LINC02269 (long intergenic non-protein coding RNA 2269) - 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 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
Advanced Search (OLGA)
Gene: LINC02269 (long intergenic non-protein coding RNA 2269) Homo sapiens
Analyze
Symbol: LINC02269
Name: long intergenic non-protein coding RNA 2269
RGD ID: 12798818
HGNC Page HGNC:53184
Description: INTERACTS WITH benzo[a]pyrene; Lasiocarpine; N-Nitrosopyrrolidine
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
GRCh384173,897,273 - 173,929,525 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl4173,699,082 - 174,001,488 (+)EnsemblGRCh38hg38GRCh38
GRCh374174,818,424 - 174,850,676 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map4q34.1NCBI
HuRef4170,365,851 - 170,523,187 (+)NCBIHuRef
CHM1_14174,596,937 - 174,754,335 (+)NCBICHM1_1
T2T-CHM13v2.04177,237,040 - 177,269,264 (+)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:23502783  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 4q32.2-35.2(chr4:162013220-189975519)x3 copy number gain See cases [RCV000050649] Chr4:162013220..189975519 [GRCh38]
Chr4:162934372..190828225 [GRCh37]
Chr4:163153822..191133668 [NCBI36]
Chr4:4q32.2-35.2		 pathogenic
GRCh38/hg38 4q34.1-35.2(chr4:173599911-188624331)x1 copy number loss See cases [RCV000050771] Chr4:173599911..188624331 [GRCh38]
Chr4:174521062..189545485 [GRCh37]
Chr4:174757637..189782479 [NCBI36]
Chr4:4q34.1-35.2		 pathogenic
GRCh38/hg38 4q26-35.2(chr4:118065569-190042639)x3 copy number gain See cases [RCV000051785] Chr4:118065569..190042639 [GRCh38]
Chr4:118986724..190828225 [GRCh37]
Chr4:119206172..191200788 [NCBI36]
Chr4:4q26-35.2		 pathogenic
GRCh38/hg38 4q27-35.2(chr4:121518223-190062270)x3 copy number gain See cases [RCV000051786] Chr4:121518223..190062270 [GRCh38]
Chr4:122439378..190828225 [GRCh37]
Chr4:122658828..191220419 [NCBI36]
Chr4:4q27-35.2		 pathogenic
GRCh38/hg38 4q31.23-35.2(chr4:148356485-189548183)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051789]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051789]|See cases [RCV000051789] Chr4:148356485..189548183 [GRCh38]
Chr4:149277637..190469337 [GRCh37]
Chr4:149497087..190706331 [NCBI36]
Chr4:4q31.23-35.2		 pathogenic
GRCh38/hg38 4q32.3-35.2(chr4:167218288-189975519)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051792]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051792]|See cases [RCV000051792] Chr4:167218288..189975519 [GRCh38]
Chr4:168139439..190828225 [GRCh37]
Chr4:168376014..191133668 [NCBI36]
Chr4:4q32.3-35.2		 pathogenic
GRCh38/hg38 4q34.1-35.2(chr4:172200228-189975519)x3 copy number gain See cases [RCV000051804] Chr4:172200228..189975519 [GRCh38]
Chr4:173121379..190828225 [GRCh37]
Chr4:173357954..191133668 [NCBI36]
Chr4:4q34.1-35.2		 pathogenic
GRCh38/hg38 4q32.1-35.2(chr4:158568335-189975660)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053325]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053325]|See cases [RCV000053325] Chr4:158568335..189975660 [GRCh38]
Chr4:159489487..190828225 [GRCh37]
Chr4:159708937..191133809 [NCBI36]
Chr4:4q32.1-35.2		 pathogenic
GRCh38/hg38 4q32.3-35.2(chr4:163651681-189975519)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053327]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053327]|See cases [RCV000053327] Chr4:163651681..189975519 [GRCh38]
Chr4:164572833..190828225 [GRCh37]
Chr4:164792283..191133668 [NCBI36]
Chr4:4q32.3-35.2		 pathogenic
GRCh38/hg38 4q32.3-35.2(chr4:164039530-189982708)x1 copy number loss See cases [RCV000053347] Chr4:164039530..189982708 [GRCh38]
Chr4:164960682..190828225 [GRCh37]
Chr4:165180132..191140857 [NCBI36]
Chr4:4q32.3-35.2		 pathogenic
GRCh38/hg38 4q34.1-35.2(chr4:171507704-189869726)x1 copy number loss See cases [RCV000053349] Chr4:171507704..189869726 [GRCh38]
Chr4:172428855..190790881 [GRCh37]
Chr4:172665430..191027875 [NCBI36]
Chr4:4q34.1-35.2		 pathogenic
GRCh38/hg38 4q34.1-35.2(chr4:172356988-189975519)x1 copy number loss See cases [RCV000053352] Chr4:172356988..189975519 [GRCh38]
Chr4:173278139..190828225 [GRCh37]
Chr4:173514714..191133668 [NCBI36]
Chr4:4q34.1-35.2		 pathogenic
GRCh38/hg38 4q34.1-35.2(chr4:173754675-189343295)x1 copy number loss See cases [RCV000053353] Chr4:173754675..189343295 [GRCh38]
Chr4:174675826..190264449 [GRCh37]
Chr4:174912401..190501443 [NCBI36]
Chr4:4q34.1-35.2		 pathogenic
GRCh38/hg38 4q31.21-35.2(chr4:145042668-189975519)x3 copy number gain See cases [RCV000135845] Chr4:145042668..189975519 [GRCh38]
Chr4:145963820..190828225 [GRCh37]
Chr4:146183270..191133668 [NCBI36]
Chr4:4q31.21-35.2		 pathogenic
GRCh38/hg38 4q34.1-35.2(chr4:173854560-189548183)x1 copy number loss See cases [RCV000136115] Chr4:173854560..189548183 [GRCh38]
Chr4:174775711..190469337 [GRCh37]
Chr4:175012286..190706331 [NCBI36]
Chr4:4q34.1-35.2		 pathogenic
GRCh38/hg38 4q31.1-35.2(chr4:138510532-189963195)x3 copy number gain See cases [RCV000136810] Chr4:138510532..189963195 [GRCh38]
Chr4:139431686..190828225 [GRCh37]
Chr4:139651136..191121344 [NCBI36]
Chr4:4q31.1-35.2		 pathogenic
GRCh38/hg38 4q32.3-35.2(chr4:166317587-190095391)x1 copy number loss See cases [RCV000137532] Chr4:166317587..190095391 [GRCh38]
Chr4:167238739..190828225 [GRCh37]
Chr4:167458189..191250527 [NCBI36]
Chr4:4q32.3-35.2		 pathogenic
GRCh38/hg38 4q33-35.2(chr4:169901205-190095391)x3 copy number gain See cases [RCV000138540] Chr4:169901205..190095391 [GRCh38]
Chr4:170822356..190828225 [GRCh37]
Chr4:171058931..191250527 [NCBI36]
Chr4:4q33-35.2		 uncertain significance
GRCh38/hg38 4q33-35.2(chr4:169873508-190018185)x1 copy number loss See cases [RCV000140396] Chr4:169873508..190018185 [GRCh38]
Chr4:170794659..190939340 [GRCh37]
Chr4:171031234..191176334 [NCBI36]
Chr4:4q33-35.2		 pathogenic
GRCh38/hg38 4q32.3-35.2(chr4:165281036-190018185)x1 copy number loss See cases [RCV000140414] Chr4:165281036..190018185 [GRCh38]
Chr4:166202188..190939340 [GRCh37]
Chr4:166421638..191176334 [NCBI36]
Chr4:4q32.3-35.2		 pathogenic
GRCh38/hg38 4q32.1-35.2(chr4:160757699-190091407)x3 copy number gain See cases [RCV000140982] Chr4:160757699..190091407 [GRCh38]
Chr4:161678851..191012562 [GRCh37]
Chr4:161898301..191246543 [NCBI36]
Chr4:4q32.1-35.2		 pathogenic
GRCh38/hg38 4q32.3-35.2(chr4:167373716-190036318)x1 copy number loss See cases [RCV000141964] Chr4:167373716..190036318 [GRCh38]
Chr4:168294867..190957473 [GRCh37]
Chr4:168531442..191194467 [NCBI36]
Chr4:4q32.3-35.2		 pathogenic
GRCh38/hg38 4q32.3-35.2(chr4:168970400-186936738)x1 copy number loss See cases [RCV000142368] Chr4:168970400..186936738 [GRCh38]
Chr4:169891551..187857892 [GRCh37]
Chr4:170128126..188094886 [NCBI36]
Chr4:4q32.3-35.2		 pathogenic
GRCh38/hg38 4q34.1-35.2(chr4:172501374-190095332)x1 copy number loss See cases [RCV000143079] Chr4:172501374..190095332 [GRCh38]
Chr4:173422525..190828225 [GRCh37]
Chr4:173659100..191250468 [NCBI36]
Chr4:4q34.1-35.2		 pathogenic
GRCh38/hg38 4q33-35.2(chr4:170899124-190036318)x1 copy number loss See cases [RCV000143232] Chr4:170899124..190036318 [GRCh38]
Chr4:171820275..190957473 [GRCh37]
Chr4:172056850..191194467 [NCBI36]
Chr4:4q33-35.2		 pathogenic
GRCh38/hg38 4q32.3-35.2(chr4:168119317-190095391)x3 copy number gain See cases [RCV000143331] Chr4:168119317..190095391 [GRCh38]
Chr4:169040468..190828225 [GRCh37]
Chr4:169277043..191250527 [NCBI36]
Chr4:4q32.3-35.2		 pathogenic
GRCh38/hg38 4q28.3-35.2(chr4:134935616-190036318)x3 copy number gain See cases [RCV000143559] Chr4:134935616..190036318 [GRCh38]
Chr4:135856771..190957473 [GRCh37]
Chr4:136076221..191194467 [NCBI36]
Chr4:4q28.3-35.2		 pathogenic
GRCh38/hg38 4q34.1-34.3(chr4:171507504-181381327)x3 copy number gain See cases [RCV000051793] Chr4:171507504..181381327 [GRCh38]
Chr4:172428655..182302480 [GRCh37]
Chr4:172665230..182539474 [NCBI36]
Chr4:4q34.1-34.3		 pathogenic
GRCh38/hg38 4q34.1-34.3(chr4:171851295-178772816)x1 copy number loss See cases [RCV000053350] Chr4:171851295..178772816 [GRCh38]
Chr4:172772446..179693970 [GRCh37]
Chr4:173009021..179930964 [NCBI36]
Chr4:4q34.1-34.3		 pathogenic
GRCh38/hg38 4q32.3-34.3(chr4:166630207-179820960) copy number loss See cases [RCV000141653] Chr4:166630207..179820960 [GRCh38]
Chr4:167551358..180742113 [GRCh37]
Chr4:167770808..180979107 [NCBI36]
Chr4:4q32.3-34.3		 pathogenic
GRCh38/hg38 4q28.3-35.2(chr4:131985253-190095391)x3 copy number gain See cases [RCV000137721] Chr4:131985253..190095391 [GRCh38]
Chr4:132906408..190828225 [GRCh37]
Chr4:133125858..191250527 [NCBI36]
Chr4:4q28.3-35.2		 pathogenic|likely benign
GRCh38/hg38 4q28.1-35.1(chr4:125432943-185761887)x3 copy number gain See cases [RCV000138578] Chr4:125432943..185761887 [GRCh38]
Chr4:126354098..186683041 [GRCh37]
Chr4:126573548..186920035 [NCBI36]
Chr4:4q28.1-35.1		 pathogenic|likely benign
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:191
Count of miRNA genes:163
Interacting mature miRNAs:166
Transcripts:ENST00000509968, ENST00000512263
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

adipose tissue
alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
entire extraembryonic component
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
326 1838 1376 2071 1355 366 430 2 59 161 50 516 3401 3339 17 1477 333 1195 229 12

Sequence


Ensembl Acc Id: ENST00000509968
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,897,241 - 173,929,522 (+)Ensembl
Ensembl Acc Id: ENST00000512263
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,897,273 - 173,929,525 (+)Ensembl
Ensembl Acc Id: ENST00000654188
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,897,213 - 173,923,611 (+)Ensembl
Ensembl Acc Id: ENST00000654333
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,699,143 - 173,929,525 (+)Ensembl
Ensembl Acc Id: ENST00000654653
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,699,143 - 173,929,525 (+)Ensembl
Ensembl Acc Id: ENST00000654916
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,699,143 - 173,929,525 (+)Ensembl
Ensembl Acc Id: ENST00000655323
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,897,259 - 173,929,480 (+)Ensembl
Ensembl Acc Id: ENST00000656512
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,699,143 - 173,929,525 (+)Ensembl
Ensembl Acc Id: ENST00000656853
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,897,243 - 174,001,488 (+)Ensembl
Ensembl Acc Id: ENST00000659294
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,699,143 - 173,929,480 (+)Ensembl
Ensembl Acc Id: ENST00000659629
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,699,143 - 173,929,525 (+)Ensembl
Ensembl Acc Id: ENST00000660497
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,699,082 - 173,703,062 (+)Ensembl
Ensembl Acc Id: ENST00000660997
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,897,220 - 173,929,525 (+)Ensembl
Ensembl Acc Id: ENST00000661458
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,699,143 - 173,929,526 (+)Ensembl
Ensembl Acc Id: ENST00000661951
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,897,241 - 173,929,525 (+)Ensembl
Ensembl Acc Id: ENST00000664651
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,897,259 - 173,929,525 (+)Ensembl
Ensembl Acc Id: ENST00000664849
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,897,234 - 173,929,474 (+)Ensembl
Ensembl Acc Id: ENST00000665324
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,699,142 - 173,703,060 (+)Ensembl
Ensembl Acc Id: ENST00000665435
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,699,134 - 173,929,525 (+)Ensembl
Ensembl Acc Id: ENST00000665681
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,897,245 - 173,929,528 (+)Ensembl
Ensembl Acc Id: ENST00000665923
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,897,241 - 173,929,525 (+)Ensembl
Ensembl Acc Id: ENST00000667443
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,897,241 - 173,929,480 (+)Ensembl
Ensembl Acc Id: ENST00000667922
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,897,213 - 173,929,525 (+)Ensembl
Ensembl Acc Id: ENST00000670652
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,925,601 - 173,929,525 (+)Ensembl
Ensembl Acc Id: ENST00000670956
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,699,136 - 173,929,525 (+)Ensembl
Ensembl Acc Id: ENST00000781415
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,699,138 - 173,923,624 (+)Ensembl
Ensembl Acc Id: ENST00000781416
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,699,142 - 173,923,624 (+)Ensembl
Ensembl Acc Id: ENST00000781417
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,699,143 - 173,923,611 (+)Ensembl
Ensembl Acc Id: ENST00000781418
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,897,241 - 173,929,530 (+)Ensembl
Ensembl Acc Id: ENST00000781419
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,897,241 - 173,929,471 (+)Ensembl
Ensembl Acc Id: ENST00000781420
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,925,689 - 173,929,525 (+)Ensembl
Ensembl Acc Id: ENST00000781421
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,699,143 - 173,702,720 (+)Ensembl
RefSeq Acc Id: NR_146487
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh384173,897,273 - 173,929,525 (+)NCBI
T2T-CHM13v2.04177,237,040 - 177,269,264 (+)NCBI
Sequence:
Promoters
RGD ID:15095827
Promoter ID:EPDNEWNC_H662
Type:initiation region
Name:LINC02269_1
Description:long intergenic non-protein coding RNA 2269 [Source:HGNCSymbol;Acc:HGNC:53184]
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
GRCh384173,897,241 - 173,897,301EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC LINC02269 COSMIC
Ensembl Genes ENSG00000250708 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000512263 ENTREZGENE
GTEx ENSG00000250708 GTEx
HGNC ID HGNC:53184 ENTREZGENE
Human Proteome Map LINC02269 Human Proteome Map
NCBI Gene LINC02269 ENTREZGENE
RNAcentral URS0000077758 RNACentral
  URS0000373903 RNACentral
  URS0000EEB0E5 RNACentral
  URS0000EEBE0A RNACentral
  URS0000EEE6E9 RNACentral
  URS0000EEE8B4 RNACentral
  URS0000EEEAB7 RNACentral
  URS0000EEF1B3 RNACentral
  URS0000EEF9CD RNACentral
  URS0000EEFFF1 RNACentral
  URS0000EF0A24 RNACentral
  URS0000EF17D1 RNACentral
  URS0000EF17DD RNACentral
  URS0000EF1C64 RNACentral
  URS0000EF1E8D RNACentral
  URS0000EF1FA7 RNACentral
  URS0000EF274F RNACentral
  URS0000EF276C RNACentral
  URS0000EF3228 RNACentral
  URS0000EF3302 RNACentral
  URS0000EF3CF9 RNACentral
  URS0000EF6E7D RNACentral
  URS0000EF6FC7 RNACentral
  URS0000EF7259 RNACentral
  URS00022B702C RNACentral