LINC02728 (long intergenic non-protein coding RNA 2728) - 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: LINC02728 (long intergenic non-protein coding RNA 2728) Homo sapiens
Analyze
Symbol: LINC02728
Name: long intergenic non-protein coding RNA 2728
RGD ID: 14694859
HGNC Page HGNC:54245
Description: INTERACTS WITH 17beta-estradiol; titanium dioxide
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
GRCh381178,423,982 - 78,429,836 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1178,423,982 - 78,429,836 (-)EnsemblGRCh38hg38GRCh38
GRCh371178,135,028 - 78,140,882 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map11q14.1NCBI
HuRef1174,432,136 - 74,438,093 (-)NCBIHuRef
CHM1_11178,018,170 - 78,024,127 (-)NCBICHM1_1
T2T-CHM13v2.01178,357,277 - 78,363,131 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 11q14.1-14.2(chr11:78362208-86165380)x3 copy number gain See cases [RCV000053637] Chr11:78362208..86165380 [GRCh38]
Chr11:78073254..85876422 [GRCh37]
Chr11:77750902..85554070 [NCBI36]
Chr11:11q14.1-14.2		 pathogenic
GRCh38/hg38 11q13.5-22.1(chr11:75941754-98357960)x1 copy number loss See cases [RCV000133838] Chr11:75941754..98357960 [GRCh38]
Chr11:75652798..98228688 [GRCh37]
Chr11:75330446..97733898 [NCBI36]
Chr11:11q13.5-22.1		 pathogenic
GRCh38/hg38 11q14.1-22.3(chr11:78232836-106779420)x1 copy number loss See cases [RCV000052710] Chr11:78232836..106779420 [GRCh38]
Chr11:77943882..106650146 [GRCh37]
Chr11:77621530..106155356 [NCBI36]
Chr11:11q14.1-22.3		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:52
Count of miRNA genes:49
Interacting mature miRNAs:50
Transcripts:ENST00000513207
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 55 2 6 2
Low 1103 942 1036 260 954 138 3090 428 1110 116 1129 1206 129 810 1713 2
Below cutoff 1294 1787 643 328 736 292 1194 1661 2113 246 294 380 41 386 1015 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000513207
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1178,423,982 - 78,429,836 (-)Ensembl
RefSeq Acc Id: ENST00000660634
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1178,424,386 - 78,427,966 (-)Ensembl
RefSeq Acc Id: ENST00000664831
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1178,424,614 - 78,427,810 (-)Ensembl
RefSeq Acc Id: NR_120564
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381178,423,982 - 78,429,836 (-)NCBI
T2T-CHM13v2.01178,357,277 - 78,363,131 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC02728 COSMIC
Ensembl Genes ENSG00000251323 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000513207 ENTREZGENE
GTEx ENSG00000251323 GTEx
HGNC ID HGNC:54245 ENTREZGENE
Human Proteome Map LINC02728 Human Proteome Map
NCBI Gene LINC02728 ENTREZGENE
RNAcentral URS000075ED9D RNACentral