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Aliases for CLRN1-AS1 Gene

Subcategory (RNA class) for CLRN1-AS1 Gene

non-coding RNA

Quality Score for this RNA gene is


Aliases for CLRN1-AS1 Gene

  • CLRN1 Antisense RNA 1 2 3 5
  • CLRN1 Antisense RNA 1 (Non-Protein Coding) 2 3
  • Clarin 1 Opposite Strand 2 3
  • Usher Critical Region Protein Pseudogene 3
  • CLRN1OS 3
  • UCRP 3

External Ids for CLRN1-AS1 Gene

Previous HGNC Symbols for CLRN1-AS1 Gene


Previous GeneCards Identifiers for CLRN1-AS1 Gene

  • GC03P150571

Summaries for CLRN1-AS1 Gene

GeneCards Summary for CLRN1-AS1 Gene

CLRN1-AS1 (CLRN1 Antisense RNA 1) is an RNA Gene, and is affiliated with the non-coding RNA class.

Gene Wiki entry for CLRN1-AS1 Gene

No data available for Entrez Gene Summary , UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLRN1-AS1 Gene

Genomics for CLRN1-AS1 Gene

Regulatory Elements for CLRN1-AS1 Gene

Enhancers for CLRN1-AS1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03F150888 1 Ensembl ENCODE 20.1 +37.6 37582 3.1 BCOR PKNOX1 TBL1XR1 ZMYM3 CEBPG CHAMP1 ZNF316 GATA2 CBX5 POLR2A CLRN1-AS1 ERICH6-AS1 MED12L ENSG00000243273
GH03F151012 1.3 Ensembl ENCODE 10.8 +162.4 162385 3.9 HDGF PKNOX1 ATF1 ARNT SIN3A ARID4B DMAP1 SLC30A9 GATA2 NFYC CLRN1 CLRN1-AS1 MED12L ENSG00000276055
GH03F150925 1.2 FANTOM5 Ensembl ENCODE 11 +73.4 73417 1.0 CTCF ZNF654 PKNOX1 RNF2 REST RAD21 CBX8 GATA2 SMC3 KLF13 FAM188B2 ENSG00000243273 CLRN1 CLRN1-AS1 MED12L P2RY14 ENSG00000260234 ENSG00000244382
GH03F151145 1.1 Ensembl ENCODE 10.4 +293.7 293723 1.7 GTF2F1 CTCF JUN MAX CEBPG EBF1 RAD21 YY1 GATA3 ZBTB48 MED12L P2RY14 ENSG00000243273 FAM188B2 CLRN1 CLRN1-AS1 GC03M151148
GH03F151002 0.9 ENCODE 11 +150.7 150691 1.7 ELF3 TBL1XR1 RAD21 YY1 ZNF143 FOS DEK MIXL1 ZNF654 CEBPB MED12L CLRN1 EIF2A CLRN1-AS1 SIAH2-AS1 ENSG00000243273 FAM188B2 ENSG00000276055
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CLRN1-AS1 on UCSC Golden Path with GeneCards custom track

Genomic Location for CLRN1-AS1 Gene

150,852,484 bp from pter
151,080,726 bp from pter
228,243 bases
Plus strand

Genomic View for CLRN1-AS1 Gene

Genes around CLRN1-AS1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLRN1-AS1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLRN1-AS1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLRN1-AS1 Gene

Proteins for CLRN1-AS1 Gene

Post-translational modifications for CLRN1-AS1 Gene

No Post-translational modifications

No data available for DME Specific Peptides for CLRN1-AS1 Gene

Domains & Families for CLRN1-AS1 Gene

Graphical View of Domain Structure for InterPro Entry

No data available for Gene Families , Protein Domains , Suggested Antigen Peptide Sequences and UniProtKB/Swiss-Prot for CLRN1-AS1 Gene

Function for CLRN1-AS1 Gene

Animal Model Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Phenotypes , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for CLRN1-AS1 Gene

Localization for CLRN1-AS1 Gene

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from COMPARTMENTS and Gene Ontology (GO) - Cellular Components for CLRN1-AS1 Gene

Pathways & Interactions for CLRN1-AS1 Gene

SuperPathways for CLRN1-AS1 Gene

No Data Available

Interacting Proteins for CLRN1-AS1 Gene

Gene Ontology (GO) - Biological Process for CLRN1-AS1 Gene


No data available for Pathways by source and SIGNOR curated interactions for CLRN1-AS1 Gene

Transcripts for CLRN1-AS1 Gene

mRNA/cDNA for CLRN1-AS1 Gene

(3) Additional mRNA sequences :
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CLRN1-AS1 Gene

CLRN1 antisense RNA 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for CLRN1-AS1 Gene

No ASD Table

Relevant External Links for CLRN1-AS1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CLRN1-AS1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CLRN1-AS1 Gene

mRNA differential expression in normal tissues according to GTEx for CLRN1-AS1 Gene

This gene is overexpressed in Whole Blood (x16.0), Liver (x4.9), and Uterus (x4.4).

SOURCE GeneReport for Unigene cluster for CLRN1-AS1 Gene:

genes like me logo Genes that share expression patterns with CLRN1-AS1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for CLRN1-AS1 Gene

Orthologs for CLRN1-AS1 Gene

Evolution for CLRN1-AS1 Gene

Gene Tree for CLRN1-AS1 (if available)
Gene Tree for CLRN1-AS1 (if available)

No data available for Orthologs for CLRN1-AS1 Gene

Paralogs for CLRN1-AS1 Gene

No data available for Paralogs for CLRN1-AS1 Gene

Variants for CLRN1-AS1 Gene

Sequence variations from dbSNP and Humsavar for CLRN1-AS1 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs111033258 Pathogenic 150,972,565(-) GTCAA(G/T)GCCTC nc-transcript-variant, upstream-variant-2KB, reference, missense
rs111033267 Pathogenic 150,972,520(-) CAGTA(A/C/T)GGGCT nc-transcript-variant, upstream-variant-2KB, reference, synonymous-codon, stop-gained
rs121908143 Pathogenic 150,972,591(-) TCCTC(G/T)GCAAA nc-transcript-variant, upstream-variant-2KB, reference, missense
rs374390376 Pathogenic 150,972,617(+) ACAAC(A/C/G)GTGTC nc-transcript-variant, upstream-variant-2KB, reference, missense
rs111033434 Likely pathogenic 150,972,582(-) AAACG(A/G)GAGCT nc-transcript-variant, upstream-variant-2KB, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for CLRN1-AS1 Gene

Variant ID Type Subtype PubMed ID
nsv829756 CNV gain+loss 17160897
nsv592045 CNV gain 21841781
nsv478908 CNV novel sequence insertion 20440878
esv3598168 CNV loss 21293372
esv2762349 CNV loss 21179565
esv2759188 CNV gain 17122850
esv2726050 CNV deletion 23290073
esv2726049 CNV deletion 23290073
esv2726048 CNV deletion 23290073
esv2726047 CNV deletion 23290073
esv2656706 CNV deletion 23128226

Relevant External Links for CLRN1-AS1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for CLRN1-AS1 Gene

Disorders for CLRN1-AS1 Gene

Relevant External Links for CLRN1-AS1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for CLRN1-AS1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CLRN1-AS1 Gene

Publications for CLRN1-AS1 Gene

  1. Mutations in a novel gene with transmembrane domains underlie Usher syndrome type 3. (PMID: 11524702) Joensuu T. … Sankila E.-M. (Am. J. Hum. Genet. 2001) 2 3 64
  2. Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers. (PMID: 23382691) Lauc G. … Rudan I. (PLoS Genet. 2013) 3 64
  3. Alternative splice variants of the USH3A gene Clarin 1 (CLRN1). (PMID: 20717163) Vastinsalo H. … Sankila E.M. (Eur. J. Hum. Genet. 2011) 3 64
  4. Down-regulation of UCRP and UBE2L6 in BRCA2 knocked-down human breast cells. (PMID: 15670748) Tripathi M.K. … Chaudhuri G. (Biochem. Biophys. Res. Commun. 2005) 22 64
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 64

Products for CLRN1-AS1 Gene

Sources for CLRN1-AS1 Gene

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