LINC02774 (long intergenic non-protein coding RNA 2774) - 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: LINC02774 (long intergenic non-protein coding RNA 2774) Homo sapiens
Analyze
Symbol: LINC02774
Name: long intergenic non-protein coding RNA 2774
RGD ID: 14400038
HGNC Page HGNC:27923
Description: ASSOCIATED WITH Megalencephaly-Polymicrogyria-Polydactyly-Hydrocephalus Syndrome 2; INTERACTS WITH 4,4'-sulfonyldiphenol; bisphenol A; bisphenol F
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
GRCh381243,917,402 - 244,047,317 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1243,917,402 - 244,047,317 (+)EnsemblGRCh38hg38GRCh38
GRCh371244,080,704 - 244,210,619 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map1q44NCBI
HuRef1214,464,222 - 214,594,683 (+)NCBIHuRef
CHM1_11245,353,017 - 245,482,821 (+)NCBICHM1_1
T2T-CHM13v2.01243,332,936 - 243,463,802 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:12477932   PMID:21441570   PMID:23400010  


Genomics

Variants

.
Variants in LINC02774
11 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 1q41-44(chr1:223815147-248918469)x3 copy number gain See cases [RCV000135839] Chr1:223815147..248918469 [GRCh38]
Chr1:224002849..249212668 [GRCh37]
Chr1:222069472..247179291 [NCBI36]
Chr1:1q41-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:237643281-248918469)x1 copy number loss See cases [RCV000142518] Chr1:237643281..248918469 [GRCh38]
Chr1:237806581..249212668 [GRCh37]
Chr1:235873204..247179291 [NCBI36]
Chr1:1q43-44		 pathogenic
Single allele deletion Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2 [RCV000235042] Chr1:242100310..244396371 [GRCh38]
Chr1:242263612..244559673 [GRCh37]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:239657468-248918610)x3 copy number gain See cases [RCV000051886] Chr1:239657468..248918610 [GRCh38]
Chr1:239820768..249212809 [GRCh37]
Chr1:237887391..247179432 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q32.2-44(chr1:209963625-248918469)x3 copy number gain See cases [RCV000134979] Chr1:209963625..248918469 [GRCh38]
Chr1:210136970..249212668 [GRCh37]
Chr1:208203593..247179291 [NCBI36]
Chr1:1q32.2-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:241625115-245453782)x3 copy number gain See cases [RCV000136503] Chr1:241625115..245453782 [GRCh38]
Chr1:241788417..245617084 [GRCh37]
Chr1:239855040..243683707 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:241676908-245647727)x1 copy number loss See cases [RCV000054027] Chr1:241676908..245647727 [GRCh38]
Chr1:241840210..245811029 [GRCh37]
Chr1:239906833..243877652 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q44(chr1:243786629-248918469)x1 copy number loss See cases [RCV000054061] Chr1:243786629..248918469 [GRCh38]
Chr1:243949931..249212668 [GRCh37]
Chr1:242016554..247179291 [NCBI36]
Chr1:1q44		 pathogenic
GRCh38/hg38 1q43-44(chr1:242932576-248864636)x4 copy number gain See cases [RCV000137155] Chr1:242932576..248864636 [GRCh38]
Chr1:243095878..249158835 [GRCh37]
Chr1:241162501..247125458 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q42.11-44(chr1:224022862-248918469)x3 copy number gain See cases [RCV000137769] Chr1:224022862..248918469 [GRCh38]
Chr1:224210564..249212668 [GRCh37]
Chr1:222277187..247179291 [NCBI36]
Chr1:1q42.11-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:239558430-248918469)x1 copy number loss See cases [RCV000054023] Chr1:239558430..248918469 [GRCh38]
Chr1:239721730..249212668 [GRCh37]
Chr1:237788353..247179291 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:242410569-245413313)x1 copy number loss See cases [RCV000054031] Chr1:242410569..245413313 [GRCh38]
Chr1:242573871..245576615 [GRCh37]
Chr1:240640494..243643238 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:243264192-244668463)x1 copy number loss See cases [RCV000134045] Chr1:243264192..244668463 [GRCh38]
Chr1:243427494..244831765 [GRCh37]
Chr1:241494117..242898388 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:238753749-248918467)x1 copy number loss See cases [RCV000134751] Chr1:238753749..248918467 [GRCh38]
Chr1:238917049..249212666 [GRCh37]
Chr1:236983672..247179289 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q42.12-44(chr1:225438480-248787200)x3 copy number gain See cases [RCV000142448] Chr1:225438480..248787200 [GRCh38]
Chr1:225626182..249060210 [GRCh37]
Chr1:223692805..247048022 [NCBI36]
Chr1:1q42.12-44		 pathogenic
GRCh38/hg38 1q32.3-44(chr1:214023812-248918469)x3 copy number gain See cases [RCV000050981] Chr1:214023812..248918469 [GRCh38]
Chr1:214197155..249212668 [GRCh37]
Chr1:212263778..247179291 [NCBI36]
Chr1:1q32.3-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:237906379-244022201)x1 copy number loss See cases [RCV000053990] Chr1:237906379..244022201 [GRCh38]
Chr1:238069679..244185503 [GRCh37]
Chr1:236136302..242252126 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q41-44(chr1:223887780-248891309)x3 copy number gain See cases [RCV000051880] Chr1:223887780..248891309 [GRCh38]
Chr1:224075482..249185508 [GRCh37]
Chr1:222142105..247152131 [NCBI36]
Chr1:1q41-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:241459440-247704671)x1 copy number loss See cases [RCV000054026] Chr1:241459440..247704671 [GRCh38]
Chr1:241622740..247867973 [GRCh37]
Chr1:239689363..245934596 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:243225391-245289313)x1 copy number loss See cases [RCV000054032] Chr1:243225391..245289313 [GRCh38]
Chr1:243388693..245452615 [GRCh37]
Chr1:241455316..243519238 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q44(chr1:243677224-244923447)x1 copy number loss See cases [RCV000050929] Chr1:243677224..244923447 [GRCh38]
Chr1:243840526..245086749 [GRCh37]
Chr1:241907149..243153372 [NCBI36]
Chr1:1q44		 pathogenic
GRCh38/hg38 1q41-44(chr1:223828500-248891309)x3 copy number gain See cases [RCV000051878] Chr1:223828500..248891309 [GRCh38]
Chr1:224016202..249185508 [GRCh37]
Chr1:222082825..247152131 [NCBI36]
Chr1:1q41-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:238351121-248918469)x1 copy number loss See cases [RCV000134172] Chr1:238351121..248918469 [GRCh38]
Chr1:238514421..249212668 [GRCh37]
Chr1:236581044..247179291 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:243304751-244019666)x3 copy number gain See cases [RCV000142682] Chr1:243304751..244019666 [GRCh38]
Chr1:243468053..244182968 [GRCh37]
Chr1:241534676..242249591 [NCBI36]
Chr1:1q43-44		 uncertain significance
GRCh38/hg38 1q42.11-44(chr1:224096488-248918469)x3 copy number gain See cases [RCV000051882] Chr1:224096488..248918469 [GRCh38]
Chr1:224284190..249212668 [GRCh37]
Chr1:222350813..247179291 [NCBI36]
Chr1:1q42.11-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:243145749-244433395)x1 copy number loss See cases [RCV000142668] Chr1:243145749..244433395 [GRCh38]
Chr1:243309051..244596697 [GRCh37]
Chr1:241375674..242663320 [NCBI36]
Chr1:1q43-44		 pathogenic|likely benign|uncertain significance
GRCh38/hg38 1q43-44(chr1:239629868-248924593)x1 copy number loss See cases [RCV000054024] Chr1:239629868..248924593 [GRCh38]
Chr1:239793168..249218792 [GRCh37]
Chr1:237859791..247185415 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:240465122-248918469)x1 copy number loss See cases [RCV000137260] Chr1:240465122..248918469 [GRCh38]
Chr1:240628422..249212668 [GRCh37]
Chr1:238695045..247179291 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:242240797-245200164)x1 copy number loss See cases [RCV000054030] Chr1:242240797..245200164 [GRCh38]
Chr1:242404099..245363466 [GRCh37]
Chr1:240470722..243430089 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:241967139-245542967)x3 copy number gain See cases [RCV000138233] Chr1:241967139..245542967 [GRCh38]
Chr1:242130441..245706269 [GRCh37]
Chr1:240197064..243772892 [NCBI36]
Chr1:1q43-44		 likely pathogenic
GRCh38/hg38 1q32.2-44(chr1:207346642-248930485)x3 copy number gain See cases [RCV000143727] Chr1:207346642..248930485 [GRCh38]
Chr1:207519987..249224684 [GRCh37]
Chr1:205586610..247191307 [NCBI36]
Chr1:1q32.2-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:242045279-248930485)x1 copy number loss See cases [RCV000139889] Chr1:242045279..248930485 [GRCh38]
Chr1:242208581..249224684 [GRCh37]
Chr1:240275204..247191307 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:242782194-245138126)x3 copy number gain See cases [RCV000140438] Chr1:242782194..245138126 [GRCh38]
Chr1:242945496..245301428 [GRCh37]
Chr1:241012119..243368051 [NCBI36]
Chr1:1q43-44		 uncertain significance
GRCh38/hg38 1q32.2-44(chr1:209646207-248931113)x3 copy number gain See cases [RCV000051861] Chr1:209646207..248931113 [GRCh38]
Chr1:209819552..249225312 [GRCh37]
Chr1:207886175..247191935 [NCBI36]
Chr1:1q32.2-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:242828731-248891309)x3 copy number gain See cases [RCV000053504] Chr1:242828731..248891309 [GRCh38]
Chr1:242992033..249185508 [GRCh37]
Chr1:241058656..247152131 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:241047422-248924593)x1 copy number loss See cases [RCV000054025] Chr1:241047422..248924593 [GRCh38]
Chr1:241210722..249218792 [GRCh37]
Chr1:239277345..247185415 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:241757249-248891309)x1 copy number loss See cases [RCV000054028] Chr1:241757249..248891309 [GRCh38]
Chr1:241920551..249185508 [GRCh37]
Chr1:239987174..247152131 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q42.13-44(chr1:229022909-248918469)x3 copy number gain See cases [RCV000136666] Chr1:229022909..248918469 [GRCh38]
Chr1:229158656..249212668 [GRCh37]
Chr1:227225279..247179291 [NCBI36]
Chr1:1q42.13-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:238033575-248924534)x1 copy number loss See cases [RCV000140039] Chr1:238033575..248924534 [GRCh38]
Chr1:238196875..249218733 [GRCh37]
Chr1:236263498..247185356 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:238192880-248930485)x1 copy number loss See cases [RCV000143374] Chr1:238192880..248930485 [GRCh38]
Chr1:238356180..249224684 [GRCh37]
Chr1:236422803..247191307 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q42.2-44(chr1:232097468-248918610)x1 copy number loss See cases [RCV000053985] Chr1:232097468..248918610 [GRCh38]
Chr1:232233214..249212809 [GRCh37]
Chr1:230299837..247179432 [NCBI36]
Chr1:1q42.2-44		 pathogenic
GRCh38/hg38 1q41-44(chr1:223347693-248918469)x3 copy number gain See cases [RCV000050581] Chr1:223347693..248918469 [GRCh38]
Chr1:223521035..249212668 [GRCh37]
Chr1:221587658..247179291 [NCBI36]
Chr1:1q41-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:240244444-248891309)x3 copy number gain See cases [RCV000051888] Chr1:240244444..248891309 [GRCh38]
Chr1:240407744..249185508 [GRCh37]
Chr1:238474367..247152131 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:236556082-248918469)x1 copy number loss See cases [RCV000137554] Chr1:236556082..248918469 [GRCh38]
Chr1:236719382..249212668 [GRCh37]
Chr1:234786005..247179291 [NCBI36]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:243221458-248919110)x1 copy number loss Intellectual disability, autosomal dominant 22 [RCV003327711] Chr1:243221458..248919110 [GRCh38]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:242164274-245299473)x1 copy number loss Intellectual disability, autosomal dominant 22 [RCV003327716] Chr1:242164274..245299473 [GRCh38]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q42.3-44(chr1:235215476-247005888)x1 copy number loss Intellectual disability, autosomal dominant 22 [RCV003327725] Chr1:235215476..247005888 [GRCh38]
Chr1:1q42.3-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:239907336-248919110)x1 copy number loss Intellectual disability, autosomal dominant 22 [RCV003333897] Chr1:239907336..248919110 [GRCh38]
Chr1:1q43-44		 pathogenic
GRCh38/hg38 1q43-44(chr1:242520315-246857912)x1 copy number loss Intellectual disability, autosomal dominant 22 [RCV003333898] Chr1:242520315..246857912 [GRCh38]
Chr1:1q43-44		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:153
Count of miRNA genes:151
Interacting mature miRNAs:152
Transcripts:ENST00000440494
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
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 1 1
Low 37 3 21 3 190 3 2 1626 7 335 24 1 1
Below cutoff 1156 1413 1182 310 1039 231 2011 731 1770 212 657 1078 81 629 1295 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000440494
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1243,917,402 - 244,047,317 (+)Ensembl
RefSeq Acc Id: ENST00000652928
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1243,917,451 - 244,027,213 (+)Ensembl
RefSeq Acc Id: NR_033883
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381243,917,402 - 244,047,317 (+)NCBI
T2T-CHM13v2.01243,332,936 - 243,463,802 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC02774 COSMIC
Ensembl Genes ENSG00000226828 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000440494 ENTREZGENE
GTEx ENSG00000226828 GTEx
HGNC ID HGNC:27923 ENTREZGENE
Human Proteome Map LINC02774 Human Proteome Map
NCBI Gene LINC02774 ENTREZGENE
RNAcentral URS000075BE3F RNACentral