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CLRN1-AS1 CLRN1 antisense RNA 1 [ Homo sapiens (human) ]

Gene ID: 116933, updated on 10-Oct-2023

Summary

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Official Symbol
CLRN1-AS1provided by HGNC
Official Full Name
CLRN1 antisense RNA 1provided by HGNC
Primary source
HGNC:HGNC:30895
See related
AllianceGenome:HGNC:30895
Gene type
ncRNA
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
UCRP; CLRN1OS
Expression
Low expression observed in reference dataset See more
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Genomic context

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See CLRN1-AS1 in Genome Data Viewer
Location:
3q25.1
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (150972678..151080726)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (153723762..153831789)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (150690465..150798513)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124909447 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14819 Neighboring gene SIAH2 antisense RNA 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:150523844-150524366 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:150524367-150524888 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:150539149-150539823 Neighboring gene NANOG hESC enhancer GRCh37_chr3:150566660-150567161 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14820 Neighboring gene uncharacterized LOC124909446 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14821 Neighboring gene MINDY family member 4B Neighboring gene Sharpr-MPRA regulatory region 9248 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:150643693-150644193 Neighboring gene clarin 1 Neighboring gene uncharacterized LOC124909448 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14822 Neighboring gene Sharpr-MPRA regulatory region 19 Neighboring gene mediator complex subunit 12L Neighboring gene RNA, 5S ribosomal pseudogene 145 Neighboring gene G protein-coupled receptor 171

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. FOXP1-induced lncRNA CLRN1-AS1 acts as a tumor suppressor in pituitary prolactinoma by repressing the autophagy via inactivating Wnt/β-catenin signaling pathway. Wang C, et al. Cell Death Dis, 2019 Jun 24. PMID 31235696, Free PMC Article
  2. Alternative splice variants of the USH3A gene Clarin 1 (CLRN1). Västinsalo H, et al. Eur J Hum Genet, 2011 Jan. PMID 20717163, Free PMC Article
  3. Mutations in a novel gene with transmembrane domains underlie Usher syndrome type 3. Joensuu T, et al. Am J Hum Genet, 2001 Oct. PMID 11524702, Free PMC Article
  4. Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers. Lauc G, et al. PLoS Genet, 2013. PMID 23382691, Free PMC Article
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. lncRNA CLRN1-AS1 reduces adhesion ability of human trophoblasts via CXCL10/CXCL11.
    Title: lncRNA CLRN1-AS1 reduces adhesion ability of human trophoblasts via CXCL10/CXCL11.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
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

Other Names

  • CLRN1 antisense RNA 1 (non-protein coding)
  • Usher critical region protein pseudogene
  • clarin 1 opposite strand

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_024066.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC020636, AF388367, AK126442

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    150972678..151080726
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    153723762..153831789
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NG_006573.1: Suppressed sequence

    Description
    NG_006573.1: This RefSeq was permanently suppressed because it is now thought that this gene is transcribed.
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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Chemical Information
Molecular Biology Databases