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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

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