LINC02699 (long intergenic non-protein coding RNA 2699) - Rat Genome Database

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Gene: LINC02699 (long intergenic non-protein coding RNA 2699) Homo sapiens
Analyze
Symbol: LINC02699
Name: long intergenic non-protein coding RNA 2699
RGD ID: 14398369
HGNC Page HGNC:54213
Description:
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
GRCh381125,453,600 - 25,924,451 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1125,734,757 - 25,782,017 (+)EnsemblGRCh38hg38GRCh38
GRCh371125,475,146 - 25,945,998 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map11p14.3NCBI
CHM1_11125,756,116 - 25,946,159 (+)NCBICHM1_1
T2T-CHM13v2.01125,593,334 - 26,064,876 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Genomics

Variants

.
Variants in LINC02699
11 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 11p14.3-14.1(chr11:23024064-27978597)x1 copy number loss See cases [RCV000137723] Chr11:23024064..27978597 [GRCh38]
Chr11:23045610..28000144 [GRCh37]
Chr11:23002186..27956720 [NCBI36]
Chr11:11p14.3-14.1		 likely pathogenic
GRCh38/hg38 11p15.1-13(chr11:20079474-34463996)x1 copy number loss See cases [RCV000142499] Chr11:20079474..34463996 [GRCh38]
Chr11:20101020..34485543 [GRCh37]
Chr11:20057596..34442119 [NCBI36]
Chr11:11p15.1-13		 pathogenic
GRCh38/hg38 11p15.5-13(chr11:202758-31726224)x3 copy number gain See cases [RCV000053613] Chr11:202758..31726224 [GRCh38]
Chr11:202758..31747772 [GRCh37]
Chr11:192758..31704348 [NCBI36]
Chr11:11p15.5-13		 pathogenic
GRCh38/hg38 11p15.1-14.2(chr11:21838014-26738627)x3 copy number gain See cases [RCV000137849] Chr11:21838014..26738627 [GRCh38]
Chr11:21859560..26760174 [GRCh37]
Chr11:21816136..26716750 [NCBI36]
Chr11:11p15.1-14.2		 uncertain significance
GRCh38/hg38 11p14.3-13(chr11:24595399-31096539)x3 copy number gain See cases [RCV000134877] Chr11:24595399..31096539 [GRCh38]
Chr11:24616945..31118086 [GRCh37]
Chr11:24573521..31074662 [NCBI36]
Chr11:11p14.3-13		 pathogenic
GRCh38/hg38 11p14.3-14.2(chr11:25402733-26309143)x3 copy number gain See cases [RCV000140060] Chr11:25402733..26309143 [GRCh38]
Chr11:25424279..26330690 [GRCh37]
Chr11:25380855..26287266 [NCBI36]
Chr11:11p14.3-14.2		 benign
GRCh38/hg38 11p14.3-12(chr11:22550115-38199159)x1 copy number loss See cases [RCV000052648] Chr11:22550115..38199159 [GRCh38]
Chr11:22571661..38220709 [GRCh37]
Chr11:22528237..38177285 [NCBI36]
Chr11:11p14.3-12		 pathogenic
NC_000011.10:g.25690753_25699159del deletion Large for gestational age [RCV000161624]|Normal pregnancy [RCV000161625] Chr11:25690753..25699159 [GRCh38]
Chr11:25712300..25720706 [GRCh37]
Chr11:11p14.3		 not provided
GRCh38/hg38 11p14.3(chr11:23335670-25613811)x3 copy number gain See cases [RCV000139989] Chr11:23335670..25613811 [GRCh38]
Chr11:23357216..25635357 [GRCh37]
Chr11:23313792..25591933 [NCBI36]
Chr11:11p14.3		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:377
Count of miRNA genes:334
Interacting mature miRNAs:354
Transcripts:ENST00000526327, ENST00000533049, ENST00000533942
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.


QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1576345LVC1_HLeft ventricular contractility QTL 1 (human)3.93Left ventricular contractility11797076733970767Human
2289313BW388_HBody weight QTL 388 (human)1.570.00356Body fat amountabdominal11443467130434671Human
597255953GWAS1352027_Hresponse to beta blocker QTL GWAS1352027 (human)0.0000001response to beta blocker112555295825552959Human
597031708GWAS1127782_Hattempted suicide QTL GWAS1127782 (human)0.0000009attempted suicide112586365825863659Human
597505037GWAS1601111_Hsevere acute respiratory syndrome, COVID-19 QTL GWAS1601111 (human)0.0000007severe acute respiratory syndrome, COVID-19112578032225780323Human
407389400GWAS1038376_Hnitric oxide exhalation measurement QTL GWAS1038376 (human)0.000002nitric oxide exhalation measurement112590841225908413Human
406917138GWAS566114_Hserum IgG glycosylation measurement QTL GWAS566114 (human)0.000004serum IgG glycosylation measurement112546893625468937Human
597609165GWAS1666025_Hhyperaldosteronism QTL GWAS1666025 (human)8e-12hyperaldosteronism112550141025501411Human
597245130GWAS1341204_Hprogression free survival, response to carboplatin, ovarian serous carcinoma, trait in response to paclitaxel QTL GWAS1341204 (human)0.000008progression free survival, response to carboplatin, ovarian serous carcinoma, trait in response to paclitaxelsurvival measurement (CMO:0001021)112565083525650836Human
1559107SCL32_HSerum cholesterol level QTL 32 (human)3.27Lipid levelLDL cholesterol11289243028892430Human
597330319GWAS1426393_Hable to hear with hearing aids QTL GWAS1426393 (human)0.0000002able to hear with hearing aids112548267725482678Human
1559104SCL15_HSerum cholesterol level QTL 15 (human)2.60.06Lipid levelhyperlipidemia susceptibility111589236841892368Human
1559113SCL31_HSerum cholesterol level QTL 31 (human)3.72Lipid levelLDL cholesterol11289243028892430Human
407389398GWAS1038374_Hnitric oxide exhalation measurement QTL GWAS1038374 (human)0.0000002nitric oxide exhalation measurement112590841225908413Human
597311098GWAS1407172_Hvaginal microbiome measurement QTL GWAS1407172 (human)0.000004vaginal microbiome measurement112556363425563635Human
597311096GWAS1407170_Hvaginal microbiome measurement QTL GWAS1407170 (human)0.000008vaginal microbiome measurement112564125625641257Human
597068402GWAS1164476_Hperipheral arterial disease, traffic air pollution measurement QTL GWAS1164476 (human)0.000002peripheral arterial disease, traffic air pollution measurement112554194725541948Human
597106621GWAS1202695_Hcerebellum cortex volume change measurement, age at assessment QTL GWAS1202695 (human)0.000004cerebellum cortex volume change measurement, age at assessment112562848625628487Human
597311094GWAS1407168_Hvaginal microbiome measurement QTL GWAS1407168 (human)0.000006vaginal microbiome measurement112561338425613385Human
597311095GWAS1407169_Hvaginal microbiome measurement QTL GWAS1407169 (human)0.000001vaginal microbiome measurement112563813625638137Human
597364149GWAS1460223_HQRS duration, response to sulfonylurea QTL GWAS1460223 (human)0.0000004QRS duration, response to sulfonylureaQRS duration (CMO:0000267)112577873125778732Human
597241953GWAS1338027_Hacylcarnitine measurement QTL GWAS1338027 (human)0.000002acylcarnitine measurement112550844125508442Human
597276962GWAS1373036_HAlzheimer disease, polygenic risk score QTL GWAS1373036 (human)2e-08Alzheimer disease, polygenic risk score112551674725516748Human
597333671GWAS1429745_HS-6-hydroxywarfarin to S-warfarin ratio measurement QTL GWAS1429745 (human)0.000009S-6-hydroxywarfarin to S-warfarin ratio measurement112550208025502081Human
597241959GWAS1338033_Hacylcarnitine measurement QTL GWAS1338033 (human)0.0000009acylcarnitine measurement112550844125508442Human
597214502GWAS1310576_Hbone density QTL GWAS1310576 (human)5e-09bone mineral mass (VT:0005007)bone mineral density (CMO:0001226)112562382025623821Human
597091945GWAS1188019_HAlzheimer disease, age at onset QTL GWAS1188019 (human)3e-09Alzheimer disease, age at onset112587103525871036Human


Expression

RNA-SEQ Expression

adipose tissue
alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
19 29 44 29 276 109 57 22 68 20 49 169 136 6 256 29 482 30 3

Sequence


Ensembl Acc Id: ENST00000526327
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1125,734,757 - 25,782,017 (+)Ensembl
Ensembl Acc Id: ENST00000533049
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1125,734,770 - 25,781,758 (+)Ensembl
Ensembl Acc Id: ENST00000533942
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1125,734,783 - 25,774,423 (+)Ensembl
Ensembl Acc Id: ENST00000654912
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1125,734,804 - 25,774,421 (+)Ensembl
Ensembl Acc Id: ENST00000746470
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1125,734,767 - 25,777,953 (+)Ensembl
Ensembl Acc Id: ENST00000746471
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1125,734,773 - 25,777,941 (+)Ensembl
RefSeq Acc Id: NR_183692
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381125,734,751 - 25,782,020 (+)NCBI
T2T-CHM13v2.01125,875,193 - 25,922,465 (+)NCBI
RefSeq Acc Id: NR_183693
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381125,453,600 - 25,782,020 (+)NCBI
T2T-CHM13v2.01125,593,334 - 25,922,465 (+)NCBI
RefSeq Acc Id: NR_183694
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381125,453,600 - 25,924,451 (+)NCBI
T2T-CHM13v2.01125,593,334 - 26,064,876 (+)NCBI

Additional Information

Database Acc Id Source(s)
COSMIC LINC02699 COSMIC
Ensembl Genes ENSG00000254456 Ensembl
GTEx ENSG00000254456 GTEx
HGNC ID HGNC:54213 ENTREZGENE
Human Proteome Map LINC02699 Human Proteome Map
NCBI Gene LINC02699 ENTREZGENE
RNAcentral URS0000378D36 RNACentral
  URS0000EED427 RNACentral
  URS0000EEE0BB RNACentral
  URS0000EF6928 RNACentral
  URS00026A1E7F RNACentral
  URS00026A200A RNACentral
  URS00026A2859 RNACentral