LINC02084 (long intergenic non-protein coding RNA 2084) - Rat Genome Database

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Pathways
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Gene: LINC02084 (long intergenic non-protein coding RNA 2084) Homo sapiens
Analyze
Symbol: LINC02084
Name: long intergenic non-protein coding RNA 2084
RGD ID: 11576077
HGNC Page HGNC:52934
Description:
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: MODEL
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38327,712,919 - 27,714,400 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl327,712,910 - 27,714,005 (+)EnsemblGRCh38hg38GRCh38
Cytogenetic Map3p24.1NCBI
CHM1_1327,703,650 - 27,705,475 (+)NCBICHM1_1
T2T-CHM13v2.0327,714,424 - 27,716,093 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
COVID-19  (HEP)

References

References - curated
# Reference Title Reference Citation
1. Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients. Xiong Y, etal., Emerg Microbes Infect. 2020 Dec;9(1):761-770. doi: 10.1080/22221751.2020.1747363.

Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 3p26.3-24.1(chr3:52266-29248782)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051718]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051718]|See cases [RCV000051718] Chr3:52266..29248782 [GRCh38]
Chr3:93949..29290273 [GRCh37]
Chr3:68949..29265277 [NCBI36]
Chr3:3p26.3-24.1		 pathogenic
GRCh38/hg38 3p25.3-22.2(chr3:11463328-38919543)x3 copy number gain See cases [RCV000051720] Chr3:11463328..38919543 [GRCh38]
Chr3:11504802..38961034 [GRCh37]
Chr3:11479802..38936038 [NCBI36]
Chr3:3p25.3-22.2		 pathogenic
GRCh38/hg38 3p26.3-24.1(chr3:32241-30064208)x3 copy number gain See cases [RCV000138004] Chr3:32241..30064208 [GRCh38]
Chr3:73914..30105699 [GRCh37]
Chr3:48914..30080703 [NCBI36]
Chr3:3p26.3-24.1		 pathogenic
GRCh38/hg38 3p26.3-22.2(chr3:52266-37148076)x3 copy number gain See cases [RCV000051097] Chr3:52266..37148076 [GRCh38]
Chr3:93949..37189567 [GRCh37]
Chr3:68949..37164571 [NCBI36]
Chr3:3p26.3-22.2		 pathogenic
GRCh38/hg38 3p26.3-22.1(chr3:53308-41381521)x3 copy number gain See cases [RCV000141810] Chr3:53308..41381521 [GRCh38]
Chr3:94991..41423012 [GRCh37]
Chr3:69991..41398016 [NCBI36]
Chr3:3p26.3-22.1		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:170
Count of miRNA genes:168
Interacting mature miRNAs:170
Transcripts:ENST00000606069
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 107 2 200 1 1 4 2 2
Low 562 1191 747 202 1116 173 739 173 765 184 842 972 35 518 363
Below cutoff 1615 1463 889 377 272 253 2690 1338 2042 183 510 507 128 654 1716 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000606069
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl327,712,910 - 27,714,005 (+)Ensembl
RefSeq Acc Id: XR_007073383
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0327,714,424 - 27,716,093 (+)NCBI
RefSeq Acc Id: XR_007095851
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38327,712,919 - 27,714,400 (+)NCBI
Promoters
RGD ID:15095578
Promoter ID:EPDNEWNC_H419
Type:initiation region
Name:LINC02084_1
Description:long intergenic non-protein coding RNA 2084 [Source:HGNCSymbol;Acc:HGNC:52934]
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
GRCh38327,712,894 - 27,712,954EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC LINC02084 COSMIC
Ensembl Genes ENSG00000272282 Ensembl
GTEx ENSG00000272282 GTEx
HGNC ID HGNC:52934 ENTREZGENE
Human Proteome Map LINC02084 Human Proteome Map
NCBI Gene LINC02084 ENTREZGENE