LINC02497 (long intergenic non-protein coding RNA 2497) - Rat Genome Database

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Gene: LINC02497 (long intergenic non-protein coding RNA 2497) Homo sapiens
Analyze
Symbol: LINC02497
Name: long intergenic non-protein coding RNA 2497
RGD ID: 12902695
HGNC Page HGNC:53482
Description: INTERACTS WITH permethrin
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
GRCh38431,171,144 - 31,211,675 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl431,171,013 - 31,211,678 (+)EnsemblGRCh38hg38GRCh38
GRCh37431,172,766 - 31,213,297 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map4p15.1NCBI
HuRef430,521,999 - 30,541,848 (+)NCBIHuRef
CHM1_1431,174,095 - 31,214,572 (+)NCBICHM1_1
T2T-CHM13v2.0431,160,121 - 31,200,343 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
permethrin  (EXP)

References

Genomics

Variants

.
Variants in LINC02497
5 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 4p16.3-15.1(chr4:72555-33130620)x3 copy number gain See cases [RCV000051753] Chr4:72555..33130620 [GRCh38]
Chr4:72447..33132242 [GRCh37]
Chr4:62447..32808637 [NCBI36]
Chr4:4p16.3-15.1		 pathogenic
GRCh38/hg38 4p16.3-14(chr4:85149-38700366)x3 copy number gain See cases [RCV000051757] Chr4:85149..38700366 [GRCh38]
Chr4:85040..38701987 [GRCh37]
Chr4:75040..38378382 [NCBI36]
Chr4:4p16.3-14		 pathogenic
GRCh38/hg38 4p16.3-14(chr4:72555-39477144)x3 copy number gain See cases [RCV000133677] Chr4:72555..39477144 [GRCh38]
Chr4:72447..39478764 [GRCh37]
Chr4:62447..39155159 [NCBI36]
Chr4:4p16.3-14		 pathogenic
GRCh38/hg38 4p16.3-12(chr4:36424-47491595)x3 copy number gain See cases [RCV000137261] Chr4:36424..47491595 [GRCh38]
Chr4:36424..47493612 [GRCh37]
Chr4:26424..47188369 [NCBI36]
Chr4:4p16.3-12		 pathogenic
GRCh38/hg38 4p15.1(chr4:31101685-31644046)x3 copy number gain See cases [RCV000133703] Chr4:31101685..31644046 [GRCh38]
Chr4:31103307..31645668 [GRCh37]
Chr4:30712405..31254766 [NCBI36]
Chr4:4p15.1		 uncertain significance
GRCh38/hg38 4p15.32-15.1(chr4:16925022-32113076)x1 copy number loss See cases [RCV000135806] Chr4:16925022..32113076 [GRCh38]
Chr4:16926645..32114698 [GRCh37]
Chr4:16535743..31758596 [NCBI36]
Chr4:4p15.32-15.1		 pathogenic|likely pathogenic
GRCh38/hg38 4p15.33-14(chr4:11399082-38137335) copy number loss 4p partial monosomy syndrome [RCV003155905] Chr4:11399082..38137335 [GRCh38]
Chr4:4p15.33-14		 pathogenic
GRCh38/hg38 4p16.3-q12(chr4:85624-57073230)x3 copy number gain Neurodevelopmental disorder [RCV003327613] Chr4:85624..57073230 [GRCh38]
Chr4:4p16.3-q12		 pathogenic
GRCh38/hg38 4p16.3-13(chr4:2904667-42963232)x3 copy number gain Neurodevelopmental disorder [RCV003327612] Chr4:2904667..42963232 [GRCh38]
Chr4:4p16.3-13		 pathogenic
GRCh38/hg38 4p16.3-11(chr4:1-49062177)x3 copy number gain Neurodevelopmental disorder [RCV003327611] Chr4:1..49062177 [GRCh38]
Chr4:4p16.3-11		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:82
Count of miRNA genes:80
Interacting mature miRNAs:81
Transcripts:ENST00000515292
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
Low 3 15 1 10 22 4 8 271 19 3
Below cutoff 388 506 111 14 87 7 444 205 581 29 259 159 7 19 353

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000515292
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl431,171,013 - 31,211,678 (+)Ensembl
RefSeq Acc Id: ENST00000660077
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl431,171,016 - 31,211,678 (+)Ensembl
RefSeq Acc Id: NR_125935
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38431,171,144 - 31,211,675 (+)NCBI
CHM1_1431,174,095 - 31,214,572 (+)NCBI
T2T-CHM13v2.0431,160,121 - 31,200,343 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC02497 COSMIC
Ensembl Genes ENSG00000251182 Ensembl
GTEx ENSG00000251182 GTEx
HGNC ID HGNC:53482 ENTREZGENE
Human Proteome Map LINC02497 Human Proteome Map
NCBI Gene LINC02497 ENTREZGENE
RNAcentral URS000037A92F RNACentral