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    NRXN1-DT NRXN1 divergent transcript [ Homo sapiens (human) ]

    Gene ID: 730100, updated on 10-Oct-2023

    Summary

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    Official Symbol
    NRXN1-DTprovided by HGNC
    Official Full Name
    NRXN1 divergent transcriptprovided by HGNC
    Primary source
    HGNC:HGNC:52686
    See related
    Ensembl:ENSG00000231918
    Gene type
    ncRNA
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Expression
    Low expression observed in reference dataset See more
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    Genomic context

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    See NRXN1-DT in Genome Data Viewer
    Location:
    2p16.3
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (51032601..52407917)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (51028763..52404220)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (51259739..52635055)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene neurexin 1 Neighboring gene uncharacterized LOC124906006 Neighboring gene microRNA 8485 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:51227905-51228438 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:51240083-51240639 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:51254469-51255168 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:51483602-51484801 Neighboring gene uncharacterized LOC105377627 Neighboring gene lysine rich nucleolar protein 1 pseudogene 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:52018811-52019312 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:52019313-52019812 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:52118567-52119067 Neighboring gene uncharacterized LOC105374597 Neighboring gene crystallin gamma G, pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:52281900-52282452 Neighboring gene CCDC12 pseudogene 1 Neighboring gene uncharacterized LOC124907767 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:52309986-52311185 Neighboring gene uncharacterized LOC107985766 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:52480599-52481157 Neighboring gene zinc finger protein 863, pseudogene Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:52538728-52539698 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:52562596-52563399 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:52564489-52565199 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:52667173-52667782 Neighboring gene long intergenic non-protein coding RNA 1867 Neighboring gene GGCT pseudogene 3 Neighboring gene CRTC1 pseudogene 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Heterozygous Deletion of Long Noncoding RNA AK127244 Is a Susceptibility Factor for Neurodevelopmental Delay. Coci EG, et al. Cytogenet Genome Res, 2022. PMID 36758534
    2. Two rare deletions upstream of the NRXN1 gene (2p16.3) affecting the non-coding mRNA AK127244 segregate with diverse psychopathological phenotypes in a family. Duong LT, et al. Eur J Med Genet, 2015 Dec. PMID 26563496
    3. Long non-coding RNA LOC730100 enhances proliferation and invasion of glioma cells through competitively sponging miR-760 from FOXA1 mRNA. Li Q, et al. Biochem Biophys Res Commun, 2019 May 7. PMID 30914197
    4. TSPYL5 SNPs: association with plasma estradiol concentrations and aromatase expression. Liu M, et al. Mol Endocrinol, 2013 Apr. PMID 23518928, Free PMC Article
    5. Genome-wide association analysis implicates the involvement of eight loci with response to tocilizumab for the treatment of rheumatoid arthritis. Wang J, et al. Pharmacogenomics J, 2013 Jun. PMID 22491018

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Long non-coding RNA LOC730100 is a competing endogenous RNA for miR-760 and promotes FOXA1 expression. miR-760 suppresses glioma progression by targeting FOXA1.
      Title: Long non-coding RNA LOC730100 enhances proliferation and invasion of glioma cells through competitively sponging miR-760 from FOXA1 mRNA.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB.
    EBI GWAS Catalog
    Common genetic variants associated with cognitive performance identified using the proxy-phenotype method.
    EBI GWAS Catalog
    Genome-wide association analysis implicates the involvement of eight loci with response to tocilizumab for the treatment of rheumatoid arthritis.
    EBI GWAS Catalog
    TSPYL5 SNPs: association with plasma estradiol concentrations and aromatase expression.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    General gene information

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    Markers

    Clone Names

    • AC007682.1

    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.

    RNA

    1. NR_135237.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC007402, AC064868, AC087073, AC139712, AK127244
      Related
      ENST00000440698.1

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      51032601..52407917
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      51028763..52404220
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    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