LINC02098 (long intergenic non-protein coding RNA 2098) - Rat Genome Database

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Gene: LINC02098 (long intergenic non-protein coding RNA 2098) Homo sapiens
Analyze
Symbol: LINC02098
Name: long intergenic non-protein coding RNA 2098
RGD ID: 11575886
HGNC Page HGNC:52950
Description: ASSOCIATED WITH Schizophrenia; schizophrenia; INTERACTS WITH aflatoxin B1
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
GRCh3811128,208,766 - 128,241,441 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl11128,208,749 - 128,241,441 (+)EnsemblGRCh38hg38GRCh38
GRCh3711128,078,661 - 128,111,336 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map11q24.3NCBI
CHM1_111127,963,072 - 127,996,954 (+)NCBICHM1_1
T2T-CHM13v2.011128,242,033 - 128,274,698 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
schizophrenia  (IAGP)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
aflatoxin B1  (EXP)

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
Schizophrenia  (IAGP)
References
Additional References at PubMed
PMID:27714034  


Genomics

Variants

.
Variants in LINC02098
2 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 11q24.1-25(chr11:121611476-135068576)x1 copy number loss See cases [RCV000142185] Chr11:121611476..135068576 [GRCh38]
Chr11:121482185..134938470 [GRCh37]
Chr11:120987395..134443680 [NCBI36]
Chr11:11q24.1-25		 pathogenic
GRCh38/hg38 11q24.1-25(chr11:121806547-135068576)x1 copy number loss See cases [RCV000142210] Chr11:121806547..135068576 [GRCh38]
Chr11:121677255..134938470 [GRCh37]
Chr11:121182465..134443680 [NCBI36]
Chr11:11q24.1-25		 pathogenic
GRCh38/hg38 11q24.2-25(chr11:126046358-134998513)x1 copy number loss See cases [RCV000136595] Chr11:126046358..134998513 [GRCh38]
Chr11:125916253..134868407 [GRCh37]
Chr11:125421463..134373617 [NCBI36]
Chr11:11q24.2-25		 pathogenic
GRCh38/hg38 11q24.2-25(chr11:125241472-134998513)x1 copy number loss See cases [RCV000136612] Chr11:125241472..134998513 [GRCh38]
Chr11:125111368..134868407 [GRCh37]
Chr11:124616578..134373617 [NCBI36]
Chr11:11q24.2-25		 pathogenic
GRCh38/hg38 11q24.3-25(chr11:127915964-135068576)x1 copy number loss See cases [RCV000143755] Chr11:127915964..135068576 [GRCh38]
Chr11:127785859..134938470 [GRCh37]
Chr11:127291069..134443680 [NCBI36]
Chr11:11q24.3-25		 pathogenic
GRCh38/hg38 11q23.3-25(chr11:116868935-135075271)x3 copy number gain See cases [RCV000137453] Chr11:116868935..135075271 [GRCh38]
Chr11:116739651..134945165 [GRCh37]
Chr11:116244861..134450377 [NCBI36]
Chr11:11q23.3-25		 pathogenic|conflicting data from submitters
GRCh38/hg38 11q23.2-25(chr11:112864326-131189315)x3 copy number gain See cases [RCV000137582] Chr11:112864326..131189315 [GRCh38]
Chr11:112832130..131059210 [GRCh37]
Chr11:112240259..130564420 [NCBI36]
Chr11:11q23.2-25		 pathogenic
GRCh38/hg38 11q23.3-25(chr11:116851395-134998513)x3 copy number gain See cases [RCV000148276] Chr11:116851395..134998513 [GRCh38]
Chr11:116722111..134868407 [GRCh37]
Chr11:116227321..134373617 [NCBI36]
Chr11:11q23.3-25		 pathogenic
GRCh38/hg38 11q23.3-25(chr11:119215032-134998654)x1 copy number loss See cases [RCV000052715] Chr11:119215032..134998654 [GRCh38]
Chr11:119085742..134868548 [GRCh37]
Chr11:118590952..134373758 [NCBI36]
Chr11:11q23.3-25		 pathogenic
GRCh38/hg38 11q23.3-25(chr11:120507265-134576266)x1 copy number loss See cases [RCV000052716] Chr11:120507265..134576266 [GRCh38]
Chr11:120377974..134446160 [GRCh37]
Chr11:119883184..133951370 [NCBI36]
Chr11:11q23.3-25		 pathogenic
GRCh38/hg38 11q24.2-25(chr11:126433740-135040246)x1 copy number loss See cases [RCV000052741] Chr11:126433740..135040246 [GRCh38]
Chr11:126303635..134910140 [GRCh37]
Chr11:125808845..134415350 [NCBI36]
Chr11:11q24.2-25		 pathogenic
GRCh38/hg38 11q24.1-25(chr11:121780459-135075271)x1 copy number loss See cases [RCV000138014] Chr11:121780459..135075271 [GRCh38]
Chr11:121651167..134945165 [GRCh37]
Chr11:121156377..134450377 [NCBI36]
Chr11:11q24.1-25		 pathogenic
GRCh38/hg38 11q24.2-25(chr11:126046358-135075271)x1 copy number loss See cases [RCV000138163] Chr11:126046358..135075271 [GRCh38]
Chr11:125916253..134945165 [GRCh37]
Chr11:125421463..134450377 [NCBI36]
Chr11:11q24.2-25		 pathogenic
GRCh38/hg38 11q23.3-25(chr11:116806268-135075271)x3 copy number gain See cases [RCV000138307] Chr11:116806268..135075271 [GRCh38]
Chr11:116676984..134945165 [GRCh37]
Chr11:116182194..134450377 [NCBI36]
Chr11:11q23.3-25		 pathogenic
GRCh38/hg38 11q23.3-25(chr11:120515759-135075271)x1 copy number loss See cases [RCV000138373] Chr11:120515759..135075271 [GRCh38]
Chr11:120386468..134945165 [GRCh37]
Chr11:119891678..134450377 [NCBI36]
Chr11:11q23.3-25		 pathogenic
GRCh38/hg38 11q24.1-25(chr11:123963074-135075271)x1 copy number loss See cases [RCV000138544] Chr11:123963074..135075271 [GRCh38]
Chr11:123833781..134945165 [GRCh37]
Chr11:123338991..134450377 [NCBI36]
Chr11:11q24.1-25		 pathogenic
GRCh38/hg38 11q22.1-25(chr11:100348599-135040246)x3 copy number gain See cases [RCV000053638] Chr11:100348599..135040246 [GRCh38]
Chr11:100219331..134910140 [GRCh37]
Chr11:99724541..134415350 [NCBI36]
Chr11:11q22.1-25		 pathogenic
GRCh38/hg38 11q23.3-25(chr11:120236432-135040246)x3 copy number gain See cases [RCV000053643] Chr11:120236432..135040246 [GRCh38]
Chr11:120107141..134910140 [GRCh37]
Chr11:119612351..134415350 [NCBI36]
Chr11:11q23.3-25		 pathogenic
GRCh38/hg38 11q24.1-25(chr11:123753493-134998513)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053645]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053645]|See cases [RCV000053645] Chr11:123753493..134998513 [GRCh38]
Chr11:123624201..134868407 [GRCh37]
Chr11:123129411..134373617 [NCBI36]
Chr11:11q24.1-25		 pathogenic
GRCh38/hg38 11q23.3-25(chr11:116851395-134998513)x3 copy number gain See cases [RCV000050331] Chr11:116851395..134998513 [GRCh38]
Chr11:116722111..134868407 [GRCh37]
Chr11:116227321..134373617 [NCBI36]
Chr11:11q23.3-25		 pathogenic
GRCh38/hg38 11q24.2-25(chr11:124315025-134818116)x1 copy number loss See cases [RCV000139907] Chr11:124315025..134818116 [GRCh38]
Chr11:124184921..134688010 [GRCh37]
Chr11:123690131..134193220 [NCBI36]
Chr11:11q24.2-25		 pathogenic
GRCh38/hg38 11q24.2-25(chr11:127604660-134998454)x1 copy number loss See cases [RCV000050843] Chr11:127604660..134998454 [GRCh38]
Chr11:127474555..134868348 [GRCh37]
Chr11:126979765..134373558 [NCBI36]
Chr11:11q24.2-25		 pathogenic
GRCh38/hg38 11q24.2-25(chr11:124155723-134998513)x1 copy number loss See cases [RCV000050865] Chr11:124155723..134998513 [GRCh38]
Chr11:124026430..134868407 [GRCh37]
Chr11:123531640..134373617 [NCBI36]
Chr11:11q24.2-25		 pathogenic
GRCh38/hg38 11q23.3-25(chr11:119433909-134998513)x1 copy number loss See cases [RCV000050905] Chr11:119433909..134998513 [GRCh38]
Chr11:119304619..134868407 [GRCh37]
Chr11:118809829..134373617 [NCBI36]
Chr11:11q23.3-25		 pathogenic
GRCh38/hg38 11q24.2-24.3(chr11:125891315-129072391)x1 copy number loss See cases [RCV000050926] Chr11:125891315..129072391 [GRCh38]
Chr11:125761210..128942286 [GRCh37]
Chr11:125266420..128447496 [NCBI36]
Chr11:11q24.2-24.3		 pathogenic
GRCh38/hg38 11q23.3-25(chr11:116851372-134998526)x3 copy number gain See cases [RCV000134064] Chr11:116851372..134998526 [GRCh38]
Chr11:116722088..134868420 [GRCh37]
Chr11:116227298..134373630 [NCBI36]
Chr11:11q23.3-25		 pathogenic
GRCh38/hg38 11q23.3-25(chr11:118789765-134998513)x3 copy number gain See cases [RCV000051213] Chr11:118789765..134998513 [GRCh38]
Chr11:118660474..134868407 [GRCh37]
Chr11:118165684..134373617 [NCBI36]
Chr11:11q23.3-25		 pathogenic
GRCh38/hg38 11q24.1-25(chr11:123799938-134998526)x1 copy number loss See cases [RCV000134708] Chr11:123799938..134998526 [GRCh38]
Chr11:123670646..134868420 [GRCh37]
Chr11:123175856..134373630 [NCBI36]
Chr11:11q24.1-25		 pathogenic
GRCh38/hg38 11q24.2-25(chr11:126199589-135075271)x1 copy number loss See cases [RCV000139117] Chr11:126199589..135075271 [GRCh38]
Chr11:126069484..134945165 [GRCh37]
Chr11:125574694..134450377 [NCBI36]
Chr11:11q24.2-25		 pathogenic
GRCh38/hg38 11q24.2-25(chr11:126445805-134998513)x3 copy number gain See cases [RCV000051162] Chr11:126445805..134998513 [GRCh38]
Chr11:126315700..134868407 [GRCh37]
Chr11:125820910..134373617 [NCBI36]
Chr11:11q24.2-25		 pathogenic
GRCh38/hg38 11q24.2-25(chr11:124205225-134998526)x1 copy number loss See cases [RCV000134731] Chr11:124205225..134998526 [GRCh38]
Chr11:124075932..134868420 [GRCh37]
Chr11:123581142..134373630 [NCBI36]
Chr11:11q24.2-25		 pathogenic
GRCh38/hg38 11q24.2-25(chr11:127564482-135075271)x1 copy number loss See cases [RCV000137719] Chr11:127564482..135075271 [GRCh38]
Chr11:127434377..134945165 [GRCh37]
Chr11:126939587..134450377 [NCBI36]
Chr11:11q24.2-25		 pathogenic|likely benign
GRCh38/hg38 11q24.2-25(chr11:124940059-135075271)x1 copy number loss See cases [RCV000138675] Chr11:124940059..135075271 [GRCh38]
Chr11:124809955..134945165 [GRCh37]
Chr11:124315165..134450377 [NCBI36]
Chr11:11q24.2-25		 pathogenic|likely benign
GRCh38/hg38 11q23.3-25(chr11:119424297-135075271)x1 copy number loss See cases [RCV000138947] Chr11:119424297..135075271 [GRCh38]
Chr11:119295007..134945165 [GRCh37]
Chr11:118800217..134450377 [NCBI36]
Chr11:11q23.3-25		 pathogenic|likely benign
GRCh38/hg38 11q24.1-25(chr11:121689052-135075271)x1 copy number loss See cases [RCV000139622] Chr11:121689052..135075271 [GRCh38]
Chr11:121559760..134945165 [GRCh37]
Chr11:121064970..134450377 [NCBI36]
Chr11:11q24.1-25		 pathogenic|likely benign
Single allele duplication Schizophrenia [RCV000754124] Chr11:118989374..135076622 [GRCh38]
Chr11:11q23.3-25		 likely pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:66
Count of miRNA genes:33
Interacting mature miRNAs:33
Transcripts:ENST00000608492, ENST00000609260
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
High
Medium 3
Low 1 1 1 1 1 330 3
Below cutoff 29 33 33 14 26 14 54 21 40 28 76 51 2 32 23

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000608492
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl11128,208,829 - 128,241,441 (+)Ensembl
RefSeq Acc Id: ENST00000609260
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl11128,208,780 - 128,241,441 (+)Ensembl
RefSeq Acc Id: ENST00000650607
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl11128,208,749 - 128,241,433 (+)Ensembl
RefSeq Acc Id: ENST00000667926
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl11128,208,784 - 128,241,441 (+)Ensembl
RefSeq Acc Id: NR_146647
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh3811128,208,766 - 128,241,441 (+)NCBI
T2T-CHM13v2.011128,242,033 - 128,274,698 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC02098 COSMIC
Ensembl Genes ENSG00000272575 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000608492 ENTREZGENE
GTEx ENSG00000272575 GTEx
HGNC ID HGNC:52950 ENTREZGENE
Human Proteome Map LINC02098 Human Proteome Map
NCBI Gene LINC02098 ENTREZGENE
RNAcentral URS0000BC4413 RNACentral