LINC01858 (long intergenic non-protein coding RNA 1858) - Rat Genome Database

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Gene: LINC01858 (long intergenic non-protein coding RNA 1858) Homo sapiens
Analyze
Symbol: LINC01858
Name: long intergenic non-protein coding RNA 1858
RGD ID: 11569839
HGNC Page HGNC:52676
Description:
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
GRCh381923,054,823 - 23,061,265 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1923,046,958 - 23,063,705 (-)EnsemblGRCh38hg38GRCh38
GRCh371923,237,625 - 23,244,067 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map19p12NCBI
HuRef1922,778,539 - 22,784,982 (-)NCBIHuRef
CHM1_11923,237,362 - 23,243,816 (-)NCBICHM1_1
T2T-CHM13v2.01923,190,027 - 23,196,469 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:12477932  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 19p12(chr19:22987611-23189484)x1 copy number loss See cases [RCV000140874] Chr19:22987611..23189484 [GRCh38]
Chr19:23170413..23372286 [GRCh37]
Chr19:22962253..23164126 [NCBI36]
Chr19:19p12		 uncertain significance
GRCh38/hg38 19p13.12-q11(chr19:13974677-27839676)x3 copy number gain See cases [RCV000052912] Chr19:13974677..27839676 [GRCh38]
Chr19:14085489..28330584 [GRCh37]
Chr19:13946489..33022424 [NCBI36]
Chr19:19p13.12-q11		 pathogenic
GRCh38/hg38 19p13.11-q13.11(chr19:17176767-34924150)x3 copy number gain See cases [RCV000050635] Chr19:17176767..34924150 [GRCh38]
Chr19:17287576..35415054 [GRCh37]
Chr19:17148576..40106894 [NCBI36]
Chr19:19p13.11-q13.11		 pathogenic
GRCh38/hg38 19p13.2-q13.31(chr19:11227942-44626354)x3 copy number gain See cases [RCV000133888] Chr19:11227942..44626354 [GRCh38]
Chr19:11338618..45129651 [GRCh37]
Chr19:11199618..49821491 [NCBI36]
Chr19:19p13.2-q13.31		 pathogenic
GRCh38/hg38 19p13.12-12(chr19:15133594-24193591)x3 copy number gain See cases [RCV000136696] Chr19:15133594..24193591 [GRCh38]
Chr19:15244405..24376393 [GRCh37]
Chr19:15105405..24168233 [NCBI36]
Chr19:19p13.12-12		 pathogenic|likely pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:201
Count of miRNA genes:192
Interacting mature miRNAs:201
Transcripts:ENST00000564534, ENST00000593985
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 28
Low 8 42 32 1 9 1 34 5 48 9 441 9 1 1
Below cutoff 1290 1159 712 152 332 79 1391 795 2584 146 697 763 83 348 787 3

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000564534
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1923,054,823 - 23,061,265 (-)Ensembl
RefSeq Acc Id: ENST00000593985
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1923,046,958 - 23,061,752 (-)Ensembl
RefSeq Acc Id: ENST00000653153
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1923,056,604 - 23,063,236 (-)Ensembl
RefSeq Acc Id: ENST00000654127
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1923,056,993 - 23,063,705 (-)Ensembl
RefSeq Acc Id: ENST00000668302
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1923,059,913 - 23,060,878 (-)Ensembl
RefSeq Acc Id: NR_110745
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381923,054,823 - 23,061,265 (-)NCBI
CHM1_11923,237,362 - 23,243,816 (-)NCBI
T2T-CHM13v2.01923,190,027 - 23,196,469 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC01858 COSMIC
Ensembl Genes ENSG00000261615 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000564534 ENTREZGENE
GTEx ENSG00000261615 GTEx
HGNC ID HGNC:52676 ENTREZGENE
Human Proteome Map LINC01858 Human Proteome Map
NCBI Gene LINC01858 ENTREZGENE
RNAcentral URS000075ED48 RNACentral