LINC02789 (long intergenic non-protein coding RNA 2789) - Rat Genome Database

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Gene: LINC02789 (long intergenic non-protein coding RNA 2789) Homo sapiens
Analyze
Symbol: LINC02789
Name: long intergenic non-protein coding RNA 2789
RGD ID: 14400109
HGNC Page HGNC:54310
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
GRCh381199,148,598 - 199,393,307 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1199,148,598 - 199,393,307 (+)EnsemblGRCh38hg38GRCh38
GRCh371199,117,726 - 199,362,435 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map1q32.1NCBI
HuRef1170,284,784 - 170,529,666 (+)NCBIHuRef
CHM1_11200,540,028 - 200,784,801 (+)NCBICHM1_1
T2T-CHM13v2.01198,407,317 - 198,652,058 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:14702039   PMID:21546767  


Genomics

Variants

.
Variants in LINC02789
10 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 1q31.1-32.1(chr1:189034483-199615866)x1 copy number loss See cases [RCV000135590] Chr1:189034483..199615866 [GRCh38]
Chr1:189003614..199584994 [GRCh37]
Chr1:187270237..197851617 [NCBI36]
Chr1:1q31.1-32.1		 pathogenic
GRCh38/hg38 1q25.2-32.1(chr1:179032905-199724897)x1 copy number loss See cases [RCV000053948] Chr1:179032905..199724897 [GRCh38]
Chr1:179002040..199694025 [GRCh37]
Chr1:177268663..197960648 [NCBI36]
Chr1:1q25.2-32.1		 pathogenic
GRCh38/hg38 1q31.1-42.11(chr1:187143981-224299417)x3 copy number gain See cases [RCV000051857] Chr1:187143981..224299417 [GRCh38]
Chr1:187113113..224487119 [GRCh37]
Chr1:185379736..222553742 [NCBI36]
Chr1:1q31.1-42.11		 pathogenic
GRCh38/hg38 1q31.3-32.1(chr1:198608514-199646718)x1 copy number loss See cases [RCV000053951] Chr1:198608514..199646718 [GRCh38]
Chr1:198577644..199615846 [GRCh37]
Chr1:196844267..197882469 [NCBI36]
Chr1:1q31.3-32.1		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:66
Count of miRNA genes:66
Interacting mature miRNAs:66
Transcripts:ENST00000452199
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
Low 2 3 4 1 4 2 1
Below cutoff 40 65 38 11 90 7 155 82 105 8 152 46 5 92 76

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000452199
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1199,148,598 - 199,393,307 (+)Ensembl
RefSeq Acc Id: NR_147896
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381199,148,598 - 199,393,307 (+)NCBI
T2T-CHM13v2.01198,407,317 - 198,652,058 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC02789 COSMIC
Ensembl Genes ENSG00000231718 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000452199 ENTREZGENE
GTEx ENSG00000231718 GTEx
HGNC ID HGNC:54310 ENTREZGENE
Human Proteome Map LINC02789 Human Proteome Map
NCBI Gene LINC02789 ENTREZGENE
RNAcentral URS00004AE46A RNACentral