LINC02542 (long intergenic non-protein coding RNA 2542) - Rat Genome Database

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Gene: LINC02542 (long intergenic non-protein coding RNA 2542) Homo sapiens
Analyze
Symbol: LINC02542
Name: long intergenic non-protein coding RNA 2542
RGD ID: 12910210
HGNC Page HGNC:53576
Description: INTERACTS WITH benzo[a]pyrene
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
GRCh38681,843,781 - 82,101,765 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl681,844,602 - 82,169,391 (-)EnsemblGRCh38hg38GRCh38
GRCh37682,553,498 - 82,811,482 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map6q14.1NCBI
HuRef679,771,252 - 79,865,813 (-)NCBIHuRef
CHM1_1682,651,123 - 82,893,216 (-)NCBICHM1_1
T2T-CHM13v2.0683,053,185 - 83,311,151 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:16344560  


Genomics

Variants

.
Variants in LINC02542
15 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 6q13-24.1(chr6:74382807-142040500)x3 copy number gain See cases [RCV000139729] Chr6:74382807..142040500 [GRCh38]
Chr6:75092523..142361637 [GRCh37]
Chr6:75149243..142403330 [NCBI36]
Chr6:6q13-24.1
pathogenic
GRCh38/hg38 6q12-14.2(chr6:64549655-83426791)x1 copy number loss See cases [RCV000142527] Chr6:64549655..83426791 [GRCh38]
Chr6:65259548..84136510 [GRCh37]
Chr6:65316269..84193229 [NCBI36]
Chr6:6q12-14.2
pathogenic
GRCh38/hg38 6q14.1-16.1(chr6:75926199-92710793)x1 copy number loss See cases [RCV000143505] Chr6:75926199..92710793 [GRCh38]
Chr6:76635916..93420511 [GRCh37]
Chr6:76692636..93477232 [NCBI36]
Chr6:6q14.1-16.1
pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:65
Count of miRNA genes:64
Interacting mature miRNAs:64
Transcripts:ENST00000418567
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 19 48 75 19 49 4 2 1 11 24 63 27
Low 493 1474 482 496 344 366 1750 310 283 140 829 434 142 350 986 3
Below cutoff 1498 855 893 49 556 47 1816 1088 1838 194 444 822 2 754 1109 1

Sequence


RefSeq Acc Id: ENST00000418567
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl681,844,604 - 81,933,578 (-)Ensembl
RefSeq Acc Id: ENST00000658218
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl681,844,604 - 81,860,397 (-)Ensembl
RefSeq Acc Id: ENST00000660534
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl681,844,606 - 81,938,437 (-)Ensembl
RefSeq Acc Id: ENST00000660637
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl681,844,604 - 82,101,800 (-)Ensembl
RefSeq Acc Id: ENST00000663543
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl681,844,604 - 82,169,391 (-)Ensembl
RefSeq Acc Id: ENST00000665153
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl681,844,604 - 81,895,717 (-)Ensembl
RefSeq Acc Id: ENST00000666226
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl681,844,604 - 82,101,765 (-)Ensembl
RefSeq Acc Id: ENST00000667666
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl681,844,602 - 82,169,338 (-)Ensembl
RefSeq Acc Id: ENST00000668266
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl681,844,604 - 82,101,792 (-)Ensembl
RefSeq Acc Id: ENST00000668303
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl681,844,604 - 82,160,755 (-)Ensembl
RefSeq Acc Id: ENST00000684960
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl681,845,540 - 81,938,452 (-)Ensembl
RefSeq Acc Id: ENST00000702318
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl681,845,547 - 81,938,468 (-)Ensembl
RefSeq Acc Id: NR_149134
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38681,843,781 - 81,938,421 (-)NCBI
T2T-CHM13v2.0683,053,185 - 83,147,737 (-)NCBI
Sequence:
RefSeq Acc Id: NR_149135
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38681,843,781 - 82,101,765 (-)NCBI
T2T-CHM13v2.0683,053,185 - 83,311,151 (-)NCBI
Sequence:
RefSeq Acc Id: NR_149136
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38681,843,781 - 81,933,480 (-)NCBI
T2T-CHM13v2.0683,053,185 - 83,142,795 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC02542 COSMIC
Ensembl Genes ENSG00000226453 Ensembl
GTEx ENSG00000226453 GTEx
HGNC ID HGNC:53576 ENTREZGENE
Human Proteome Map LINC02542 Human Proteome Map
NCBI Gene LINC02542 ENTREZGENE
RNAcentral URS0000BC4515 RNACentral
  URS0000BC4554 RNACentral
  URS0000BC45C5 RNACentral