124.7 (50067443..50139617, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 13 NC_007124.6 (49753659..49826565, complement)

    Chromosome 13 - NC_007124.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC137487446 Neighboring gene G protein subunit gamma 4 Neighboring gene lysosomal trafficking regulator Neighboring gene G protein-coupled receptor 137Ba Neighboring gene eukaryotic translation initiation factor 2-alpha kinase 2 Neighboring gene protein kinase containing Z-DNA binding domains

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Collective cell migration during optic cup formation features changing cell-matrix interactions linked to matrix topology. Soans KG, et al. Curr Biol, 2022 Nov 21. PMID 36208624
    2. Short body length phenotype is compensated by the upregulation of nidogen family members in a deleterious nid1a mutation of zebrafish. Zhu P, et al. J Genet Genomics, 2017 Nov 20. PMID 29169924
    3. Optic cup morphogenesis requires neural crest-mediated basement membrane assembly. Bryan CD, et al. Development, 2020 Feb 21. PMID 31988185, Free PMC Article
    4. Temporal characterization of optic fissure basement membrane composition suggests nidogen may be an initial target of remodeling. Carrara N, et al. Dev Biol, 2019 Aug 1. PMID 31034836
    5. Common responses of fish embryos to metals: an integrated analysis of transcriptomes and methylomes in zebrafish embryos under the stress of copper ions or silver nanoparticles. Tai Z, et al. Metallomics, 2019 Sep 1. PMID 31468037

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 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

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in animal organ development IEA
    Inferred from Electronic Annotation
    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
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    nidogen-1
    Names
    nidogen 1

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007124.7 Reference GRCz11 Primary Assembly

      Range
      50067443..50139617 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_686064.9 → 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

    1. NW_018394890.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      249856..267603 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_021472743.2 → 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
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Molecular Biology Databases
    Research Materials
    Tools