LINC00654 (long intergenic non-protein coding RNA 654) - 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: LINC00654 (long intergenic non-protein coding RNA 654) Homo sapiens
Analyze
Symbol: LINC00654
Name: long intergenic non-protein coding RNA 654
RGD ID: 6892865
HGNC Page HGNC:27154
Description: INTERACTS WITH benzo[a]pyrene; methylmercury chloride; sotorasib
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
GRCh38205,496,067 - 5,504,596 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl205,482,736 - 5,526,709 (-)EnsemblGRCh38hg38GRCh38
GRCh37205,476,713 - 5,485,242 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36205,424,711 - 5,433,242 (-)NCBINCBI36Build 36hg18NCBI36
Celera205,550,059 - 5,556,083 (-)NCBICelera
Cytogenetic Map20p12.3NCBI
HuRef205,434,887 - 5,440,911 (-)NCBIHuRef
CHM1_1205,479,927 - 5,485,935 (-)NCBICHM1_1
T2T-CHM13v2.0205,536,974 - 5,545,197 (-)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:12477932   PMID:19204726  


Genomics

Variants

.
Variants in LINC00654
1 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 20p13-q11.1(chr20:80106-30227427)x3 copy number gain See cases [RCV000133996] Chr20:80106..30227427 [GRCh38]
Chr20:60747..29462103 [GRCh37]
Chr20:8747..28075764 [NCBI36]
Chr20:20p13-q11.1		 pathogenic
GRCh38/hg38 20p13-q13.33(chr20:99557-64277321)x3 copy number gain See cases [RCV000135859] Chr20:99557..64277321 [GRCh38]
Chr20:80198..62908674 [GRCh37]
Chr20:28198..62379118 [NCBI36]
Chr20:20p13-q13.33		 pathogenic
GRCh38/hg38 20p13-12.3(chr20:4343033-6911730)x1 copy number loss See cases [RCV000137695] Chr20:4343033..6911730 [GRCh38]
Chr20:4323680..6892377 [GRCh37]
Chr20:4271680..6840377 [NCBI36]
Chr20:20p13-12.3		 pathogenic
GRCh38/hg38 20p12.3(chr20:5491535-5781055)x3 copy number gain See cases [RCV000137218] Chr20:5491535..5781055 [GRCh38]
Chr20:5472181..5761701 [GRCh37]
Chr20:5420181..5709701 [NCBI36]
Chr20:20p12.3		 benign
GRCh38/hg38 20p13-12.3(chr20:5039774-5645855)x3 copy number gain See cases [RCV000137853] Chr20:5039774..5645855 [GRCh38]
Chr20:5020420..5626501 [GRCh37]
Chr20:4968420..5574501 [NCBI36]
Chr20:20p13-12.3		 uncertain significance
GRCh38/hg38 20p13-12.1(chr20:80106-13029401)x3 copy number gain See cases [RCV000138677] Chr20:80106..13029401 [GRCh38]
Chr20:60747..13010049 [GRCh37]
Chr20:8747..12958049 [NCBI36]
Chr20:20p13-12.1		 pathogenic
GRCh38/hg38 20p13-12.3(chr20:80093-6386012)x3 copy number gain See cases [RCV000139597] Chr20:80093..6386012 [GRCh38]
Chr20:60734..6366659 [GRCh37]
Chr20:8734..6314659 [NCBI36]
Chr20:20p13-12.3		 pathogenic
GRCh38/hg38 20p13-12.3(chr20:4926195-5543771)x3 copy number gain See cases [RCV000139625] Chr20:4926195..5543771 [GRCh38]
Chr20:4906841..5524417 [GRCh37]
Chr20:4854841..5472417 [NCBI36]
Chr20:20p13-12.3		 uncertain significance
GRCh38/hg38 20p13-12.3(chr20:84402-6159078)x3 copy number gain See cases [RCV000141348] Chr20:84402..6159078 [GRCh38]
Chr20:65043..6139725 [GRCh37]
Chr20:13043..6087725 [NCBI36]
Chr20:20p13-12.3		 pathogenic
GRCh38/hg38 20p13-11.1(chr20:80927-26324843)x3 copy number gain See cases [RCV000142017] Chr20:80927..26324843 [GRCh38]
Chr20:61568..26305479 [GRCh37]
Chr20:9568..26253479 [NCBI36]
Chr20:20p13-11.1		 pathogenic
GRCh38/hg38 20p13-12.3(chr20:1269303-8626911)x3 copy number gain See cases [RCV000142917] Chr20:1269303..8626911 [GRCh38]
Chr20:1249947..8607558 [GRCh37]
Chr20:1197947..8555558 [NCBI36]
Chr20:20p13-12.3		 pathogenic
GRCh38/hg38 20p13-11.23(chr20:80928-18688031)x3 copy number gain See cases [RCV000143426] Chr20:80928..18688031 [GRCh38]
Chr20:61569..18668675 [GRCh37]
Chr20:9569..18616675 [NCBI36]
Chr20:20p13-11.23		 pathogenic
GRCh38/hg38 20p13-11.21(chr20:89939-25697564)x3 copy number gain See cases [RCV000051227] Chr20:89939..25697564 [GRCh38]
Chr20:70580..25678200 [GRCh37]
Chr20:18580..25626200 [NCBI36]
Chr20:20p13-11.21		 pathogenic
GRCh38/hg38 20p13-11.23(chr20:89939-19146279)x3 copy number gain See cases [RCV000051041] Chr20:89939..19146279 [GRCh38]
Chr20:70580..19126923 [GRCh37]
Chr20:18580..19074923 [NCBI36]
Chr20:20p13-11.23		 pathogenic
GRCh38/hg38 20p13-11.23(chr20:89939-19071495)x3 copy number gain See cases [RCV000052995] Chr20:89939..19071495 [GRCh38]
Chr20:70580..19052139 [GRCh37]
Chr20:18580..19000139 [NCBI36]
Chr20:20p13-11.23		 pathogenic
GRCh38/hg38 20p13-11.22(chr20:89939-21787252)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052996]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052996]|See cases [RCV000052996] Chr20:89939..21787252 [GRCh38]
Chr20:70580..21767890 [GRCh37]
Chr20:18580..21715890 [NCBI36]
Chr20:20p13-11.22		 pathogenic
GRCh38/hg38 20p13-12.1(chr20:89939-14818511)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052997]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052997]|See cases [RCV000052997] Chr20:89939..14818511 [GRCh38]
Chr20:70580..14799157 [GRCh37]
Chr20:18580..14747157 [NCBI36]
Chr20:20p13-12.1		 pathogenic
GRCh38/hg38 20p13-11.21(chr20:87153-23635465)x3 copy number gain Renal agenesis [RCV003327640] Chr20:87153..23635465 [GRCh38]
Chr20:20p13-11.21		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:347
Count of miRNA genes:309
Interacting mature miRNAs:330
Transcripts:ENST00000379053, ENST00000589201
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
RH12029  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37205,480,147 - 5,480,293UniSTSGRCh37
Build 36205,428,147 - 5,428,293RGDNCBI36
Celera205,550,988 - 5,551,134RGD
Cytogenetic Map20p12.3UniSTS
HuRef205,435,816 - 5,435,962UniSTS
GeneMap99-GB4 RH Map2031.8UniSTS
NCBI RH Map2079.8UniSTS
A008V36  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37205,481,241 - 5,481,462UniSTSGRCh37
Build 36205,429,241 - 5,429,462RGDNCBI36
Celera205,552,082 - 5,552,303RGD
Cytogenetic Map20p12.3UniSTS
HuRef205,436,910 - 5,437,131UniSTS
GeneMap99-GB4 RH Map2032.79UniSTS
NCBI RH Map2079.8UniSTS


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 6 5 1 4 1 2 2 18 1 366 17
Low 2145 2362 1332 231 1039 94 2812 1613 3340 246 901 1448 141 1191 1838 3
Below cutoff 237 620 365 374 831 352 1504 564 338 144 147 94 25 13 950 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000379053
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl205,496,067 - 5,504,613 (-)Ensembl
RefSeq Acc Id: ENST00000589201
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl205,500,329 - 5,504,582 (-)Ensembl
RefSeq Acc Id: ENST00000650928
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl205,482,736 - 5,526,606 (-)Ensembl
RefSeq Acc Id: ENST00000654011
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl205,501,073 - 5,504,609 (-)Ensembl
RefSeq Acc Id: ENST00000660858
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl205,501,074 - 5,510,842 (-)Ensembl
RefSeq Acc Id: ENST00000661996
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl205,482,736 - 5,489,233 (-)Ensembl
RefSeq Acc Id: ENST00000663299
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl205,501,290 - 5,526,696 (-)Ensembl
RefSeq Acc Id: ENST00000664106
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl205,499,436 - 5,504,665 (-)Ensembl
RefSeq Acc Id: ENST00000665765
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl205,500,329 - 5,526,709 (-)Ensembl
RefSeq Acc Id: NR_015406
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38205,496,067 - 5,504,596 (-)NCBI
GRCh37205,479,218 - 5,485,242 (-)NCBI
HuRef205,434,887 - 5,440,911 (-)NCBI
CHM1_1205,477,417 - 5,485,935 (-)NCBI
T2T-CHM13v2.0205,536,974 - 5,545,197 (-)NCBI
Sequence:
Protein Sequences
GenBank Protein BAF82659 (Get FASTA)   NCBI Sequence Viewer  
  BAF84175 (Get FASTA)   NCBI Sequence Viewer  
  BAF84955 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences

Promoters
RGD ID:15097250
Promoter ID:EPDNEWNC_H2092
Type:initiation region
Name:LINC00654_1
Description:long intergenic non-protein coding RNA 654 [Source:HGNCSymbol;Acc:HGNC:27154]
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
GRCh38205,504,585 - 5,504,645EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC LINC00654 COSMIC
Ensembl Genes ENSG00000205181 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000379053 ENTREZGENE
GTEx ENSG00000205181 GTEx
HGNC ID HGNC:27154 ENTREZGENE
Human Proteome Map LINC00654 Human Proteome Map
NCBI Gene LINC00654 ENTREZGENE
RNAcentral URS0000A775BD RNACentral