LINC01789 (long intergenic non-protein coding RNA 1789) - Rat Genome Database
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Gene: LINC01789 (long intergenic non-protein coding RNA 1789) Homo sapiens
Analyze
Symbol: LINC01789
Name: long intergenic non-protein coding RNA 1789
RGD ID: 11563892
HGNC Page HGNC
Description: ASSOCIATED WITH schizophrenia; INTERACTS WITH sodium arsenite
Type: ncrna
RefSeq Status: MODEL
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2107,254,691 - 107,365,873 (-)EnsemblGRCh38hg38GRCh38
GRCh382107,260,700 - 107,365,691 (-)NCBIGRCh38GRCh38hg38GRCh38
Cytogenetic Map2q12.3NCBI
CHM1_12107,875,543 - 107,986,709 (-)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
schizophrenia  (IAGP)

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

Genomics

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:266
Count of miRNA genes:245
Interacting mature miRNAs:253
Transcripts:ENST00000443123, ENST00000455614
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
High
Medium 96 19 1 96
Low 523 2 2 91 2 525
Below cutoff 60 85 102 16 45 10 146 60 210 92 172 115 6 44 95

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000443123
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2107,254,691 - 107,365,873 (-)Ensembl
RefSeq Acc Id: ENST00000455614
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2107,266,153 - 107,365,543 (-)Ensembl
RefSeq Acc Id: XR_001739630
RefSeq Status:
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382107,260,700 - 107,270,428 (-)NCBI
Sequence:
RefSeq Acc Id: XR_002959413
RefSeq Status:
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382107,260,700 - 107,365,691 (-)NCBI
Sequence:
RefSeq Acc Id: XR_923156
RefSeq Status:
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382107,260,700 - 107,365,691 (-)NCBI
Sequence:
Promoters
RGD ID:15095473
Promoter ID:EPDNEWNC_H298
Type:initiation region
Name:LINC01789_1
Description:long intergenic non-protein coding RNA 1789 [Source:HGNCSymbol;Acc:HGNC:52578]
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
GRCh382107,365,573 - 107,365,633EPDNEWNC

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
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 2q12.2-12.3(chr2:105828398-108080417)x3 copy number gain See cases [RCV000052691] Chr2:105828398..108080417 [GRCh38]
Chr2:106444854..108696873 [GRCh37]
Chr2:105811286..108063305 [NCBI36]
Chr2:2q12.2-12.3		 uncertain 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 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
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 2q12.2-13(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 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 2q12.2-14.1(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 2q12.2-12.3(chr2:106260759-107904531)x1 copy number loss See cases [RCV000051289] Chr2:106260759..107904531 [GRCh38]
Chr2:106877215..108520987 [GRCh37]
Chr2:106243647..107887419 [NCBI36]
Chr2:2q12.2-12.3		 uncertain significance
GRCh38/hg38 2q12.2-12.3(chr2:106261594-107786796)x1 copy number loss See cases [RCV000051290] Chr2:106261594..107786796 [GRCh38]
Chr2:106878050..108403252 [GRCh37]
Chr2:106244482..107769684 [NCBI36]
Chr2:2q12.2-12.3		 uncertain significance
NC_000002.12:g.(?_106480385)_(107825992_?)del deletion Schizophrenia [RCV000416711] Chr2:106480385..107825992 [GRCh38]
Chr2:107096841..108442448 [GRCh37]
Chr2:106463273..107808880 [NCBI36]
Chr2:2q12.2-12.3		 likely pathogenic
NC_000002.12:g.(?_106287425)_(107812162_?)dup duplication Schizophrenia [RCV000416938] Chr2:106287425..107812162 [GRCh38]
Chr2:106903881..108428618 [GRCh37]
Chr2:106270313..107795050 [NCBI36]
Chr2:2q12.2-12.3		 likely pathogenic
Single allele deletion not provided [RCV000677995] Chr2:106312802..107890728 [GRCh38]
Chr2:106929257..108507183 [GRCh37]
Chr2:2q12.2-12.3		 uncertain significance
NC_000002.12:g.(?_106445028)_(107839483_?)del deletion Schizophrenia [RCV000754224] Chr2:106445028..107839483 [GRCh38]
Chr2:2q12.2-12.3		 likely pathogenic

Additional Information

Database Acc Id Source(s)
COSMIC LINC01789 COSMIC
Ensembl Genes ENSG00000229457 Ensembl
GTEx ENSG00000229457 GTEx
HGNC ID HGNC:52578 ENTREZGENE
Human Proteome Map LINC01789 Human Proteome Map
NCBI Gene LINC01789 ENTREZGENE