LINC01180 (long intergenic non-protein coding RNA 1180) - Rat Genome Database

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Gene: LINC01180 (long intergenic non-protein coding RNA 1180) Homo sapiens
Analyze
Symbol: LINC01180
Name: long intergenic non-protein coding RNA 1180
RGD ID: 7825709
HGNC Page HGNC:49558
Description:
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: RP11-1072C15.2
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381744,646,364 - 44,650,349 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1744,646,364 - 44,650,349 (-)EnsemblGRCh38hg38GRCh38
GRCh371742,723,732 - 42,727,717 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map17q21.31NCBI
HuRef1738,488,609 - 38,492,594 (-)NCBIHuRef
CHM1_11742,959,835 - 42,963,814 (-)NCBICHM1_1
T2T-CHM13v2.01745,500,306 - 45,504,291 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:12477932  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 17q21.31(chr17:43934167-44854025)x1 copy number loss See cases [RCV000134949] Chr17:43934167..44854025 [GRCh38]
Chr17:42011535..42931393 [GRCh37]
Chr17:39367061..40286919 [NCBI36]
Chr17:17q21.31		 pathogenic
GRCh38/hg38 17q23.1-25.1(chr17:36449220-75053130)x3 copy number gain See cases [RCV000137437] Chr17:36449220..75053130 [GRCh38]
Chr17:57595736..73049225 [GRCh37]
Chr17:54950518..70560820 [NCBI36]
Chr17:17q23.1-25.1		 pathogenic
GRCh38/hg38 17q21.33-24.2(chr17:36449220-68170214)x3 copy number gain See cases [RCV000050957] Chr17:36449220..68170214 [GRCh38]
Chr17:48563237..65936105 [GRCh37]
Chr17:45918236..63677950 [NCBI36]
Chr17:17q21.33-24.2		 pathogenic
GRCh38/hg38 17q23.2-25.3(chr17:36449220-83086677)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052483]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052483]|See cases [RCV000052483] Chr17:36449220..83086677 [GRCh38]
Chr17:58617905..81044553 [GRCh37]
Chr17:55972687..78637842 [NCBI36]
Chr17:17q23.2-25.3		 pathogenic
GRCh38/hg38 17q21.31(chr17:43570878-44762377)x1 copy number loss See cases [RCV000053429] Chr17:43570878..44762377 [GRCh38]
Chr17:41648246..42839745 [GRCh37]
Chr17:39003772..40195271 [NCBI36]
Chr17:17q21.31		 pathogenic
GRCh38/hg38 17q12-21.31(chr17:39199873-45629579)x3 copy number gain See cases [RCV000052479] Chr17:39199873..45629579 [GRCh38]
Chr17:37356126..43706945 [GRCh37]
Chr17:34609652..41062728 [NCBI36]
Chr17:17q12-21.31		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:115
Count of miRNA genes:107
Interacting mature miRNAs:109
Transcripts:ENST00000589259
Prediction methods:Microtar, 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 11
Low 4 5 1 5 1 1 2 1 8 372 5 1
Below cutoff 411 578 348 90 394 66 839 291 1477 102 269 441 27 204 504 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000589259
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1744,646,364 - 44,650,349 (-)Ensembl
RefSeq Acc Id: NR_110661
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381744,646,364 - 44,650,349 (-)NCBI
CHM1_11742,959,835 - 42,963,814 (-)NCBI
T2T-CHM13v2.01745,500,306 - 45,504,291 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC01180 COSMIC
Ensembl Genes ENSG00000266979 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000589259 ENTREZGENE
GTEx ENSG00000266979 GTEx
HGNC ID HGNC:49558 ENTREZGENE
Human Proteome Map LINC01180 Human Proteome Map
NCBI Gene LINC01180 ENTREZGENE
RNAcentral URS000075D35D RNACentral