Aliases for CLRN1-AS1 Gene

Subcategory (RNA class) for CLRN1-AS1 Gene


Number of RNA Genes sources:

3 / 14

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
  • CLRN1-AS1 2 168
  • Usher Critical Region Protein Pseudogene 3
  • NONHSAG036394 92
  • HSALNG0029809 167
  • 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 lncRNA class. Diseases associated with CLRN1-AS1 include Usher Syndrome and Usher Syndrome, Type I.

Gene Wiki entry for CLRN1-AS1 Gene

Rfam classification for CLRN1-AS1 Gene

  • CLRN1 antisense RNA 1 conserved region

Additional gene information for CLRN1-AS1 Gene

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

Genomics for CLRN1-AS1 Gene

GeneHancer (GH) Regulatory Elements for CLRN1-AS1 Gene

Promoters and enhancers for CLRN1-AS1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J150888 Promoter/Enhancer 0.8 Ensembl ENCODE 20.1 +37.6 37582 3.1 CEBPG CEBPB SPI1 HLF PKNOX1 CTCF ENSG00000243273 CLRN1-AS1 ERICH6-AS1 MED12L lnc-MINDY4B-1 MINDY4B piR-32651-009 ENSG00000260234
GH03J151145 Enhancer 0.9 ENCODE dbSUPER 10.4 +293.7 293723 1.7 CTCF JUND REST RAD21 TRIM22 SMC3 MXI1 DEK GATA3 CEBPG MED12L P2RY14 MINDY4B ENSG00000243273 CLRN1 CLRN1-AS1 RF00994-691 lnc-SELENOT-5
GH03J151002 Enhancer 0.7 Ensembl ENCODE 11 +150.7 150690 1.7 ZNF316 MAFF MAFK SMAD4 BCL6 GLIS1 JUND FOS GATAD2A CREB1 RF00017-4140 CLRN1 MED12L CLRN1-AS1 MINDY4B ENSG00000243273 piR-41306-194
GH03J151012 Enhancer 0.6 Ensembl ENCODE 10.8 +162.2 162229 4.2 EP300 MXI1 FOS MAX CEBPB CLRN1 CLRN1-AS1 MED12L RF00017-4141 RF00017-4140 ENSG00000243273
GH03J150925 Enhancer 0.5 FANTOM5 11 +73.1 73075 0.2 CTCF CTBP1 SIN3A XRCC5 RBM39 RNF2 CREB1 TRIM22 ZNF444 MINDY4B ENSG00000243273 CLRN1 CLRN1-AS1 MED12L P2RY14 ENSG00000260234
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

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

Genomic Locations for CLRN1-AS1 Gene

Genomic Locations for CLRN1-AS1 Gene
228,243 bases
Plus strand
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

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

Function for CLRN1-AS1 Gene

Phenotypes From GWAS Catalog for CLRN1-AS1 Gene

Animal Model Products

CRISPR 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 , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for CLRN1-AS1 Gene

Pathways & Interactions for CLRN1-AS1 Gene

PathCards logo

SuperPathways for CLRN1-AS1 Gene

No Data Available

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


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

Drugs & Compounds for CLRN1-AS1 Gene

No Compound Related Data Available

Transcripts for CLRN1-AS1 Gene

mRNA/cDNA for CLRN1-AS1 Gene

4 RNACentral transcripts :
2 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :
2 NONCODE transcripts :
3 LncBook transcripts :
1 LNCipedia transcripts :

CRISPR Products

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

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).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CLRN1-AS1

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 , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer 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, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CLRN1-AS1 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
730216 Likely Benign: not provided 150,972,689(+) T/A MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
rs1057517224 Likely Pathogenic: Usher syndrome, type 3A 150,972,696(+) G/A NONSENSE,NON_CODING_TRANSCRIPT_VARIANT
rs111033422 Benign/Likely Benign: Usher syndrome, type 3A; Retinitis pigmentosa-deafness syndrome; not specified; Retinitis Pigmentosa, Dominant; not provided 150,972,703(+) T/G NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
rs1553776132 Likely Pathogenic: Usher syndrome, type 3A 150,972,706(+) C/T INITIATIOR_CODON_VARIANT,MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
rs1553776135 Likely Pathogenic: Usher syndrome, type 3A 150,972,707(+) A/G INITIATIOR_CODON_VARIANT,MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT

Additional dbSNP identifiers (rs#s) for CLRN1-AS1 Gene

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

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

Additional Variant Information 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

MalaCards: The human disease database

(3) MalaCards diseases for CLRN1-AS1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
usher syndrome
  • retinitis pigmentosa-deafness syndrome
usher syndrome, type i
  • ush1
retinitis pigmentosa
  • retinitis pigmentosa 1
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for CLRN1-AS1

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

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

Publications for CLRN1-AS1 Gene

  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. (PMID: 31235696) Wang C … Wang X (Cell death & disease 2019) 2 3 54
  2. Mutations in a novel gene with transmembrane domains underlie Usher syndrome type 3. (PMID: 11524702) Joensuu T … Sankila EM (American journal of human genetics 2001) 2 3 54
  3. Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers. (PMID: 23382691) Lauc G … Rudan I (PLoS genetics 2013) 3 54
  4. Alternative splice variants of the USH3A gene Clarin 1 (CLRN1). (PMID: 20717163) Västinsalo H … Sankila EM (European journal of human genetics : EJHG 2011) 3 54
  5. Down-regulation of UCRP and UBE2L6 in BRCA2 knocked-down human breast cells. (PMID: 15670748) Tripathi MK … Chaudhuri G (Biochemical and biophysical research communications 2005) 23 54

Products for CLRN1-AS1 Gene

Sources for CLRN1-AS1 Gene