LINC01593 (long intergenic non-protein coding RNA 1593) - Rat Genome Database
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Pathways
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Gene: LINC01593 (long intergenic non-protein coding RNA 1593) Homo sapiens
Analyze
Symbol: LINC01593
Name: long intergenic non-protein coding RNA 1593
RGD ID: 10769211
HGNC Page HGNC
Description: ASSOCIATED WITH distal hereditary motor neuronopathy type 7A
Type: ncrna
RefSeq Status: VALIDATED
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2108,049,200 - 108,052,755 (-)EnsemblGRCh38hg38GRCh38
GRCh382108,049,200 - 108,052,755 (-)NCBIGRCh38GRCh38hg38GRCh38
Cytogenetic Map2q12.3NCBI
CHM1_12108,669,953 - 108,673,508 (-)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References

Genomics

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:41
Count of miRNA genes:41
Interacting mature miRNAs:41
Transcripts:ENST00000424355
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
High
Medium 6 1 1 2
Low 105 3 23 8 11 8 35 3 23 183 80 33 8 16
Below cutoff 298 112 224 31 99 28 312 65 355 101 354 209 4 158 178

Sequence

Nucleotide Sequences
RefSeq Transcripts NR_135071 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC023672 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000424355
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2108,049,200 - 108,052,755 (-)Ensembl
RefSeq Acc Id: NR_135071
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382108,049,200 - 108,052,755 (-)NCBI
CHM1_12108,669,953 - 108,673,508 (-)NCBI
Sequence:

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 2q11.2-13(chr2:101710825-110791418)x3 copy number gain See cases [RCV000138645] Chr2:101710825..110791418 [GRCh38]
Chr2:102327287..111548995 [GRCh37]
Chr2:101693719..111265466 [NCBI36]
Chr2:2q11.2-13		 pathogenic
GRCh38/hg38 2q12.3(chr2:107924122-108472871)x3 copy number gain See cases [RCV000139122] Chr2:107924122..108472871 [GRCh38]
Chr2:108540578..109089327 [GRCh37]
Chr2:107907010..108455759 [NCBI36]
Chr2:2q12.3		 uncertain significance
GRCh38/hg38 2q11.1-13(chr2:94678532-110602409)x3 copy number gain See cases [RCV000141075] Chr2:94678532..110602409 [GRCh38]
Chr2:95344257..111359986 [GRCh37]
Chr2:94707984..111076455 [NCBI36]
Chr2:2q11.1-13		 pathogenic
GRCh38/hg38 2q12.3(chr2:107901810-108472871)x3 copy number gain See cases [RCV000141241] Chr2:107901810..108472871 [GRCh38]
Chr2:108518266..109089327 [GRCh37]
Chr2:107884698..108455759 [NCBI36]
Chr2:2q12.3		 uncertain significance
GRCh38/hg38 2q12.2-13(chr2:106516472-110576905)x3 copy number gain See cases [RCV000139569] Chr2:106516472..110576905 [GRCh38]
Chr2:107132928..111334482 [GRCh37]
Chr2:106499360..110857227 [NCBI36]
Chr2:2q12.2-13		 uncertain significance
GRCh38/hg38 2q12.2-14.1(chr2:106428663-112379067)x3 copy number gain See cases [RCV000140834] Chr2:106428663..112379067 [GRCh38]
Chr2:107045119..113136644 [GRCh37]
Chr2:106411551..112853115 [NCBI36]
Chr2:2q12.2-14.1		 uncertain significance
GRCh38/hg38 2q11.2-12.3(chr2:100378510-108472871)x3 copy number gain See cases [RCV000050836] Chr2:100378510..108472871 [GRCh38]
Chr2:100994972..109089327 [GRCh37]
Chr2:100361404..108455759 [NCBI36]
Chr2:2q11.2-12.3		 pathogenic
GRCh38/hg38 2q12.2-12.3(chr2:105828398-108080417)x3 copy number gain See cases [RCV000052691] Chr2:105828398..108080417 [GRCh38]
Chr2:106444854..108696873 [GRCh37]
Chr2:105811286..108063305 [NCBI36]
Chr2:2q12.2-12.3		 uncertain significance
GRCh38/hg38 2q11.2-13(chr2:97672522-110211318)x3 copy number gain See cases [RCV000052947] Chr2:97672522..110211318 [GRCh38]
Chr2:98288985..110968895 [GRCh37]
Chr2:97655417..110326184 [NCBI36]
Chr2:2q11.2-13		 pathogenic
GRCh38/hg38 2q12.2-13(chr2:106696282-110223328)x3 copy number gain See cases [RCV000053141] Chr2:106696282..110223328 [GRCh38]
Chr2:107312738..110980905 [GRCh37]
Chr2:106679170..110338194 [NCBI36]
Chr2:2q12.2-13		 uncertain significance
GRCh38/hg38 2q12.3(chr2:107924122-108509089)x1 copy number loss See cases [RCV000137577] Chr2:107924122..108509089 [GRCh38]
Chr2:108540578..109125545 [GRCh37]
Chr2:107907010..108491977 [NCBI36]
Chr2:2q12.3		 uncertain significance
Single allele duplication Neuronopathy, distal hereditary motor, type viia [RCV000534213] Chr2:107988136..108963283 [GRCh38]
Chr2:2q12.3-13		 uncertain significance
GRCh38/hg38 2q12.3-13(chr2:107962353-109700179)x1 copy number loss See cases [RCV000134167] Chr2:107962353..109700179 [GRCh38]
Chr2:108578809..110457756 [GRCh37]
Chr2:107945241..109815045 [NCBI36]
Chr2:2q12.3-13		 pathogenic|uncertain significance

Additional Information

Database Acc Id Source(s)
COSMIC LINC01593 COSMIC
Ensembl Genes ENSG00000231221 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000424355 ENTREZGENE
GTEx ENSG00000231221 GTEx
HGNC ID HGNC:51583 ENTREZGENE
Human Proteome Map LINC01593 Human Proteome Map
NCBI Gene LINC01593 ENTREZGENE
RNAcentral URS00003091F8 RNACentral