LINC01616 (long intergenic non-protein coding RNA 1616) - Rat Genome Database

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Pathways
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Gene: LINC01616 (long intergenic non-protein coding RNA 1616) Homo sapiens
Analyze
Symbol: LINC01616
Name: long intergenic non-protein coding RNA 1616
RGD ID: 10401054
HGNC Page HGNC:51900
Description:
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: n341006
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381129,980,120 - 29,982,393 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1129,980,113 - 29,982,392 (-)EnsemblGRCh38hg38GRCh38
GRCh371130,001,667 - 30,003,940 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map11p14.1NCBI
CHM1_11130,000,568 - 30,002,841 (-)NCBICHM1_1
T2T-CHM13v2.01130,114,216 - 30,116,489 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:14702039   PMID:16344560   PMID:26318290  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 11p15.1-13(chr11:20079474-34463996)x1 copy number loss See cases [RCV000142499] Chr11:20079474..34463996 [GRCh38]
Chr11:20101020..34485543 [GRCh37]
Chr11:20057596..34442119 [NCBI36]
Chr11:11p15.1-13		 pathogenic
GRCh38/hg38 11p14.3-12(chr11:22550115-38199159)x1 copy number loss See cases [RCV000052648] Chr11:22550115..38199159 [GRCh38]
Chr11:22571661..38220709 [GRCh37]
Chr11:22528237..38177285 [NCBI36]
Chr11:11p14.3-12		 pathogenic
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 11p14.3-13(chr11:24595399-31096539)x3 copy number gain See cases [RCV000134877] Chr11:24595399..31096539 [GRCh38]
Chr11:24616945..31118086 [GRCh37]
Chr11:24573521..31074662 [NCBI36]
Chr11:11p14.3-13		 pathogenic
GRCh38/hg38 11p14.2-13(chr11:26368962-35252976)x1 copy number loss See cases [RCV000135295] Chr11:26368962..35252976 [GRCh38]
Chr11:26390509..35274523 [GRCh37]
Chr11:26347085..35231099 [NCBI36]
Chr11:11p14.2-13		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:38
Count of miRNA genes:37
Interacting mature miRNAs:37
Transcripts:ENST00000561816
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 4 310
Low 6 145 478 4 132 114 1857 2 21 71 1 311 57
Below cutoff 1212 1141 249 48 203 14 1902 917 1215 99 559 663 34 703 1163 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000561816
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1129,980,113 - 29,982,392 (-)Ensembl
RefSeq Acc Id: NR_132652
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381129,980,120 - 29,982,393 (-)NCBI
CHM1_11130,000,568 - 30,002,841 (-)NCBI
T2T-CHM13v2.01130,114,216 - 30,116,489 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC01616 COSMIC
Ensembl Genes ENSG00000261340 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000561816 ENTREZGENE
GTEx ENSG00000261340 GTEx
HGNC ID HGNC:51900 ENTREZGENE
Human Proteome Map LINC01616 Human Proteome Map
NCBI Gene LINC01616 ENTREZGENE
RNAcentral URS00008E3A00 RNACentral