LINC01520 (long intergenic non-protein coding RNA 1520) - Rat Genome Database

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Gene: LINC01520 (long intergenic non-protein coding RNA 1520) Homo sapiens
Analyze
Symbol: LINC01520
Name: long intergenic non-protein coding RNA 1520
RGD ID: 8698837
HGNC Page HGNC:51218
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
GRCh381085,449,592 - 85,492,001 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1085,449,592 - 85,492,001 (+)EnsemblGRCh38hg38GRCh38
GRCh371087,209,349 - 87,251,758 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map10q23.1NCBI
HuRef1081,055,323 - 81,097,736 (+)NCBIHuRef
CHM1_11087,491,490 - 87,533,893 (+)NCBICHM1_1
T2T-CHM13v2.01086,329,829 - 86,372,242 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
Additional References at PubMed
PMID:11329013  


Genomics

Variants

.
Variants in LINC01520
2 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NR_120671.1(LINC01520):n.1208+2789G>A single nucleotide variant Lung cancer [RCV000109437] Chr10:85464486 [GRCh38]
Chr10:87224243 [GRCh37]
Chr10:10q23.1
uncertain significance
GRCh38/hg38 10q22.3-23.2(chr10:79925613-86951708)x1 copy number loss See cases [RCV000135348] Chr10:79925613..86951708 [GRCh38]
Chr10:81685369..88711465 [GRCh37]
Chr10:81675349..88701445 [NCBI36]
Chr10:10q22.3-23.2
pathogenic
GRCh38/hg38 10q22.3-23.2(chr10:79802022-87068261)x1 copy number loss See cases [RCV000136565] Chr10:79802022..87068261 [GRCh38]
Chr10:81561459..88828018 [GRCh37]
Chr10:81263385..88817998 [NCBI36]
Chr10:10q22.3-23.2
pathogenic
GRCh38/hg38 10q11.23-23.2(chr10:50729367-87147204)x3 copy number gain See cases [RCV000138007] Chr10:50729367..87147204 [GRCh38]
Chr10:52489127..88906961 [GRCh37]
Chr10:52159133..88896941 [NCBI36]
Chr10:10q11.23-23.2
pathogenic
GRCh38/hg38 10q22.3-23.2(chr10:79689360-87223773)x1 copy number loss See cases [RCV000141724] Chr10:79689360..87223773 [GRCh38]
Chr10:81449116..88983530 [GRCh37]
Chr10:81119122..88973510 [NCBI36]
Chr10:10q22.3-23.2
pathogenic
GRCh38/hg38 10q22.3-23.2(chr10:79881238-87180672)x1 copy number loss See cases [RCV000143178] Chr10:79881238..87180672 [GRCh38]
Chr10:81640994..88940429 [GRCh37]
Chr10:81630974..88930409 [NCBI36]
Chr10:10q22.3-23.2
pathogenic
GRCh38/hg38 10q22.3-23.2(chr10:79882162-87068261)x1 copy number loss See cases [RCV000148069] Chr10:79882162..87068261 [GRCh38]
Chr10:81641918..88828018 [GRCh37]
Chr10:81631898..88817998 [NCBI36]
Chr10:10q22.3-23.2
pathogenic
GRCh38/hg38 10q22.3-23.2(chr10:79719429-87358394)x1 copy number loss See cases [RCV000052534] Chr10:79719429..87358394 [GRCh38]
Chr10:81479185..89118151 [GRCh37]
Chr10:81149191..89108131 [NCBI36]
Chr10:10q22.3-23.2
pathogenic
GRCh38/hg38 10q22.3-23.2(chr10:79802022-87358394)x1 copy number loss See cases [RCV000052537] Chr10:79802022..87358394 [GRCh38]
Chr10:81561459..89118151 [GRCh37]
Chr10:81541288..89108131 [NCBI36]
Chr10:10q22.3-23.2
pathogenic
GRCh38/hg38 10q22.3-23.2(chr10:79882162-87068261)x1 copy number loss See cases [RCV000052539] Chr10:79882162..87068261 [GRCh38]
Chr10:81641918..88828018 [GRCh37]
Chr10:81631898..88817998 [NCBI36]
Chr10:10q22.3-23.2
pathogenic|conflicting data from submitters
GRCh38/hg38 10q22.3-23.2(chr10:79898516-86964367)x1 copy number loss See cases [RCV000052541] Chr10:79898516..86964367 [GRCh38]
Chr10:81658272..88724124 [GRCh37]
Chr10:81648252..88714104 [NCBI36]
Chr10:10q22.3-23.2
pathogenic
GRCh38/hg38 10q22.3-23.2(chr10:79898516-87358394)x1 copy number loss See cases [RCV000052542] Chr10:79898516..87358394 [GRCh38]
Chr10:81658272..89118151 [GRCh37]
Chr10:81648252..89108131 [NCBI36]
Chr10:10q22.3-23.2
pathogenic
GRCh38/hg38 10q22.3-23.2(chr10:79898516-87109827)x1 copy number loss See cases [RCV000052544] Chr10:79898516..87109827 [GRCh38]
Chr10:81658272..88869584 [GRCh37]
Chr10:81648252..88859564 [NCBI36]
Chr10:10q22.3-23.2
pathogenic
GRCh38/hg38 10q23.1-23.31(chr10:84925492-88002064)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052546]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052546]|See cases [RCV000052546] Chr10:84925492..88002064 [GRCh38]
Chr10:86685248..89761821 [GRCh37]
Chr10:86675228..89751801 [NCBI36]
Chr10:10q23.1-23.31
pathogenic
GRCh38/hg38 10q22.3-23.2(chr10:79881238-87182117)x3 copy number gain See cases [RCV000053558] Chr10:79881238..87182117 [GRCh38]
Chr10:81640994..88941874 [GRCh37]
Chr10:81630974..88931854 [NCBI36]
Chr10:10q22.3-23.2
pathogenic
GRCh38/hg38 10q23.1-23.31(chr10:84434981-89150802)x3 copy number gain See cases [RCV000053559] Chr10:84434981..89150802 [GRCh38]
Chr10:86194737..90910559 [GRCh37]
Chr10:86184717..90900539 [NCBI36]
Chr10:10q23.1-23.31
pathogenic
GRCh37/hg19 10q23.1-23.31(chr10:86766571-92609514)x1 copy number loss See cases [RCV000447104] Chr10:86766571..92609514 [GRCh37]
Chr10:10q23.1-23.31
pathogenic
GRCh37/hg19 10q22.3-23.2(chr10:81630468-88975551)x1 copy number loss See cases [RCV000447214] Chr10:81630468..88975551 [GRCh37]
Chr10:10q22.3-23.2
pathogenic
GRCh37/hg19 10q22.3-23.2(chr10:81892411-88722952)x1 copy number loss See cases [RCV000447520] Chr10:81892411..88722952 [GRCh37]
Chr10:10q22.3-23.2
pathogenic
GRCh37/hg19 10q23.1-25.1(chr10:85557432-105804295)x1 copy number loss Poly (ADP-Ribose) polymerase inhibitor response [RCV000431909] Chr10:85557432..105804295 [GRCh37]
Chr10:10q23.1-25.1
pathogenic|drug response
GRCh37/hg19 10q22.3-23.2(chr10:81630468-88973570)x3 copy number gain See cases [RCV000448704] Chr10:81630468..88973570 [GRCh37]
Chr10:10q22.3-23.2
pathogenic
GRCh37/hg19 10p15.3-q26.3(chr10:93297-135378918)x3 copy number gain See cases [RCV000448750] Chr10:93297..135378918 [GRCh37]
Chr10:10p15.3-q26.3
pathogenic
GRCh37/hg19 10q22.3-23.2(chr10:81597767-88951347)x1 copy number loss See cases [RCV000511644] Chr10:81597767..88951347 [GRCh37]
Chr10:10q22.3-23.2
pathogenic
GRCh37/hg19 10q23.1-23.2(chr10:82013260-89166455)x1 copy number loss See cases [RCV000511659] Chr10:82013260..89166455 [GRCh37]
Chr10:10q23.1-23.2
pathogenic
GRCh37/hg19 10q22.3-23.2(chr10:81617260-88980961)x1 copy number loss See cases [RCV000511693] Chr10:81617260..88980961 [GRCh37]
Chr10:10q22.3-23.2
pathogenic
GRCh37/hg19 10p15.3-q26.3(chr10:100027-135427143) copy number gain See cases [RCV000511389] Chr10:100027..135427143 [GRCh37]
Chr10:10p15.3-q26.3
pathogenic|uncertain significance
GRCh37/hg19 10p15.3-q26.3(chr10:100027-135427143)x3 copy number gain See cases [RCV000510861] Chr10:100027..135427143 [GRCh37]
Chr10:10p15.3-q26.3
pathogenic
GRCh37/hg19 10q22.3-23.2(chr10:81697811-88768847) copy number loss not provided [RCV000767565] Chr10:81697811..88768847 [GRCh37]
Chr10:10q22.3-23.2
pathogenic
GRCh37/hg19 10q11.21-26.3(chr10:42347406-135534747)x1 copy number loss Poly (ADP-Ribose) polymerase inhibitor response [RCV000626438] Chr10:42347406..135534747 [GRCh37]
Chr10:10q11.21-26.3
drug response
GRCh37/hg19 10q22.3-23.2(chr10:81644079-88973306)x3 copy number gain not provided [RCV000683282] Chr10:81644079..88973306 [GRCh37]
Chr10:10q22.3-23.2
pathogenic|likely pathogenic
GRCh37/hg19 10q23.1-23.32(chr10:83379241-93219169)x1 copy number loss not provided [RCV000683284] Chr10:83379241..93219169 [GRCh37]
Chr10:10q23.1-23.32
pathogenic
GRCh37/hg19 10q21.3-23.32(chr10:69040366-93194993)x3 copy number gain not provided [RCV000683289] Chr10:69040366..93194993 [GRCh37]
Chr10:10q21.3-23.32
pathogenic
GRCh37/hg19 10q23.1(chr10:87243040-87249036)x0 copy number loss not provided [RCV000749726] Chr10:87243040..87249036 [GRCh37]
Chr10:10q23.1
benign
GRCh37/hg19 10p15.3-q26.3(chr10:73232-135524321)x3 copy number gain not provided [RCV000749464] Chr10:73232..135524321 [GRCh37]
Chr10:10p15.3-q26.3
pathogenic
GRCh37/hg19 10p15.3-q26.3(chr10:98087-135477883)x3 copy number gain not provided [RCV000749465] Chr10:98087..135477883 [GRCh37]
Chr10:10p15.3-q26.3
pathogenic
GRCh37/hg19 10q22.3-23.2(chr10:81617260-88980961)x1 copy number loss not provided [RCV001006339] Chr10:81617260..88980961 [GRCh37]
Chr10:10q22.3-23.2
pathogenic
GRCh37/hg19 10q22.3-23.2(chr10:81617260-89146780)x1 copy number loss not provided [RCV001258450] Chr10:81617260..89146780 [GRCh37]
Chr10:10q22.3-23.2
pathogenic
GRCh37/hg19 10q22.3-23.2(chr10:81630468-88980961) copy number loss Chromosome 10q23 deletion syndrome [RCV002280714] Chr10:81630468..88980961 [GRCh37]
Chr10:10q22.3-23.2
pathogenic
Single allele deletion not provided [RCV001260503] Chr10:81585301..89101700 [GRCh37]
Chr10:10q22.3-23.2
pathogenic
GRCh37/hg19 10q22.3-23.2(chr10:81457752-89253430)x1 copy number loss not provided [RCV001258451] Chr10:81457752..89253430 [GRCh37]
Chr10:10q22.3-23.2
pathogenic
GRCh37/hg19 10q23.1-23.31(chr10:87232436-89649679)x1 copy number loss not provided [RCV001827740] Chr10:87232436..89649679 [GRCh37]
Chr10:10q23.1-23.31
pathogenic
GRCh37/hg19 10q23.1-23.31(chr10:83533660-91913077)x1 copy number loss See cases [RCV002287561] Chr10:83533660..91913077 [GRCh37]
Chr10:10q23.1-23.31
pathogenic
GRCh37/hg19 10q22.3-23.31(chr10:80585057-89721049)x3 copy number gain not provided [RCV002266548] Chr10:80585057..89721049 [GRCh37]
Chr10:10q22.3-23.31
not provided
GRCh37/hg19 10q23.1-23.32(chr10:82595472-93542416)x1 copy number loss not provided [RCV002472429] Chr10:82595472..93542416 [GRCh37]
Chr10:10q23.1-23.32
pathogenic
GRCh37/hg19 10p14-q26.3(chr10:11138692-135427143) copy number gain Distal trisomy 10q [RCV003319593] Chr10:11138692..135427143 [GRCh37]
Chr10:10p14-q26.3
pathogenic
GRCh37/hg19 10p13-q26.3(chr10:12829206-135427143) copy number loss Distal 10q deletion syndrome [RCV003319583] Chr10:12829206..135427143 [GRCh37]
Chr10:10p13-q26.3
pathogenic
GRCh37/hg19 10q22.3-23.2(chr10:81611360-89264122)x3 copy number gain See cases [RCV003329515] Chr10:81611360..89264122 [GRCh37]
Chr10:10q22.3-23.2
pathogenic
GRCh37/hg19 10q11.21-24.2(chr10:42709645-100834951)x3 copy number gain not provided [RCV003484798] Chr10:42709645..100834951 [GRCh37]
Chr10:10q11.21-24.2
pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:92
Count of miRNA genes:87
Interacting mature miRNAs:87
Transcripts:ENST00000441457
Prediction methods:Microtar, 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 3 197 1
Below cutoff 32 27 75 5 33 4 102 30 189 13 194 30 1 13 73

Sequence


RefSeq Acc Id: ENST00000441457
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1085,449,592 - 85,491,996 (+)Ensembl
RefSeq Acc Id: ENST00000652859
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1085,449,664 - 85,492,001 (+)Ensembl
RefSeq Acc Id: ENST00000659541
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1085,449,802 - 85,492,001 (+)Ensembl
RefSeq Acc Id: NR_120671
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381085,449,592 - 85,492,001 (+)NCBI
CHM1_11087,491,490 - 87,533,898 (+)NCBI
T2T-CHM13v2.01086,329,829 - 86,372,242 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC01520 COSMIC
Ensembl Genes ENSG00000230962 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000441457 ENTREZGENE
GTEx ENSG00000230962 GTEx
HGNC ID HGNC:51218 ENTREZGENE
Human Proteome Map LINC01520 Human Proteome Map
NCBI Gene LINC01520 ENTREZGENE
RNAcentral URS000075B6C0 RNACentral