LINC01857 (long intergenic non-protein coding RNA 1857) - Rat Genome Database

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Gene: LINC01857 (long intergenic non-protein coding RNA 1857) Homo sapiens
Analyze
Symbol: LINC01857
Name: long intergenic non-protein coding RNA 1857
RGD ID: 11569268
HGNC Page HGNC:52673
Description: INTERACTS WITH lipopolysaccharide; S-(1,2-dichlorovinyl)-L-cysteine
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382207,662,384 - 207,679,122 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2207,662,375 - 207,679,116 (+)EnsemblGRCh38hg38GRCh38
GRCh372208,527,108 - 208,543,846 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map2q33.3NCBI
HuRef2200,375,113 - 200,385,770 (+)NCBIHuRef
CHM1_12208,532,895 - 208,550,050 (+)NCBICHM1_1
T2T-CHM13v2.02208,136,456 - 208,153,623 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:28424495   PMID:30628071   PMID:31049960   PMID:31405785   PMID:32329840   PMID:34793477   PMID:35468304  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 2q33.3(chr2:207661540-207876453)x3 copy number gain See cases [RCV000135368] Chr2:207661540..207876453 [GRCh38]
Chr2:208526264..208741177 [GRCh37]
Chr2:208234509..208449422 [NCBI36]
Chr2:2q33.3		 uncertain significance
GRCh38/hg38 2q32.2-37.3(chr2:189436149-241841232)x3 copy number gain See cases [RCV000142307] Chr2:189436149..241841232 [GRCh38]
Chr2:190300875..242783384 [GRCh37]
Chr2:190009120..242432057 [NCBI36]
Chr2:2q32.2-37.3		 pathogenic
GRCh38/hg38 2q33.1-34(chr2:199937273-210031924)x1 copy number loss See cases [RCV000143301] Chr2:199937273..210031924 [GRCh38]
Chr2:200801996..210896648 [GRCh37]
Chr2:200510241..210604893 [NCBI36]
Chr2:2q33.1-34		 pathogenic
GRCh38/hg38 2q33.1-34(chr2:198095810-211803453)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052603]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052603]|See cases [RCV000052603] Chr2:198095810..211803453 [GRCh38]
Chr2:198960534..212668178 [GRCh37]
Chr2:198668779..212376423 [NCBI36]
Chr2:2q33.1-34		 pathogenic
GRCh38/hg38 2q33.2-35(chr2:203010732-214671878)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052607]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052607]|See cases [RCV000052607] Chr2:203010732..214671878 [GRCh38]
Chr2:203875455..215536602 [GRCh37]
Chr2:203583700..215244847 [NCBI36]
Chr2:2q33.2-35		 pathogenic
GRCh38/hg38 2q32.2-37.3(chr2:188818195-242065208)x3 copy number gain See cases [RCV000052958] Chr2:188818195..242065208 [GRCh38]
Chr2:189682921..243007359 [GRCh37]
Chr2:189391166..242656032 [NCBI36]
Chr2:2q32.2-37.3		 pathogenic
GRCh38/hg38 2q32.2-37.3(chr2:190310736-241892770)x3 copy number gain See cases [RCV000052959] Chr2:190310736..241892770 [GRCh38]
Chr2:191175462..242834921 [GRCh37]
Chr2:190883707..242483594 [NCBI36]
Chr2:2q32.2-37.3		 pathogenic
GRCh38/hg38 2q32.3-37.3(chr2:193122313-241074980)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052960]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052960]|See cases [RCV000052960] Chr2:193122313..241074980 [GRCh38]
Chr2:193987039..242014395 [GRCh37]
Chr2:193695284..241663068 [NCBI36]
Chr2:2q32.3-37.3		 pathogenic
GRCh38/hg38 2q33.3-34(chr2:207058886-211245603)x1 copy number loss See cases [RCV000139325] Chr2:207058886..211245603 [GRCh38]
Chr2:207923610..212110328 [GRCh37]
Chr2:207631855..211818573 [NCBI36]
Chr2:2q33.3-34		 pathogenic
GRCh38/hg38 2q31.3-36.2(chr2:180513793-224302848)x3 copy number gain See cases [RCV000139446] Chr2:180513793..224302848 [GRCh38]
Chr2:181378520..225167565 [GRCh37]
Chr2:181086765..224875809 [NCBI36]
Chr2:2q31.3-36.2		 pathogenic
GRCh38/hg38 2q33.3-34(chr2:204906843-210031449)x1 copy number loss See cases [RCV000139629] Chr2:204906843..210031449 [GRCh38]
Chr2:205771566..210896173 [GRCh37]
Chr2:205479811..210604418 [NCBI36]
Chr2:2q33.3-34		 pathogenic
GRCh38/hg38 2q33.1-34(chr2:199946494-209985195)x1 copy number loss See cases [RCV000141076] Chr2:199946494..209985195 [GRCh38]
Chr2:200811217..210849919 [GRCh37]
Chr2:200519462..210558164 [NCBI36]
Chr2:2q33.1-34		 pathogenic
GRCh38/hg38 2q32.3-37.3(chr2:194898783-236473913)x3 copy number gain See cases [RCV000051119] Chr2:194898783..236473913 [GRCh38]
Chr2:195763507..237382556 [GRCh37]
Chr2:195471752..237047295 [NCBI36]
Chr2:2q32.3-37.3		 pathogenic
GRCh38/hg38 2q32.3-35(chr2:192938826-215705052)x1 copy number loss See cases [RCV000141254] Chr2:192938826..215705052 [GRCh38]
Chr2:193803552..216569775 [GRCh37]
Chr2:193511797..216278020 [NCBI36]
Chr2:2q32.3-35		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:67
Count of miRNA genes:63
Interacting mature miRNAs:64
Transcripts:ENST00000429730
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 entire extraembryonic component pharyngeal arch
High 1
Medium 64 60 10 3 932 3 4 1 7 9 19 4 2
Low 269 823 252 170 757 130 268 16 101 143 240 680 40 261 85 1 1
Below cutoff 444 458 494 194 128 140 686 207 556 135 415 349 55 451 352 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000429730
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2207,662,375 - 207,667,333 (+)Ensembl
RefSeq Acc Id: ENST00000691648
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2207,662,376 - 207,679,116 (+)Ensembl
RefSeq Acc Id: NR_135566
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382207,662,384 - 207,679,122 (+)NCBI
CHM1_12208,532,895 - 208,550,050 (+)NCBI
T2T-CHM13v2.02208,136,456 - 208,153,623 (+)NCBI
Sequence:
RefSeq Acc Id: NR_135567
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382207,662,430 - 207,667,024 (+)NCBI
CHM1_12208,532,941 - 208,537,535 (+)NCBI
T2T-CHM13v2.02208,136,502 - 208,141,094 (+)NCBI
Sequence:
Promoters
RGD ID:15095538
Promoter ID:EPDNEWNC_H361
Type:single initiation site
Name:LINC01857_1
Description:long intergenic non-protein coding RNA 1857 [Source:HGNCSymbol;Acc:HGNC:52673]
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
GRCh382207,662,378 - 207,662,438EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC LINC01857 COSMIC
Ensembl Genes ENSG00000224137 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000691648 ENTREZGENE
GTEx ENSG00000224137 GTEx
HGNC ID HGNC:52673 ENTREZGENE
Human Proteome Map LINC01857 Human Proteome Map
NCBI Gene LINC01857 ENTREZGENE
RNAcentral URS0000A76B57 RNACentral
  URS0000A77076 RNACentral