LINC01376 (long intergenic non-protein coding RNA 1376) - Rat Genome Database

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Gene: LINC01376 (long intergenic non-protein coding RNA 1376) Homo sapiens
Analyze
Symbol: LINC01376
Name: long intergenic non-protein coding RNA 1376
RGD ID: 11039105
HGNC Page HGNC:50637
Description: INTERACTS WITH 2-hydroxypropanoic acid; rac-lactic acid; sodium arsenite
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
GRCh38218,986,451 - 19,026,971 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl218,986,451 - 19,348,067 (-)EnsemblGRCh38hg38GRCh38
GRCh37219,167,729 - 19,226,726 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36219,031,210 - 19,090,207 (-)NCBINCBI36Build 36hg18NCBI36
Celera219,048,679 - 19,089,174 (-)NCBICelera
Cytogenetic Map2p24.2-p24.1NCBI
HuRef218,942,749 - 18,983,665 (-)NCBIHuRef
CHM1_1219,096,463 - 19,155,853 (-)NCBICHM1_1
T2T-CHM13v2.0219,019,224 - 19,059,747 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:14702039   PMID:36973940  


Genomics

Variants

.
Variants in LINC01376
3 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 2p25.3-23.1(chr2:30141-31766749)x3 copy number gain See cases [RCV000052929] Chr2:30141..31766749 [GRCh38]
Chr2:30141..31991818 [GRCh37]
Chr2:20141..31845322 [NCBI36]
Chr2:2p25.3-23.1		 pathogenic
GRCh38/hg38 2p25.3-23.2(chr2:30341-28419664)x3 copy number gain See cases [RCV000135398] Chr2:30341..28419664 [GRCh38]
Chr2:30341..28642531 [GRCh37]
Chr2:20341..28496035 [NCBI36]
Chr2:2p25.3-23.2		 pathogenic
GRCh38/hg38 2p25.3-23.3(chr2:17019-26318846)x3 copy number gain See cases [RCV000137344] Chr2:17019..26318846 [GRCh38]
Chr2:17019..26541714 [GRCh37]
Chr2:7019..26395218 [NCBI36]
Chr2:2p25.3-23.3		 pathogenic
GRCh38/hg38 2p25.3-24.1(chr2:1664615-23664142)x3 copy number gain See cases [RCV000137913] Chr2:1664615..23664142 [GRCh38]
Chr2:1668387..23887012 [GRCh37]
Chr2:1647394..23740517 [NCBI36]
Chr2:2p25.3-24.1		 pathogenic|likely pathogenic
GRCh38/hg38 2p24.2-24.1(chr2:16723596-21600734)x1 copy number loss See cases [RCV000139451] Chr2:16723596..21600734 [GRCh38]
Chr2:16904863..21823606 [GRCh37]
Chr2:16768344..21677111 [NCBI36]
Chr2:2p24.2-24.1		 pathogenic|likely pathogenic
GRCh38/hg38 2p25.3-24.1(chr2:17019-20001056)x3 copy number gain See cases [RCV000141226] Chr2:17019..20001056 [GRCh38]
Chr2:17019..20200817 [GRCh37]
Chr2:7019..20064298 [NCBI36]
Chr2:2p25.3-24.1		 pathogenic
GRCh38/hg38 2p25.3-22.3(chr2:12770-33711509)x3 copy number gain See cases [RCV000141829] Chr2:12770..33711509 [GRCh38]
Chr2:12770..33936576 [GRCh37]
Chr2:2770..33790080 [NCBI36]
Chr2:2p25.3-22.3		 pathogenic
GRCh38/hg38 2p25.3-23.3(chr2:12770-25039694)x3 copy number gain See cases [RCV000141877] Chr2:12770..25039694 [GRCh38]
Chr2:12770..25262563 [GRCh37]
Chr2:2770..25116067 [NCBI36]
Chr2:2p25.3-23.3		 pathogenic
GRCh38/hg38 2p24.2-24.1(chr2:18439073-19428650)x1 copy number loss See cases [RCV000143366] Chr2:18439073..19428650 [GRCh38]
Chr2:18620339..19628411 [GRCh37]
Chr2:18483820..19491892 [NCBI36]
Chr2:2p24.2-24.1		 uncertain significance
GRCh38/hg38 2p25.3-21(chr2:236816-45983232)x3 copy number gain See cases [RCV000143682] Chr2:236816..45983232 [GRCh38]
Chr2:236816..46210371 [GRCh37]
Chr2:226816..46063875 [NCBI36]
Chr2:2p25.3-21		 pathogenic
GRCh38/hg38 2p25.3-16.1(chr2:66097-55570637)x3 copy number gain See cases [RCV000052933] Chr2:66097..55570637 [GRCh38]
Chr2:66097..55797773 [GRCh37]
Chr2:56097..55651277 [NCBI36]
Chr2:2p25.3-16.1		 pathogenic
GRCh38/hg38 2p25.1-11.2(chr2:7495123-87705899)x3 copy number gain See cases [RCV000141494] Chr2:7495123..87705899 [GRCh38]
Chr2:7635254..88005418 [GRCh37]
Chr2:7552705..87786533 [NCBI36]
Chr2:2p25.1-11.2		 benign
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:362
Count of miRNA genes:316
Interacting mature miRNAs:329
Transcripts:ENST00000418165, ENST00000424895, ENST00000432142, ENST00000449124
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 1 3 3
Low 1347 1188 1104 161 406 92 3111 798 1141 213 1190 1378 79 816 1881 3
Below cutoff 1081 1489 609 451 1211 362 1242 1389 2550 204 253 224 91 388 905 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000418165
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl219,026,660 - 19,306,037 (-)Ensembl
RefSeq Acc Id: ENST00000424895
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl218,986,451 - 19,026,971 (-)Ensembl
RefSeq Acc Id: ENST00000432142
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl219,022,449 - 19,306,054 (-)Ensembl
RefSeq Acc Id: ENST00000449124
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl219,044,866 - 19,346,748 (-)Ensembl
RefSeq Acc Id: ENST00000650025
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl218,986,474 - 19,348,067 (-)Ensembl
RefSeq Acc Id: ENST00000702731
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl219,347,249 - 19,348,014 (-)Ensembl
RefSeq Acc Id: NR_135287
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38218,986,451 - 19,026,971 (-)NCBI
CHM1_1219,097,128 - 19,156,119 (-)NCBI
T2T-CHM13v2.0219,019,224 - 19,059,747 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC01376 COSMIC
Ensembl Genes ENSG00000236204 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000424895 ENTREZGENE
GTEx ENSG00000236204 GTEx
HGNC ID HGNC:50637 ENTREZGENE
Human Proteome Map LINC01376 Human Proteome Map
NCBI Gene LINC01376 ENTREZGENE
RNAcentral URS0000770BFF RNACentral