LINC02082 (long intergenic non-protein coding RNA 2082) - Rat Genome Database

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Gene: LINC02082 (long intergenic non-protein coding RNA 2082) Homo sapiens
Analyze
Symbol: LINC02082
Name: long intergenic non-protein coding RNA 2082
RGD ID: 11575417
HGNC Page HGNC:52931
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
GRCh383168,901,945 - 168,921,996 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3168,902,194 - 168,924,590 (+)EnsemblGRCh38hg38GRCh38
GRCh373168,619,733 - 168,639,784 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map3q26.2NCBI
HuRef3165,991,706 - 166,010,249 (+)NCBIHuRef
CHM1_13168,584,047 - 168,602,591 (+)NCBICHM1_1
T2T-CHM13v2.03171,685,869 - 171,705,921 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:37932992  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 3q22.3-29(chr3:137126982-198110178)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051723]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051723]|See cases [RCV000051723] Chr3:137126982..198110178 [GRCh38]
Chr3:136845824..197837049 [GRCh37]
Chr3:138328514..199321446 [NCBI36]
Chr3:3q22.3-29		 pathogenic
GRCh38/hg38 3q24-26.32(chr3:147442566-178522531)x3 copy number gain See cases [RCV000051724] Chr3:147442566..178522531 [GRCh38]
Chr3:147160353..178240319 [GRCh37]
Chr3:148643043..179723013 [NCBI36]
Chr3:3q24-26.32		 pathogenic
GRCh38/hg38 3q24-29(chr3:147521892-198096565)x3 copy number gain See cases [RCV000051725] Chr3:147521892..198096565 [GRCh38]
Chr3:147239679..197823436 [GRCh37]
Chr3:148722369..199307833 [NCBI36]
Chr3:3q24-29		 pathogenic
GRCh38/hg38 3q13.11-29(chr3:103426882-198110178)x3 copy number gain See cases [RCV000134948] Chr3:103426882..198110178 [GRCh38]
Chr3:103145726..197837049 [GRCh37]
Chr3:104628416..199321446 [NCBI36]
Chr3:3q13.11-29		 pathogenic
GRCh38/hg38 3q26.1-28(chr3:167717962-188365272)x3 copy number gain See cases [RCV000142107] Chr3:167717962..188365272 [GRCh38]
Chr3:167435750..188083060 [GRCh37]
Chr3:168918444..189565754 [NCBI36]
Chr3:3q26.1-28		 likely pathogenic
GRCh38/hg38 3q25.31-29(chr3:157293378-198134727)x3 copy number gain See cases [RCV000051726] Chr3:157293378..198134727 [GRCh38]
Chr3:157011167..197861598 [GRCh37]
Chr3:158493861..199345995 [NCBI36]
Chr3:3q25.31-29		 pathogenic
GRCh38/hg38 3q25.32-26.31(chr3:158141556-172788324)x3 copy number gain See cases [RCV000051735] Chr3:158141556..172788324 [GRCh38]
Chr3:157859345..172506114 [GRCh37]
Chr3:159342039..173988808 [NCBI36]
Chr3:3q25.32-26.31		 pathogenic
GRCh38/hg38 3q25.31-29(chr3:156118441-198125115)x3 copy number gain See cases [RCV000142310] Chr3:156118441..198125115 [GRCh38]
Chr3:155836230..197851986 [GRCh37]
Chr3:157318924..199336383 [NCBI36]
Chr3:3q25.31-29		 pathogenic
GRCh38/hg38 3q26.1-26.2(chr3:166831737-170631211)x3 copy number gain See cases [RCV000136642] Chr3:166831737..170631211 [GRCh38]
Chr3:166549525..170349000 [GRCh37]
Chr3:168032219..171831694 [NCBI36]
Chr3:3q26.1-26.2		 uncertain significance
GRCh38/hg38 3q26.2-29(chr3:168167568-198110178)x3 copy number gain See cases [RCV000137106] Chr3:168167568..198110178 [GRCh38]
Chr3:167885356..197837049 [GRCh37]
Chr3:169368050..199321446 [NCBI36]
Chr3:3q26.2-29		 pathogenic
GRCh38/hg38 3q26.1-29(chr3:166137209-198125115)x3 copy number gain See cases [RCV000143694] Chr3:166137209..198125115 [GRCh38]
Chr3:165854997..197851986 [GRCh37]
Chr3:167337691..199336383 [NCBI36]
Chr3:3q26.1-29		 pathogenic
GRCh38/hg38 3q26.1-26.33(chr3:165158611-180130168)x3 copy number gain See cases [RCV000139359] Chr3:165158611..180130168 [GRCh38]
Chr3:164876399..179847956 [GRCh37]
Chr3:166359093..181330650 [NCBI36]
Chr3:3q26.1-26.33		 pathogenic
GRCh38/hg38 3q25.1-29(chr3:152100512-198118383)x3 copy number gain See cases [RCV000139435] Chr3:152100512..198118383 [GRCh38]
Chr3:151818301..197845254 [GRCh37]
Chr3:153300991..199329651 [NCBI36]
Chr3:3q25.1-29		 pathogenic
GRCh38/hg38 3q25.31-29(chr3:156321878-198113452)x3 copy number gain See cases [RCV000140849] Chr3:156321878..198113452 [GRCh38]
Chr3:156039667..197840323 [GRCh37]
Chr3:157522361..199324720 [NCBI36]
Chr3:3q25.31-29		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:31
Count of miRNA genes:31
Interacting mature miRNAs:31
Transcripts:ENST00000484765
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 5 22 1 1 1 31 2 12 6 4
Low 214 129 379 47 143 43 559 154 1906 90 360 408 5 579 291 2
Below cutoff 1305 1113 587 216 321 119 1710 859 1554 213 450 718 98 507 1054

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000484765
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3168,903,366 - 168,921,996 (+)Ensembl
RefSeq Acc Id: ENST00000664865
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3168,902,194 - 168,924,590 (+)Ensembl
RefSeq Acc Id: NR_109989
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh383168,901,945 - 168,921,996 (+)NCBI
CHM1_13168,582,629 - 168,602,678 (+)NCBI
T2T-CHM13v2.03171,685,869 - 171,705,921 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC02082 COSMIC
Ensembl Genes ENSG00000242268 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000484765 ENTREZGENE
GTEx ENSG00000242268 GTEx
HGNC ID HGNC:52931 ENTREZGENE
Human Proteome Map LINC02082 Human Proteome Map
NCBI Gene LINC02082 ENTREZGENE
RNAcentral URS000075C391 RNACentral