LINC01831 (long intergenic non-protein coding RNA 1831) - Rat Genome Database
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Pathways
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Gene: LINC01831 (long intergenic non-protein coding RNA 1831) Homo sapiens
Analyze
Symbol: LINC01831
Name: long intergenic non-protein coding RNA 1831
RGD ID: 11565233
HGNC Page HGNC
Description: INTERACTS WITH benzo[a]pyrene; sodium arsenite
Type: ncrna
RefSeq Status: VALIDATED
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2104,412,146 - 104,414,195 (-)EnsemblGRCh38hg38GRCh38
GRCh382104,412,152 - 104,414,031 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372105,028,610 - 105,030,499 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map2q12.1NCBI
HuRef298,794,053 - 98,795,942 (-)NCBIHuRef
CHM1_12105,032,919 - 105,034,798 (-)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Genomics

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:153
Count of miRNA genes:136
Interacting mature miRNAs:137
Transcripts:ENST00000449772
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
High
Medium 231 231 231 3 1 1 2
Low 1 10 171 170 20 170 2 1 248 50 22 9 2
Below cutoff 41 82 45 11 70 9 41 24 1336 33 173 39 3 15 23

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000449772
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2104,412,227 - 104,414,008 (-)Ensembl
RefSeq Acc Id: ENST00000658461
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2104,412,151 - 104,414,031 (-)Ensembl
RefSeq Acc Id: ENST00000661379
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2104,412,146 - 104,414,195 (-)Ensembl
RefSeq Acc Id: NR_135589
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382104,412,152 - 104,414,031 (-)NCBI
CHM1_12105,032,919 - 105,034,798 (-)NCBI
Sequence:
Promoters
RGD ID:15095455
Promoter ID:EPDNEWNC_H294
Type:initiation region
Name:LINC01831_1
Description:long intergenic non-protein coding RNA 1831 [Source:HGNCSymbol;Acc:HGNC:52637]
SO ACC ID:SO:0000170
Source:EPDNEWNC (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh382104,414,029 - 104,414,089EPDNEWNC

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 2q11.2-13(chr2:97672522-110211318)x3 copy number gain See cases [RCV000052947] Chr2:97672522..110211318 [GRCh38]
Chr2:98288985..110968895 [GRCh37]
Chr2:97655417..110326184 [NCBI36]
Chr2:2q11.2-13		 pathogenic
GRCh38/hg38 2q11.1-13(chr2:94678532-110602409)x3 copy number gain See cases [RCV000141075] Chr2:94678532..110602409 [GRCh38]
Chr2:95344257..111359986 [GRCh37]
Chr2:94707984..111076455 [NCBI36]
Chr2:2q11.1-13		 pathogenic
GRCh38/hg38 2q12.1-12.3(chr2:104381722-107312459)x1 copy number loss See cases [RCV000135282] Chr2:104381722..107312459 [GRCh38]
Chr2:104998180..107928915 [GRCh37]
Chr2:104364612..107295347 [NCBI36]
Chr2:2q12.1-12.3		 likely pathogenic
GRCh38/hg38 2q11.2-12.3(chr2:100378510-108472871)x3 copy number gain See cases [RCV000050836] Chr2:100378510..108472871 [GRCh38]
Chr2:100994972..109089327 [GRCh37]
Chr2:100361404..108455759 [NCBI36]
Chr2:2q11.2-12.3		 pathogenic
GRCh38/hg38 2q12.1-12.2(chr2:103739593-105485794)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052690]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052690]|See cases [RCV000052690] Chr2:103739593..105485794 [GRCh38]
Chr2:104356051..106102251 [GRCh37]
Chr2:103722483..105468683 [NCBI36]
Chr2:2q12.1-12.2		 uncertain significance
GRCh38/hg38 2q11.2-12.2(chr2:102084275-106085903)x1 copy number loss See cases [RCV000134974] Chr2:102084275..106085903 [GRCh38]
Chr2:102700735..106702359 [GRCh37]
Chr2:102067167..106068791 [NCBI36]
Chr2:2q11.2-12.2		 likely pathogenic
GRCh38/hg38 2q11.2-13(chr2:101710825-110791418)x3 copy number gain See cases [RCV000138645] Chr2:101710825..110791418 [GRCh38]
Chr2:102327287..111548995 [GRCh37]
Chr2:101693719..111265466 [NCBI36]
Chr2:2q11.2-13		 pathogenic
GRCh38/hg38 2q12.1(chr2:103897882-104834336)x1 copy number loss See cases [RCV000139814] Chr2:103897882..104834336 [GRCh38]
Chr2:104514340..105450794 [GRCh37]
Chr2:103880772..104817226 [NCBI36]
Chr2:2q12.1		 likely benign
GRCh38/hg38 2q11.2-12.2(chr2:100478285-106498909)x3 copy number gain See cases [RCV000141445] Chr2:100478285..106498909 [GRCh38]
Chr2:101094747..107115365 [GRCh37]
Chr2:100461179..106481797 [NCBI36]
Chr2:2q11.2-12.2		 uncertain significance
GRCh38/hg38 2q11.2-12.2(chr2:101234070-105679157)x1 copy number loss See cases [RCV000142969] Chr2:101234070..105679157 [GRCh38]
Chr2:101850532..106295614 [GRCh37]
Chr2:101216964..105662046 [NCBI36]
Chr2:2q11.2-12.2		 pathogenic

Additional Information

Database Acc Id Source(s)
COSMIC LINC01831 COSMIC
Ensembl Genes ENSG00000225765 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000449772 ENTREZGENE
GTEx ENSG00000225765 GTEx
HGNC ID HGNC:52637 ENTREZGENE
Human Proteome Map LINC01831 Human Proteome Map
NCBI Gene LINC01831 ENTREZGENE
RNAcentral URS0000A765EC RNACentral