LINC02709 (long intergenic non-protein coding RNA 2709) - Rat Genome Database

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Gene: LINC02709 (long intergenic non-protein coding RNA 2709) Homo sapiens
Analyze
Symbol: LINC02709
Name: long intergenic non-protein coding RNA 2709
RGD ID: 14694877
HGNC Page HGNC:54226
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
GRCh38119,754,770 - 9,759,533 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl119,754,770 - 9,759,533 (-)EnsemblGRCh38hg38GRCh38
GRCh37119,776,317 - 9,781,080 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map11p15.4NCBI
HuRef119,448,933 - 9,453,694 (-)NCBIHuRef
CHM1_1119,775,635 - 9,780,398 (-)NCBICHM1_1
T2T-CHM13v2.0119,839,482 - 9,844,242 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:12477932   PMID:14702039  


Genomics

Variants

.
Variants in LINC02709
4 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 11p15.5-13(chr11:202758-31726224)x3 copy number gain See cases [RCV000053613] Chr11:202758..31726224 [GRCh38]
Chr11:202758..31747772 [GRCh37]
Chr11:192758..31704348 [NCBI36]
Chr11:11p15.5-13		 pathogenic
GRCh38/hg38 11p15.4(chr11:7995676-10437205)x3 copy number gain See cases [RCV000143490] Chr11:7995676..10437205 [GRCh38]
Chr11:8017223..10458752 [GRCh37]
Chr11:7973799..10415328 [NCBI36]
Chr11:11p15.4		 uncertain significance
GRCh38/hg38 11p15.5-15.4(chr11:61793-10727969)x3 copy number gain See cases [RCV000139987] Chr11:61793..10727969 [GRCh38]
Chr11:61793..10749516 [GRCh37]
Chr11:51793..10706092 [NCBI36]
Chr11:11p15.5-15.4		 pathogenic
GRCh38/hg38 11p15.5-15.1(chr11:446754-18904742)x3 copy number gain See cases [RCV000133997] Chr11:446754..18904742 [GRCh38]
Chr11:446754..18926289 [GRCh37]
Chr11:436754..18882865 [NCBI36]
Chr11:11p15.5-15.1		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:294
Count of miRNA genes:272
Interacting mature miRNAs:278
Transcripts:ENST00000500698, ENST00000525154
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 4 3 2 1 2 2 2 3 1 2 11 1
Low 254 36 102 93 603 69 1112 136 197 218 639 287 35 447 463 3
Below cutoff 2107 2601 1540 475 1125 341 3143 1946 3292 194 782 1285 135 752 2230 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000500698
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl119,754,770 - 9,759,533 (-)Ensembl
RefSeq Acc Id: ENST00000525154
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl119,755,129 - 9,758,164 (-)Ensembl
RefSeq Acc Id: NR_033972
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38119,754,770 - 9,759,533 (-)NCBI
T2T-CHM13v2.0119,839,482 - 9,844,242 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC02709 COSMIC
Ensembl Genes ENSG00000245522 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000500698 ENTREZGENE
GTEx ENSG00000245522 GTEx
HGNC ID HGNC:54226 ENTREZGENE
Human Proteome Map LINC02709 Human Proteome Map
NCBI Gene LINC02709 ENTREZGENE
RNAcentral URS0000565587 RNACentral