LINC01886 (long intergenic non-protein coding RNA 1886) - Rat Genome Database
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Gene: LINC01886 (long intergenic non-protein coding RNA 1886) Homo sapiens
Analyze
Symbol: LINC01886
Name: long intergenic non-protein coding RNA 1886
RGD ID: 11569124
HGNC Page HGNC
Description: ASSOCIATED WITH schizophrenia
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 Ensembl2107,529,292 - 107,556,499 (+)EnsemblGRCh38hg38GRCh38
GRCh382107,529,419 - 107,556,496 (+)NCBIGRCh38GRCh38hg38GRCh38
Cytogenetic Map2q12.3NCBI
CHM1_12108,150,268 - 108,177,457 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

References

Genomics

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:274
Count of miRNA genes:262
Interacting mature miRNAs:265
Transcripts:ENST00000439893, ENST00000443205
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 1 228 2 1 16 15 237 1
Low 18 60 464 8 4 3 710 375 301 141 438 492 6 175 542
Below cutoff 647 808 123 105 139 42 1656 868 1750 130 258 157 65 461 1121

Sequence

Nucleotide Sequences
RefSeq Transcripts NR_146968 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC096669 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000439893
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2107,542,749 - 107,555,639 (+)Ensembl
RefSeq Acc Id: ENST00000443205
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2107,529,452 - 107,556,312 (+)Ensembl
RefSeq Acc Id: ENST00000658627
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2107,542,495 - 107,556,484 (+)Ensembl
RefSeq Acc Id: ENST00000660653
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2107,529,292 - 107,556,499 (+)Ensembl
RefSeq Acc Id: ENST00000662038
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2107,529,480 - 107,556,499 (+)Ensembl
RefSeq Acc Id: ENST00000665591
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2107,529,483 - 107,556,496 (+)Ensembl
RefSeq Acc Id: ENST00000666630
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2107,529,411 - 107,531,981 (+)Ensembl
RefSeq Acc Id: ENST00000669483
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2107,529,419 - 107,556,498 (+)Ensembl
RefSeq Acc Id: NR_146968
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382107,529,419 - 107,556,496 (+)NCBI
Sequence:
Promoters
RGD ID:15095472
Promoter ID:EPDNEWNC_H299
Type:initiation region
Name:LINC01886_1
Description:long intergenic non-protein coding RNA 1886 [Source:HGNCSymbol;Acc:HGNC:52705]
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
GRCh382107,529,512 - 107,529,572EPDNEWNC

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
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 LINC01886 COSMIC
Ensembl Genes ENSG00000224568 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000443205 ENTREZGENE
GTEx ENSG00000224568 GTEx
HGNC ID HGNC:52705 ENTREZGENE
Human Proteome Map LINC01886 Human Proteome Map
NCBI Gene LINC01886 ENTREZGENE
RNAcentral URS0000BC455B RNACentral