LINC01123 (long intergenic non-protein coding RNA 1123) - Rat Genome Database
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Gene: LINC01123 (long intergenic non-protein coding RNA 1123) Homo sapiens
Analyze
Symbol: LINC01123
Name: long intergenic non-protein coding RNA 1123
RGD ID: 7383653
HGNC Page HGNC
Description: ASSOCIATED WITH autism spectrum disorder; INTERACTS WITH triclosan
Type: ncrna
RefSeq Status: VALIDATED
Also known as: AC013268.5
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2109,987,063 - 109,996,140 (+)EnsemblGRCh38hg38GRCh38
GRCh382109,986,980 - 109,995,281 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372110,744,557 - 110,752,858 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map2q13NCBI
CHM1_12110,750,181 - 110,757,073 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
triclosan  (EXP)

References

References - curated
1. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
Additional References at PubMed
PMID:12477932   PMID:14702039   PMID:15342556   PMID:16344560   PMID:31488218  


Genomics

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:303
Count of miRNA genes:272
Interacting mature miRNAs:284
Transcripts:ENST00000336905, ENST00000419296
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 19 13 21 3 1 148 2 33 22 1
Low 1382 1346 1138 246 238 118 2601 407 2968 353 1122 1478 138 850 1574
Below cutoff 1013 1061 518 334 566 303 1582 1649 507 61 276 92 31 353 1113 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000336905
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2109,988,272 - 109,996,140 (+)Ensembl
RefSeq Acc Id: ENST00000419296
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2109,987,063 - 109,995,281 (+)Ensembl
RefSeq Acc Id: NR_046110
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382109,986,980 - 109,995,281 (+)NCBI
GRCh372110,744,557 - 110,752,858 (+)NCBI
CHM1_12110,750,181 - 110,757,073 (+)NCBI
Sequence:
RefSeq Acc Id: NR_046111
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382109,986,980 - 109,995,281 (+)NCBI
GRCh372110,744,557 - 110,752,858 (+)NCBI
CHM1_12110,750,181 - 110,757,073 (+)NCBI
Sequence:
RefSeq Acc Id: NR_046112
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382109,986,980 - 109,995,281 (+)NCBI
GRCh372110,744,557 - 110,752,858 (+)NCBI
CHM1_12110,756,190 - 110,757,073 (+)NCBI
Sequence:
Promoters
RGD ID:15095468
Promoter ID:EPDNEWNC_H302
Type:initiation region
Name:LINC01123_1
Description:long intergenic non-protein coding RNA 1123 [Source:HGNCSymbol;Acc:HGNC:49269]
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
GRCh382109,987,063 - 109,987,123EPDNEWNC

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 2q13(chr2:109623720-110207160)x1 copy number loss See cases [RCV000133772] Chr2:109623720..110207160 [GRCh38]
Chr2:110381297..110964737 [GRCh37]
Chr2:109738586..110322026 [NCBI36]
Chr2:2q13
benign
GRCh38/hg38 2q13(chr2:109959903-110360538)x3 copy number gain See cases [RCV000134235] Chr2:109959903..110360538 [GRCh38]
Chr2:110717480..111118115 [GRCh37]
Chr2:110074769..110552653 [NCBI36]
Chr2:2q13
benign
GRCh38/hg38 2q13(chr2:108719125-110611314)x3 copy number gain See cases [RCV000137361] Chr2:108719125..110611314 [GRCh38]
Chr2:109335581..111368891 [GRCh37]
Chr2:108702013..111085360 [NCBI36]
Chr2:2q13
uncertain significance
GRCh38/hg38 2q13(chr2:109975055-110576905)x3 copy number gain See cases [RCV000137971] Chr2:109975055..110576905 [GRCh38]
Chr2:110732632..111334482 [GRCh37]
Chr2:110089921..110775582 [NCBI36]
Chr2:2q13
likely benign
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 2q13(chr2:109975072-110207198)x3 copy number gain See cases [RCV000138513] Chr2:109975072..110207198 [GRCh38]
Chr2:110732649..110964775 [GRCh37]
Chr2:110089938..110322064 [NCBI36]
Chr2:2q13
benign
GRCh38/hg38 2q12.2-13(chr2:106516472-110576905)x3 copy number gain See cases [RCV000139569] Chr2:106516472..110576905 [GRCh38]
Chr2:107132928..111334482 [GRCh37]
Chr2:106499360..110857227 [NCBI36]
Chr2:2q12.2-13
uncertain significance
GRCh38/hg38 2q12.2-14.1(chr2:106428663-112379067)x3 copy number gain See cases [RCV000140834] Chr2:106428663..112379067 [GRCh38]
Chr2:107045119..113136644 [GRCh37]
Chr2:106411551..112853115 [NCBI36]
Chr2:2q12.2-14.1
uncertain significance
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 2q13(chr2:109975055-110207160)x1 copy number loss See cases [RCV000141492] Chr2:109975055..110207160 [GRCh38]
Chr2:110732632..110964737 [GRCh37]
Chr2:110089921..110322026 [NCBI36]
Chr2:2q13
benign
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 2q13(chr2:109936618-110452159)x1 copy number loss See cases [RCV000053606] Chr2:109936618..110452159 [GRCh38]
Chr2:110694195..111209736 [GRCh37]
Chr2:110051484..110644273 [NCBI36]
Chr2:2q13
benign
GRCh38/hg38 2q12.2-13(chr2:106696282-110223328)x3 copy number gain See cases [RCV000053141] Chr2:106696282..110223328 [GRCh38]
Chr2:107312738..110980905 [GRCh37]
Chr2:106679170..110338194 [NCBI36]
Chr2:2q12.2-13
uncertain significance
Single allele duplication Autism spectrum disorder [RCV000208724] Chr2:109696399..110327308 [GRCh38]
Chr2:110453976..111084885 [GRCh37]
Chr2:2q13
uncertain significance

Additional Information

Database Acc Id Source(s)
COSMIC LINC01123 COSMIC
Ensembl Genes ENSG00000204588 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000419296 ENTREZGENE
GTEx ENSG00000204588 GTEx
HGNC ID HGNC:49269 ENTREZGENE
Human Proteome Map LINC01123 Human Proteome Map
NCBI Gene LINC01123 ENTREZGENE
RNAcentral URS000075D3B0 RNACentral
  URS000075DA1D RNACentral
  URS000075E510 RNACentral
UniGene Hs.516403 ENTREZGENE