LINC01106 (long intergenic non-protein coding RNA 1106) - Rat Genome Database
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Gene: LINC01106 (long intergenic non-protein coding RNA 1106) Homo sapiens
Analyze
Symbol: LINC01106
Name: long intergenic non-protein coding RNA 1106
RGD ID: 2304400
HGNC Page HGNC
Description: INTERACTS WITH 2-hydroxypropanoic acid; rac-lactic acid
Type: ncrna
RefSeq Status: VALIDATED
Also known as: DKFZp686K04236; FLJ38359
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2110,375,138 - 110,384,442 (-)EnsemblGRCh38hg38GRCh38
GRCh382110,375,109 - 110,384,536 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372111,132,686 - 111,142,113 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362110,569,034 - 110,569,923 (-)NCBINCBI36hg18NCBI36
Celera2104,743,689 - 104,745,411 (-)NCBI
Cytogenetic Map2q13NCBI
HuRef2104,187,233 - 104,187,570 (-)NCBIHuRef
CHM1_12111,136,848 - 111,146,273 (-)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:12477932   PMID:14702039   PMID:15342556   PMID:16344560   PMID:32990221  


Genomics

Position Markers
STS-R37430  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372111,139,784 - 111,140,031UniSTSGRCh37
GRCh372110,746,629 - 110,746,876UniSTSGRCh37
Build 362110,103,918 - 110,104,165RGDNCBI36
Celera2102,789,634 - 102,789,881RGD
Cytogenetic Map2q13UniSTS
HuRef2104,204,074 - 104,204,321UniSTS
WI-21119  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372111,139,989 - 111,140,066UniSTSGRCh37
GRCh372110,746,594 - 110,746,671UniSTSGRCh37
Build 362110,103,883 - 110,103,960RGDNCBI36
Celera2102,789,599 - 102,789,676RGD
Cytogenetic Map2q13UniSTS
HuRef2104,204,279 - 104,204,356UniSTS
GeneMap99-GB4 RH Map2388.24UniSTS
Whitehead-RH Map2617.7UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:212
Count of miRNA genes:127
Interacting mature miRNAs:129
Transcripts:ENST00000436665, ENST00000448359
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 38 8 9 6 6 75 2 56 11
Low 1554 1445 1305 373 298 258 2931 557 3094 388 1071 1538 126 976 1747 1
Below cutoff 832 1043 389 229 627 186 1349 1575 478 28 308 47 43 228 1003 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000436665
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2110,375,138 - 110,384,442 (-)Ensembl
RefSeq Acc Id: ENST00000448359
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2110,375,156 - 110,383,233 (-)Ensembl
RefSeq Acc Id: ENST00000654118
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2110,375,627 - 110,383,516 (-)Ensembl
RefSeq Acc Id: ENST00000665250
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2110,375,747 - 110,383,496 (-)Ensembl
RefSeq Acc Id: NR_027244
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382110,375,109 - 110,384,536 (-)NCBI
GRCh372111,132,686 - 111,142,113 (-)RGD
Celera2104,743,689 - 104,745,411 (-)RGD
HuRef2104,187,233 - 104,187,570 (-)ENTREZGENE
CHM1_12111,136,848 - 111,146,273 (-)NCBI
Sequence:
Protein Sequences
GenBank Protein BAC04604 (Get FASTA)   NCBI Sequence Viewer  
  CAH18204 (Get FASTA)   NCBI Sequence Viewer  
  EAW50645 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences

Promoters
RGD ID:15095469
Promoter ID:EPDNEWNC_H303
Type:initiation region
Name:LINC01106_1
Description:long intergenic non-protein coding RNA 1106 [Source:HGNCSymbol;Acc:HGNC:26769]
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
GRCh382110,384,442 - 110,384,502EPDNEWNC

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 2q13(chr2:110104900-110611314)x3 copy number gain See cases [RCV000050514] Chr2:110104900..110611314 [GRCh38]
Chr2:110862477..111368891 [GRCh37]
Chr2:110219766..111085360 [NCBI36]
Chr2:2q13
benign
GRCh38/hg38 2q13(chr2:110104900-110611314)x1 copy number loss See cases [RCV000135500] Chr2:110104900..110611314 [GRCh38]
Chr2:110862477..111368891 [GRCh37]
Chr2:110219766..111085360 [NCBI36]
Chr2:2q13
benign
GRCh38/hg38 2q13(chr2:110025681-110576905)x1 copy number loss See cases [RCV000136417] Chr2:110025681..110576905 [GRCh38]
Chr2:110783258..111334482 [GRCh37]
Chr2:110140547..110811832 [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(chr2:110049995-110576905)x3 copy number gain See cases [RCV000138366] Chr2:110049995..110576905 [GRCh38]
Chr2:110807572..111334482 [GRCh37]
Chr2:110164861..110775582 [NCBI36]
Chr2:2q13
likely 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(chr2:109936618-110452159)x1 copy number loss See cases [RCV000053606] Chr2:109936618..110452159 [GRCh38]
Chr2:110694195..111209736 [GRCh37]
Chr2:110051484..110644273 [NCBI36]
Chr2:2q13
benign
GRCh38/hg38 2q13(chr2:110084138-110611314)x1 copy number loss See cases [RCV000053608] Chr2:110084138..110611314 [GRCh38]
Chr2:110841715..111368891 [GRCh37]
Chr2:110199004..111085360 [NCBI36]
Chr2:2q13
benign

Additional Information

Database Acc Id Source(s)
COSMIC LINC01106 COSMIC
Ensembl Genes ENSG00000175772 Ensembl
GTEx ENSG00000175772 GTEx
HGNC ID HGNC:26769 ENTREZGENE
Human Proteome Map LINC01106 Human Proteome Map
NCBI Gene 151009 ENTREZGENE
RNAcentral URS000075EE95 RNACentral
UniGene Hs.643369 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-10-22 LINC01106  long intergenic non-protein coding RNA 1106  LOC151009  uncharacterized LOC151009  Symbol and/or name change 5135510 APPROVED
2011-11-01 LOC151009  uncharacterized LOC151009  LOC151009  hypothetical LOC151009  Symbol and/or name change 5135510 APPROVED