LINC01352 (long intergenic non-protein coding RNA 1352) - Rat Genome Database

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Gene: LINC01352 (long intergenic non-protein coding RNA 1352) Homo sapiens
Analyze
Symbol: LINC01352
Name: long intergenic non-protein coding RNA 1352
RGD ID: 8656230
HGNC Page HGNC:50578
Description: ASSOCIATED WITH Usher syndrome
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381220,829,255 - 220,832,429 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1220,829,255 - 220,832,429 (+)EnsemblGRCh38hg38GRCh38
GRCh371221,002,597 - 221,005,771 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map1q41NCBI
HuRef1191,677,218 - 191,680,392 (+)NCBIHuRef
CHM1_11222,275,064 - 222,278,238 (+)NCBICHM1_1
T2T-CHM13v2.01220,068,972 - 220,072,146 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
Usher syndrome  (IAGP)

References
Additional References at PubMed
PMID:12477932  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 1q32.2-44(chr1:209963625-248918469)x3 copy number gain See cases [RCV000134979] Chr1:209963625..248918469 [GRCh38]
Chr1:210136970..249212668 [GRCh37]
Chr1:208203593..247179291 [NCBI36]
Chr1:1q32.2-44		 pathogenic
GRCh38/hg38 1q41(chr1:220673535-223683512)x1 copy number loss See cases [RCV000135795] Chr1:220673535..223683512 [GRCh38]
Chr1:220846877..223871214 [GRCh37]
Chr1:218913500..221937837 [NCBI36]
Chr1:1q41		 pathogenic
GRCh38/hg38 1q32.1-42.12(chr1:204764914-225408698)x3 copy number gain See cases [RCV000142054] Chr1:204764914..225408698 [GRCh38]
Chr1:204734042..225596400 [GRCh37]
Chr1:203000665..223663023 [NCBI36]
Chr1:1q32.1-42.12		 pathogenic
GRCh38/hg38 1q32.2-44(chr1:207346642-248930485)x3 copy number gain See cases [RCV000143727] Chr1:207346642..248930485 [GRCh38]
Chr1:207519987..249224684 [GRCh37]
Chr1:205586610..247191307 [NCBI36]
Chr1:1q32.2-44		 pathogenic
GRCh38/hg38 1q41(chr1:215206760-222004068)x1 copy number loss See cases [RCV000148255] Chr1:215206760..222004068 [GRCh38]
Chr1:215380103..222177410 [GRCh37]
Chr1:213446726..220244033 [NCBI36]
Chr1:1q41		 pathogenic
GRCh38/hg38 1q32.3-44(chr1:214023812-248918469)x3 copy number gain See cases [RCV000050981] Chr1:214023812..248918469 [GRCh38]
Chr1:214197155..249212668 [GRCh37]
Chr1:212263778..247179291 [NCBI36]
Chr1:1q32.3-44		 pathogenic
GRCh38/hg38 1q41(chr1:215206760-222004068)x1 copy number loss See cases [RCV000050298] Chr1:215206760..222004068 [GRCh38]
Chr1:215380103..222177410 [GRCh37]
Chr1:213446726..220244033 [NCBI36]
Chr1:1q41		 pathogenic
GRCh38/hg38 1q31.1-42.11(chr1:187143981-224299417)x3 copy number gain See cases [RCV000051857] Chr1:187143981..224299417 [GRCh38]
Chr1:187113113..224487119 [GRCh37]
Chr1:185379736..222553742 [NCBI36]
Chr1:1q31.1-42.11		 pathogenic
GRCh38/hg38 1q32.2-44(chr1:209646207-248931113)x3 copy number gain See cases [RCV000051861] Chr1:209646207..248931113 [GRCh38]
Chr1:209819552..249225312 [GRCh37]
Chr1:207886175..247191935 [NCBI36]
Chr1:1q32.2-44		 pathogenic
GRCh38/hg38 1q41(chr1:215447347-221971832)x3 copy number gain See cases [RCV000051874] Chr1:215447347..221971832 [GRCh38]
Chr1:215620690..222145174 [GRCh37]
Chr1:213687313..220211797 [NCBI36]
Chr1:1q41		 pathogenic
Single allele deletion Usher syndrome [RCV000505151] Chr1:216066818..222607612 [GRCh38]
Chr1:216240159..222780953 [GRCh37]
Chr1:1q41		 likely pathogenic
GRCh38/hg38 1q32.2-42.13(chr1:228006998-228061271)x2 copy number loss Orofacial cleft 2 [RCV002481175] Chr1:228006998..228061271 [GRCh38]
Chr1:1q32.2-42.13		 association
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:102
Count of miRNA genes:101
Interacting mature miRNAs:102
Transcripts:ENST00000431347
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system adipose tissue appendage entire extraembryonic component
High
Medium 1 1 1 1 1 1
Low 1096 1212 403 101 315 89 2383 862 1006 124 506 753 13 910 1670 3
Below cutoff 1115 1424 1120 410 849 282 1711 1204 2333 214 788 692 131 284 1076 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000431347
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1220,829,255 - 220,832,429 (+)Ensembl
RefSeq Acc Id: NR_110797
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381220,829,255 - 220,832,429 (+)NCBI
CHM1_11222,275,064 - 222,278,238 (+)NCBI
T2T-CHM13v2.01220,068,972 - 220,072,146 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC01352 COSMIC
Ensembl Genes ENSG00000238078 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000431347 ENTREZGENE
GTEx ENSG00000238078 GTEx
HGNC ID HGNC:50578 ENTREZGENE
Human Proteome Map LINC01352 Human Proteome Map
NCBI Gene LINC01352 ENTREZGENE
RNAcentral URS000014FB6A RNACentral