LINC00518 (long intergenic non-protein coding RNA 518) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: LINC00518 (long intergenic non-protein coding RNA 518) Homo sapiens
Analyze
Symbol: LINC00518
Name: long intergenic non-protein coding RNA 518
RGD ID: 1602284
HGNC Page HGNC:28626
Description: INTERACTS WITH benzo[e]pyrene; methapyrilene; permethrin
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: C6orf218; LENOX; MGC40222; RP1-290I10.8
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38610,427,785 - 10,434,822 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl610,429,255 - 10,435,015 (-)EnsemblGRCh38hg38GRCh38
GRCh37610,428,018 - 10,435,055 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36610,537,663 - 10,542,760 (-)NCBINCBI36Build 36hg18NCBI36
Celera611,656,497 - 11,663,529 (-)NCBICelera
Cytogenetic Map6p24.3NCBI
HuRef610,303,776 - 10,310,807 (-)NCBIHuRef
CHM1_1610,430,265 - 10,437,301 (-)NCBICHM1_1
T2T-CHM13v2.0610,295,518 - 10,302,554 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Molecular Function

References
Additional References at PubMed
PMID:12477932   PMID:24906614   PMID:25416956   PMID:30001527   PMID:30462844   PMID:30611858   PMID:30720156   PMID:31391242   PMID:31712557   PMID:32814053   PMID:33371395   PMID:33664256  
PMID:36214632  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 6p25.3-24.1(chr6:164360-13339881)x3 copy number gain See cases [RCV000134022] Chr6:164360..13339881 [GRCh38]
Chr6:164360..13340113 [GRCh37]
Chr6:109360..13448092 [NCBI36]
Chr6:6p25.3-24.1		 pathogenic
GRCh38/hg38 6p25.2-24.1(chr6:4068792-13267799)x1 copy number loss See cases [RCV000136132] Chr6:4068792..13267799 [GRCh38]
Chr6:4069026..13268031 [GRCh37]
Chr6:4014025..13376010 [NCBI36]
Chr6:6p25.2-24.1		 pathogenic
GRCh38/hg38 6p25.3-22.3(chr6:152634-15732163)x3 copy number gain See cases [RCV000138121] Chr6:152634..15732163 [GRCh38]
Chr6:152634..15732394 [GRCh37]
Chr6:97634..15840373 [NCBI36]
Chr6:6p25.3-22.3		 likely benign
GRCh38/hg38 6p25.2-21.33(chr6:3224310-30657190)x3 copy number gain See cases [RCV000138956] Chr6:3224310..30657190 [GRCh38]
Chr6:3224544..30624967 [GRCh37]
Chr6:3169543..30732946 [NCBI36]
Chr6:6p25.2-21.33		 pathogenic
GRCh38/hg38 6p25.3-22.3(chr6:155807-17058414)x3 copy number gain See cases [RCV000140307] Chr6:155807..17058414 [GRCh38]
Chr6:155807..17058645 [GRCh37]
Chr6:100807..17166624 [NCBI36]
Chr6:6p25.3-22.3		 pathogenic
GRCh38/hg38 6p25.3-24.2(chr6:156974-11550817)x3 copy number gain See cases [RCV000142295] Chr6:156974..11550817 [GRCh38]
Chr6:156974..11551050 [GRCh37]
Chr6:101974..11659036 [NCBI36]
Chr6:6p25.3-24.2		 likely pathogenic
GRCh38/hg38 6p25.2-22.3(chr6:2862640-16697788)x1 copy number loss See cases [RCV000142435] Chr6:2862640..16697788 [GRCh38]
Chr6:2862874..16698019 [GRCh37]
Chr6:2807873..16805998 [NCBI36]
Chr6:6p25.2-22.3		 pathogenic
GRCh38/hg38 6p25.3-23(chr6:152634-14417003)x3 copy number gain See cases [RCV000143334] Chr6:152634..14417003 [GRCh38]
Chr6:152634..14417234 [GRCh37]
Chr6:97634..14525213 [NCBI36]
Chr6:6p25.3-23		 pathogenic
GRCh38/hg38 6p25.3-24.1(chr6:156974-13081201)x3 copy number gain See cases [RCV000143698] Chr6:156974..13081201 [GRCh38]
Chr6:156974..13081433 [GRCh37]
Chr6:101974..13189419 [NCBI36]
Chr6:6p25.3-24.1		 likely pathogenic
GRCh38/hg38 6p25.3-23(chr6:156974-13855925)x1 copy number loss See cases [RCV000143782] Chr6:156974..13855925 [GRCh38]
Chr6:156974..13856156 [GRCh37]
Chr6:101974..13964135 [NCBI36]
Chr6:6p25.3-23		 pathogenic
GRCh38/hg38 6p25.3-12.3(chr6:156974-46789291)x3 copy number gain See cases [RCV000143497] Chr6:156974..46789291 [GRCh38]
Chr6:156974..46757028 [GRCh37]
Chr6:101974..46864987 [NCBI36]
Chr6:6p25.3-12.3		 pathogenic
GRCh38/hg38 6p25.3-22.3(chr6:106431-18360595)x3 copy number gain See cases [RCV000051869] Chr6:106431..18360595 [GRCh38]
Chr6:106431..18360826 [GRCh37]
Chr6:51431..18468805 [NCBI36]
Chr6:6p25.3-22.3		 pathogenic
GRCh38/hg38 6p25.3-23(chr6:389423-13474956)x3 copy number gain See cases [RCV000051896] Chr6:389423..13474956 [GRCh38]
Chr6:389423..13475188 [GRCh37]
Chr6:334423..13583167 [NCBI36]
Chr6:6p25.3-23		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:272
Count of miRNA genes:184
Interacting mature miRNAs:191
Transcripts:ENST00000472178, ENST00000479822, ENST00000487130, ENST00000491317, ENST00000496285
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.

Markers in Region
RH94060  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37610,428,151 - 10,428,340UniSTSGRCh37
Build 36610,536,137 - 10,536,326RGDNCBI36
Celera611,656,630 - 11,656,819RGD
Cytogenetic Map6p24.3UniSTS
HuRef610,303,909 - 10,304,098UniSTS
GeneMap99-GB4 RH Map645.89UniSTS


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 visual system adipose tissue appendage entire extraembryonic component
High
Medium 2 1 67 1 2
Low 22 9 6 2 6 686 12 14 8 369 46 11 1 295
Below cutoff 336 168 135 94 93 22 920 127 374 61 284 167 72 104 577 5

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000472178
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl610,429,709 - 10,434,495 (-)Ensembl
RefSeq Acc Id: ENST00000479822
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl610,429,262 - 10,434,835 (-)Ensembl
RefSeq Acc Id: ENST00000487130
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl610,429,548 - 10,434,874 (-)Ensembl
RefSeq Acc Id: ENST00000491317
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl610,429,796 - 10,434,817 (-)Ensembl
RefSeq Acc Id: ENST00000496285
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl610,429,255 - 10,435,003 (-)Ensembl
RefSeq Acc Id: ENST00000655125
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl610,429,255 - 10,435,015 (-)Ensembl
RefSeq Acc Id: ENST00000656574
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl610,429,257 - 10,434,477 (-)Ensembl
RefSeq Acc Id: ENST00000662081
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl610,429,263 - 10,434,957 (-)Ensembl
RefSeq Acc Id: NR_027793
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38610,427,785 - 10,434,822 (-)NCBI
GRCh37610,428,018 - 10,435,055 (-)RGD
Celera611,656,497 - 11,663,529 (-)RGD
HuRef610,303,776 - 10,310,807 (-)RGD
CHM1_1610,430,265 - 10,437,301 (-)NCBI
T2T-CHM13v2.0610,295,518 - 10,302,554 (-)NCBI
Sequence:
Reference Protein Sequences

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8N0U6-F1-model_v2 AlphaFold Q8N0U6 1-118 view protein structure

Promoters
RGD ID:15095990
Promoter ID:EPDNEWNC_H833
Type:initiation region
Name:LINC00518_1
Description:long intergenic non-protein coding RNA 518 [Source:HGNCSymbol;Acc:HGNC:28626]
SO ACC ID:SO:0000170
Source:EPDNEWNC (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38610,434,807 - 10,434,867EPDNEWNC
RGD ID:6803858
Promoter ID:HG_KWN:52293
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:K562,   Lymphoblastoid,   NB4
Transcripts:UC010JOK.1
Position:
Human AssemblyChrPosition (strand)Source
Build 36610,538,086 - 10,538,586 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
COSMIC LINC00518 COSMIC
Ensembl Genes ENSG00000183674 Ensembl
GTEx ENSG00000183674 GTEx
HGNC ID HGNC:28626 ENTREZGENE
Human Proteome Map LINC00518 Human Proteome Map
NCBI Gene 221718 ENTREZGENE
PharmGKB PA144596499 PharmGKB
RNAcentral URS000075AEC3 RNACentral
UniProt CF218_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-11-29 LINC00518  long intergenic non-protein coding RNA 518  C6orf218  chromosome 6 open reading frame 218  Symbol and/or name change 5135510 APPROVED