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    NID1 nidogen 1 [ Homo sapiens (human) ]

    Gene ID: 4811, updated on 9-Dec-2024

    Summary

    Official Symbol
    NID1provided by HGNC
    Official Full Name
    nidogen 1provided by HGNC
    Primary source
    HGNC:HGNC:7821
    See related
    Ensembl:ENSG00000116962 MIM:131390; AllianceGenome:HGNC:7821
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NID
    Summary
    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]
    Expression
    Broad expression in placenta (RPKM 93.1), gall bladder (RPKM 48.2) and 20 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See NID1 in Genome Data Viewer
    Location:
    1q42.3
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (235975830..236065090, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (235372074..235461403, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (236139130..236228390, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene lysosomal trafficking regulator Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2805 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2806 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1991 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1992 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2807 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1993 Neighboring gene uncharacterized LOC105373215 Neighboring gene RNA, U5E small nuclear 2, pseudogene Neighboring gene MPRA-validated peak780 silencer Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:236073306-236074505 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:236081529-236082028 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2808 Neighboring gene long intergenic non-protein coding RNA 2768 Neighboring gene RNA, U6 small nuclear 968, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1994 Neighboring gene MPRA-validated peak781 silencer Neighboring gene meiotic recombination hotspot NID3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2809 Neighboring gene MPRA-validated peak782 silencer Neighboring gene meiotic recombination hotspot NID2 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:236162526-236163725 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:236164752-236165460 Neighboring gene meiotic recombination hotspot NID1 Neighboring gene NANOG hESC enhancer GRCh37_chr1:236221449-236221986 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2812 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1995 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1996 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:236244555-236245056 Neighboring gene MS32 minisatellite repeat instability region Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:236259904-236261103 Neighboring gene meiotic recombination hotspot MSTM1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2813 Neighboring gene meiotic recombination hotspot MSTM2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1997 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1998 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:236306063-236306566 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:236313713-236314481 Neighboring gene ACO2 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2814 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2815 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1999 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2816 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2817 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2818 Neighboring gene G protein-coupled receptor 137B

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies nidogen 1 (NID1) as a susceptibility locus to cutaneous nevi and melanoma risk.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables collagen binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables extracellular matrix structural constituent ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables extracellular matrix structural constituent RCA
    inferred from Reviewed Computational Analysis
    more info
    PubMed 
    enables laminin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables laminin-1 binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables proteoglycan binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 

    General protein information

    Preferred Names
    nidogen-1
    Names
    NID-1
    enactin
    entactin
    epididymis secretory sperm binding protein

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_033228.1 RefSeqGene

      Range
      5092..94352
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_002508.3NP_002499.2  nidogen-1 precursor

      See identical proteins and their annotated locations for NP_002499.2

      Status: REVIEWED

      Source sequence(s)
      AL122018, AL139161, BQ549657, CN267119, DA269707, M30269
      Consensus CDS
      CCDS1608.1
      UniProtKB/Swiss-Prot
      P14543, Q14942, Q59FL2, Q5TAF2, Q5TAF3, Q86XD7
      UniProtKB/TrEMBL
      A0A384MR25
      Related
      ENSP00000264187.6, ENST00000264187.7
      Conserved Domains (8) summary
      smart00135
      Location:10141055
      LY; Low-density lipoprotein-receptor YWTD domain
      smart00179
      Location:710751
      EGF_CA; Calcium-binding EGF-like domain
      smart00539
      Location:106269
      NIDO; Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins
      cd00255
      Location:429660
      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:9921029
      Ldl_recept_b; Low-density lipoprotein receptor repeat class B
      pfam00086
      Location:849919
      Thyroglobulin_1; Thyroglobulin type-1 repeat
      pfam12947
      Location:811839
      EGF_3; EGF domain
      pfam14670
      Location:12121236
      FXa_inhibition; Coagulation Factor Xa inhibitory site

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      235975830..236065090 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      235372074..235461403 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)