Lncenc1 (long non-coding RNA, embryonic stem cells expressed 1) - Rat Genome Database

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Gene: Lncenc1 (long non-coding RNA, embryonic stem cells expressed 1) Mus musculus
Analyze
No known orthologs.
Symbol: Lncenc1
Name: long non-coding RNA, embryonic stem cells expressed 1
RGD ID: 2299758
MGI Page MGI
Description: Acts upstream of or within regulation of gene expression. Is expressed in brain. Orthologous to human LINC01157 (long intergenic non-protein coding RNA 1157).
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: ENSMUSG00000078952; Gm11019; Gm2373; Linc; linc-; linc-Enc1; Lincenc1; Pla; Platr18; predicted gene, 100039691
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391397,571,441 - 97,641,366 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1397,571,455 - 97,645,404 (+)EnsemblGRCm39 Ensembl
GRCm381397,434,970 - 97,497,664 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1397,434,970 - 97,497,007 (+)EnsemblGRCm38mm10GRCm38
MGSCv371398,204,925 - 98,266,962 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361398,252,910 - 98,259,655 (+)NCBIMGSCv36mm8
Celera13101,065,753 - 101,157,357 (+)NCBICelera
Cytogenetic Map13D1NCBI
cM Map1350.71NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

References - curated
# Reference Title Reference Citation
1. Mouse MP Annotation Import Pipeline RGD automated import pipeline
Additional References at PubMed
PMID:10512203   PMID:12466851   PMID:12477932   PMID:12520002   PMID:12904583   PMID:14610273   PMID:15840001   PMID:17967808   PMID:18799693   PMID:24316575   PMID:24381249   PMID:25909911  
PMID:26034286   PMID:30174313   PMID:33059001   PMID:33340495   PMID:36880658  


Genomics

Variants

.
Variants in Lncenc1
2533 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:276
Count of miRNA genes:170
Interacting mature miRNAs:185
Transcripts:ENSMUST00000109431, ENSMUST00000179324, ENSMUST00000180371
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.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1301949Skull20_mskull morphology 20 (mouse)Not determined136425082198250945Mouse
1357468Rplag_mreduced platelet aggregation (mouse)Not determined1395502130120883175Mouse
1300941Skl6_mskeletal size (tail length) 6 (mouse)Not determined136425082198250945Mouse
4142147Mvwf4_mmodifier of von Willebrand factor 4 (mouse)Not determined20477612112898424Mouse
1301445Listr2_mlisteriosis resistance 2 (mouse)Not determined1366744601100744746Mouse
4141728Egaq4_mearly growth adjusted QTL 4 (mouse)Not determined87901985112431103Mouse
10043997Bw40_mbody weight QTL 40 (mouse)Not determined1479239045113239162Mouse
1301142Heal2_mwound healing/regeneration 2 (mouse)Not determined1393875267120883175Mouse
4142338Skmw18_mskeletal muscle weight 18 (mouse)Not determined1394528399120883175Mouse
10402414Sgp5_mserum gp70 production 5 (mouse)Not determined1356470456105422186Mouse
4142465Pbwg17_mpostnatal body weight growth 17 (mouse)Not determined1383876060117876256Mouse
4140995Fbtq6_mfemoral bone trait QTL 6 (mouse)Not determined1386341617120341758Mouse
4141992W6q16_mweight 6 weeks QTL 16 (mouse)Not determined55720354112431103Mouse
1301593Heal8_mwound healing/regeneration 8 (mouse)Not determined1368053999102054119Mouse
4141266Mol3_mmodifier of LPS-response 3 (mouse)Not determined76132600112431103Mouse
1558741Ses10_msalmonella enteritidis susceptibility 10 (mouse)Not determined1382739968116740106Mouse
14700691Cisaq1_mcoxsackieviral infection serum ALT QTL 1 (mouse)1386148119120461536Mouse
4142241Tailq3_mtail length QTL 3 (mouse)Not determined55720354112431103Mouse
1300939Hrtfm6_mheart failure modifier 6 (mouse)Not determined1391383692120883175Mouse
14747007Mancz11_mmandible centroid size 11 (mouse)1370111284104111284Mouse
12880414V125Dq10_mvitamin D active form serum level QTL 10 (mouse)1378036508112036508Mouse
10045623Heal18_mwound healing regeneration 18 (mouse)Not determined1379239045113239162Mouse
4140959W10q17_mweight 10 weeks QTL 17 (mouse)Not determined55720354112431103Mouse
4142314Tailaq3_mtail length adjusted QTL 3 (mouse)Not determined55720354112431103Mouse
14696726Kidrq3_mkidney weight, right QTL 3 (mouse)1368217066102217066Mouse
1300876Tanidd2_mtally ho associated non-insulin dependednt diabetes mellitus 2 (mouse)Not determined1391965303120883175Mouse
1558763Gct9_mgranulosa cell tumorigenesis 9 (mouse)Not determined1395036824120883175Mouse


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000109431
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1397,571,478 - 97,633,515 (+)Ensembl
GRCm38.p6 Ensembl1397,434,970 - 97,497,007 (+)Ensembl
RefSeq Acc Id: ENSMUST00000179324
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1397,619,209 - 97,633,515 (+)Ensembl
GRCm38.p6 Ensembl1397,482,701 - 97,497,007 (+)Ensembl
RefSeq Acc Id: ENSMUST00000180371
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1397,619,463 - 97,626,208 (+)Ensembl
GRCm38.p6 Ensembl1397,482,955 - 97,489,700 (+)Ensembl
RefSeq Acc Id: ENSMUST00000242609
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1397,619,257 - 97,628,100 (+)Ensembl
RefSeq Acc Id: ENSMUST00000242928
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1397,619,259 - 97,628,094 (+)Ensembl
RefSeq Acc Id: ENSMUST00000243060
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1397,619,259 - 97,632,581 (+)Ensembl
RefSeq Acc Id: ENSMUST00000243064
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1397,619,257 - 97,623,620 (+)Ensembl
RefSeq Acc Id: ENSMUST00000244070
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1397,619,257 - 97,627,334 (+)Ensembl
RefSeq Acc Id: ENSMUST00000244290
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1397,571,455 - 97,645,404 (+)Ensembl
RefSeq Acc Id: ENSMUST00000244877
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1397,619,259 - 97,632,582 (+)Ensembl
RefSeq Acc Id: ENSMUST00000244982
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1397,619,257 - 97,627,334 (+)Ensembl
RefSeq Acc Id: ENSMUST00000245212
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1397,619,257 - 97,630,767 (+)Ensembl
RefSeq Acc Id: ENSMUST00000245625
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1397,619,257 - 97,628,094 (+)Ensembl
RefSeq Acc Id: ENSMUST00000246094
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1397,619,259 - 97,633,515 (+)Ensembl
RefSeq Acc Id: NR_110430
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391397,619,258 - 97,633,515 (+)NCBI
GRCm381397,482,701 - 97,497,664 (+)NCBI
Celera13101,065,753 - 101,157,357 (+)NCBI
Sequence:
RefSeq Acc Id: NR_110431
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391397,619,258 - 97,633,515 (+)NCBI
GRCm381397,482,701 - 97,497,664 (+)NCBI
Celera13101,065,753 - 101,157,357 (+)NCBI
Sequence:
RefSeq Acc Id: NR_110432
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391397,571,441 - 97,633,515 (+)NCBI
GRCm381397,434,970 - 97,497,664 (+)NCBI
Celera13101,065,753 - 101,157,357 (+)NCBI
Sequence:
RefSeq Acc Id: NR_188726
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391397,571,441 - 97,633,515 (+)NCBI
RefSeq Acc Id: NR_188727
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391397,619,258 - 97,633,515 (+)NCBI
RefSeq Acc Id: NR_188728
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391397,571,441 - 97,641,366 (+)NCBI
Promoters
RGD ID:8681108
Promoter ID:EPDNEW_M18579
Type:initiation region
Name:Lncenc1_2
Description:Mus musculus long non-coding RNA, embryonic stem cells expressed1 , transcript variant 2, long non-coding RNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M18580  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381397,434,933 - 97,434,993EPDNEW
RGD ID:15094352
Promoter ID:EPDNEWNC_M2260
Type:single initiation site
Name:Lncenc1_1
Description:long non-coding RNA, embryonic stem cells expressed 1[Source:MGI Symbol;Acc:MGI:3780541]
SO ACC ID:SO:0000170
Source:EPDNEWNC (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381397,482,752 - 97,482,812EPDNEWNC
RGD ID:8681098
Promoter ID:EPDNEW_M18580
Type:multiple initiation site
Name:Lncenc1_1
Description:Mus musculus long non-coding RNA, embryonic stem cells expressed1 , transcript variant 2, long non-coding RNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M18579  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381397,482,752 - 97,482,812EPDNEW
RGD ID:6823939
Promoter ID:MM_KWN:14997
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:ES_Cell
Transcripts:XM_001477186_GM2373
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361398,252,561 - 98,253,061 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:3780541 AgrOrtholog
Ensembl Genes ENSMUSG00000078952 Ensembl, ENTREZGENE
Ensembl Transcript ENSMUST00000109431 ENTREZGENE
  ENSMUST00000179324 ENTREZGENE
MGD MGI:3780541 ENTREZGENE
NCBI Gene 100039691 ENTREZGENE
PhenoGen Lncenc1 PhenoGen
RNAcentral URS00026A1A58 RNACentral
  URS00026A1D40 RNACentral
  URS00026A2591 RNACentral
  URS00026A2682 RNACentral
  URS00026A2786 RNACentral
  URS00026A27E7 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-10-27 Lncenc1  long non-coding RNA, embryonic stem cells expressed 1  Lincenc1  long intergenic non-coding RNA, embryonic stem cells expressed 1  Symbol and/or name change 5135510 APPROVED
2014-06-10 Lincenc1  long intergenic non-coding RNA, embryonic stem cells expressed 1  Gm2373  predicted gene 2373  Symbol and/or name change 5135510 APPROVED