LINC01140 (long intergenic non-protein coding RNA 1140) - Rat Genome Database

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Gene: LINC01140 (long intergenic non-protein coding RNA 1140) Homo sapiens
Analyze
Symbol: LINC01140
Name: long intergenic non-protein coding RNA 1140
RGD ID: 2303861
HGNC Page HGNC:27922
Description: INTERACTS WITH 2-palmitoylglycerol; 3-isobutyl-1-methyl-7H-xanthine; benzo[a]pyrene
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: FLJ11317; MGC161518; RP5-1052I5.1
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38187,129,765 - 87,169,204 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl187,129,765 - 87,169,198 (+)EnsemblGRCh38hg38GRCh38
GRCh37187,595,448 - 87,634,887 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36187,368,260 - 87,375,184 (+)NCBINCBI36Build 36hg18NCBI36
Celera185,841,152 - 85,880,575 (+)NCBICelera
Cytogenetic Map1p22.3NCBI
HuRef185,709,082 - 85,748,499 (+)NCBIHuRef
CHM1_1187,710,360 - 87,749,782 (+)NCBICHM1_1
T2T-CHM13v2.0186,972,495 - 87,011,921 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8889548   PMID:12477932   PMID:14702039   PMID:16344560   PMID:19247474   PMID:28444881   PMID:33234721   PMID:34587432   PMID:35307914   PMID:35988287   PMID:36299824   PMID:37602451  


Genomics

Variants

.
Variants in LINC01140
1 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 1p31.1-21.1(chr1:83457325-104273917)x3 copy number gain See cases [RCV000135654] Chr1:83457325..104273917 [GRCh38]
Chr1:83923008..104816539 [GRCh37]
Chr1:83695596..104618062 [NCBI36]
Chr1:1p31.1-21.1		 pathogenic
GRCh38/hg38 1p22.3-22.2(chr1:86228890-88466303)x1 copy number loss See cases [RCV000138370] Chr1:86228890..88466303 [GRCh38]
Chr1:86694573..88931986 [GRCh37]
Chr1:86467161..88704574 [NCBI36]
Chr1:1p22.3-22.2		 uncertain significance
GRCh38/hg38 1p31.1-22.2(chr1:76419302-88628464)x1 copy number loss See cases [RCV000138957] Chr1:76419302..88628464 [GRCh38]
Chr1:76884987..89094147 [GRCh37]
Chr1:76657575..88866735 [NCBI36]
Chr1:1p31.1-22.2		 pathogenic
GRCh38/hg38 1p31.1-13.3(chr1:72661709-107456880)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051825]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051825]|See cases [RCV000051825] Chr1:72661709..107456880 [GRCh38]
Chr1:73127392..107999502 [GRCh37]
Chr1:72899980..107801025 [NCBI36]
Chr1:1p31.1-13.3		 pathogenic
NR_026985.1(LINC01140):n.578T>C single nucleotide variant not provided [RCV003406591] Chr1:87133657 [GRCh38]
Chr1:87599340 [GRCh37]
Chr1:1p22.3		 benign
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1705
Count of miRNA genes:722
Interacting mature miRNAs:826
Transcripts:ENST00000461990, ENST00000467438, ENST00000469312, ENST00000471417, ENST00000476432, ENST00000484933, ENST00000490006, ENST00000587165, ENST00000589455, ENST00000590653
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.

Markers in Region
RH92748  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37187,599,992 - 87,600,127UniSTSGRCh37
Build 36187,372,580 - 87,372,715RGDNCBI36
Celera185,845,696 - 85,845,831RGD
Cytogenetic Map1p22.3UniSTS
HuRef185,713,626 - 85,713,761UniSTS
GeneMap99-GB4 RH Map1244.17UniSTS
SHGC-153532  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37187,633,248 - 87,633,523UniSTSGRCh37
Build 36187,405,836 - 87,406,111RGDNCBI36
Celera185,878,936 - 85,879,211RGD
Cytogenetic Map1p22.3UniSTS
HuRef185,746,860 - 85,747,135UniSTS
TNG Radiation Hybrid Map150232.0UniSTS
SHGC-75102  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37187,634,002 - 87,634,149UniSTSGRCh37
Build 36187,406,590 - 87,406,737RGDNCBI36
Celera185,879,690 - 85,879,837RGD
Cytogenetic Map1p22.3UniSTS
HuRef185,747,614 - 85,747,761UniSTS
TNG Radiation Hybrid Map150225.0UniSTS
GeneMap99-GB4 RH Map1244.91UniSTS
AW546958  
Human AssemblyChrPosition (strand)SourceJBrowse
HuRef185,726,161 - 85,727,135UniSTS
UniSTS:495279  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37187,597,680 - 87,598,718UniSTSGRCh37
Celera185,843,384 - 85,844,422UniSTS
HuRef185,711,314 - 85,712,352UniSTS


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 visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 4 66 45 1 6 338 7 101 1 35 80 1 311 102
Low 1965 2003 1058 213 474 51 3314 1750 2743 98 1197 1196 162 893 2214 3 1
Below cutoff 374 874 502 310 1238 313 681 433 860 249 168 259 7 1 472 2 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NR_026985 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_026986 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_026987 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_026988 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_026989 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC093155 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL139139 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL833352 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC030523 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC041867 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC126240 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC132861 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BI818944 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BM679066 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BM722117 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471097 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068277 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DA398164 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DA981741 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DB100426 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DB462107 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000461990
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl187,129,870 - 87,136,669 (+)Ensembl
RefSeq Acc Id: ENST00000467438
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl187,131,975 - 87,134,595 (+)Ensembl
RefSeq Acc Id: ENST00000469312
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl187,129,765 - 87,168,505 (+)Ensembl
RefSeq Acc Id: ENST00000471417
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl187,129,854 - 87,134,469 (+)Ensembl
RefSeq Acc Id: ENST00000476432
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl187,131,969 - 87,134,131 (+)Ensembl
RefSeq Acc Id: ENST00000484933
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl187,132,003 - 87,136,669 (+)Ensembl
RefSeq Acc Id: ENST00000490006
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl187,129,774 - 87,169,198 (+)Ensembl
RefSeq Acc Id: ENST00000587165
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl187,132,055 - 87,162,137 (+)Ensembl
RefSeq Acc Id: ENST00000589455
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl187,132,055 - 87,134,192 (+)Ensembl
RefSeq Acc Id: ENST00000590653
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl187,131,955 - 87,136,669 (+)Ensembl
RefSeq Acc Id: ENST00000619924
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl187,132,002 - 87,133,035 (+)Ensembl
RefSeq Acc Id: NR_026985
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38187,131,926 - 87,136,669 (+)NCBI
GRCh37187,595,448 - 87,634,887 (+)RGD
Celera185,841,152 - 85,880,575 (+)RGD
HuRef185,709,082 - 85,748,499 (+)ENTREZGENE
CHM1_1187,712,521 - 87,717,265 (+)NCBI
T2T-CHM13v2.0186,974,656 - 86,979,400 (+)NCBI
Sequence:
RefSeq Acc Id: NR_026986
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38187,131,926 - 87,136,669 (+)NCBI
GRCh37187,595,448 - 87,634,887 (+)RGD
Celera185,841,152 - 85,880,575 (+)RGD
HuRef185,709,082 - 85,748,499 (+)ENTREZGENE
CHM1_1187,712,521 - 87,717,265 (+)NCBI
T2T-CHM13v2.0186,974,656 - 86,979,400 (+)NCBI
Sequence:
RefSeq Acc Id: NR_026987
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38187,131,926 - 87,136,669 (+)NCBI
GRCh37187,595,448 - 87,634,887 (+)RGD
Celera185,841,152 - 85,880,575 (+)RGD
HuRef185,709,082 - 85,748,499 (+)ENTREZGENE
CHM1_1187,712,521 - 87,717,265 (+)NCBI
T2T-CHM13v2.0186,974,656 - 86,979,400 (+)NCBI
Sequence:
RefSeq Acc Id: NR_026988
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38187,129,765 - 87,136,669 (+)NCBI
GRCh37187,595,448 - 87,634,887 (+)RGD
Celera185,841,152 - 85,880,575 (+)RGD
HuRef185,709,082 - 85,748,499 (+)ENTREZGENE
CHM1_1187,710,360 - 87,717,265 (+)NCBI
T2T-CHM13v2.0186,972,495 - 86,979,400 (+)NCBI
Sequence:
RefSeq Acc Id: NR_026989
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38187,129,765 - 87,169,204 (+)NCBI
GRCh37187,595,448 - 87,634,887 (+)RGD
Celera185,841,152 - 85,880,575 (+)RGD
HuRef185,709,082 - 85,748,499 (+)ENTREZGENE
CHM1_1187,710,360 - 87,749,782 (+)NCBI
T2T-CHM13v2.0186,972,495 - 87,011,921 (+)NCBI
Sequence:
Protein Sequences
GenBank Protein AAI26241 (Get FASTA)   NCBI Sequence Viewer  
  EAW73175 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences

Promoters
RGD ID:15095238
Promoter ID:EPDNEWNC_H77
Type:initiation region
Name:LINC01140_1
Description:long intergenic non-protein coding RNA 1140 [Source:HGNCSymbol;Acc:HGNC:27922]
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
GRCh38187,129,844 - 87,129,904EPDNEWNC
RGD ID:15095237
Promoter ID:EPDNEWNC_H78
Type:initiation region
Name:LINC01140_2
Description:long intergenic non-protein coding RNA 1140 [Source:HGNCSymbol;Acc:HGNC:27922]
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
GRCh38187,131,968 - 87,132,028EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC LINC01140 COSMIC
Ensembl Genes ENSG00000267272 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000490006 ENTREZGENE
  ENST00000590653 ENTREZGENE
GTEx ENSG00000267272 GTEx
HGNC ID HGNC:27922 ENTREZGENE
Human Proteome Map LINC01140 Human Proteome Map
NCBI Gene 339524 ENTREZGENE
RNAcentral URS000075A0EB RNACentral
  URS000075C478 RNACentral
  URS000075CD48 RNACentral
  URS000075D2B3 RNACentral
  URS000075D36D RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-12-10 LINC01140  long intergenic non-protein coding RNA 1140  LOC339524  uncharacterized LOC339524  Symbol and/or name change 5135510 APPROVED
2011-11-01 LOC339524  uncharacterized LOC339524  LOC339524  hypothetical LOC339524  Symbol and/or name change 5135510 APPROVED