Dubr (Dppa2 upstream binding RNA) - Rat Genome Database

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Gene: Dubr (Dppa2 upstream binding RNA) Mus musculus
Analyze
Symbol: Dubr
Name: Dppa2 upstream binding RNA
RGD ID: 1620017
MGI Page MGI
Description: Acts upstream of or within negative regulation of transcription by RNA polymerase II; positive regulation of myoblast differentiation; and regulation of DNA methylation. Located in cytoplasm and nucleus. Is expressed in central nervous system and dorsal root ganglion. Orthologous to human DUBR (DPPA2 upstream binding RNA).
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: 5330426P16Rik; Dum
RGD Orthologs
Human
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391650,547,114 - 50,553,136 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1650,530,732 - 50,553,159 (-)EnsemblGRCm39 Ensembl
GRCm381650,726,751 - 50,732,773 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1650,719,294 - 50,732,773 (-)EnsemblGRCm38mm10GRCm38
MGSCv371650,726,864 - 50,732,886 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361650,644,973 - 50,760,359 (-)NCBIMGSCv36mm8
Celera1651,074,049 - 51,080,080 (-)NCBICelera
Cytogenetic Map16B5NCBI
cM Map1631.5NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IDA)
nucleus  (IDA)

Molecular Function

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:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:16141072   PMID:16141073   PMID:18799693   PMID:21267068   PMID:24316575   PMID:25253739   PMID:25686699  
PMID:30186101   PMID:32901860   PMID:33798452   PMID:36417851  


Genomics

Comparative Map Data
Dubr
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391650,547,114 - 50,553,136 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1650,530,732 - 50,553,159 (-)EnsemblGRCm39 Ensembl
GRCm381650,726,751 - 50,732,773 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1650,719,294 - 50,732,773 (-)EnsemblGRCm38mm10GRCm38
MGSCv371650,726,864 - 50,732,886 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361650,644,973 - 50,760,359 (-)NCBIMGSCv36mm8
Celera1651,074,049 - 51,080,080 (-)NCBICelera
Cytogenetic Map16B5NCBI
cM Map1631.5NCBI
DUBR
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383107,240,692 - 107,326,964 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3107,220,744 - 107,348,464 (+)EnsemblGRCh38hg38GRCh38
GRCh373106,959,539 - 107,045,811 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363108,332,055 - 108,447,045 (+)NCBINCBI36Build 36hg18NCBI36
Celera3105,358,190 - 105,442,153 (+)NCBICelera
Cytogenetic Map3q13.12NCBI
HuRef3104,334,237 - 104,419,155 (+)NCBIHuRef
CHM1_13106,923,896 - 107,010,140 (+)NCBICHM1_1
T2T-CHM13v2.03109,960,376 - 110,046,666 (+)NCBIT2T-CHM13v2.0

Variants

.
Variants in Dubr
164 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:85
Count of miRNA genes:82
Interacting mature miRNAs:83
Transcripts:ENSMUST00000169791
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
1300915Lmr12_mleishmaniasis resistance 12 (mouse)Not determined162879281362792952Mouse
26884416Bzwq5_mbi-zygomatic width QTL 5, 5 week (mouse)163732036284696888Mouse
1301070Cypr1_mcytokine production 1 (mouse)Not determined163231279566312933Mouse
26884432Zlq7_mzygomatic length QTL 7, 10 week (mouse)16381786464620363Mouse
1302096Aod1a_mautoimmune ovarian dysgenesis 1a (mouse)Not determined163544664392573008Mouse
27226768Tibl9_mtibia length 9, 5 week (mouse)16331786451420363Mouse
11059560Lmr12b_mleishmaniasis resistance 12b (mouse)162879281362792952Mouse
4141212Imraq3_mimmune response to AAV2 QTL 3 (mouse)Not determined164438335078383506Mouse
1301138Pcd4ts3_mp-glycoprotein positive CD4 T cell subset 3 (mouse)Not determined164059392374594076Mouse
11059559Lmr12a_mleishmaniasis resistance 12a (mouse)162879281362792952Mouse
1301719Remslp3_mrapid eye movement sleep 3 (mouse)Not determined164438335078383506Mouse
1357778Diobq_mdiet-induced obesity QTL (mouse)Not determined164219781782331174Mouse
14928310Manh80_mmandible shape 80 (mouse)164821984182219841Mouse
11049571Lmr12c_mleishmaniasis resistance 12c (mouse)162879281362792952Mouse
4142112Skts-fp3_mskin tumor susceptibility in FVB and PWK 3 (mouse)Not determined164005388172924385Mouse
1558836Dice1b_mdetermination of interleukin 4 commitment 1b (mouse)Not determined164551100072274485Mouse
1357763Lp1_mlymphocyte proliferation 1 (mouse)Not determined16654297965466552Mouse
1357517Bwtn1_mbody weight at necropsy 1 (mouse)Not determined162001932985600826Mouse
4141179Ipng3_mimprinted postnatal growth 3 (mouse)Not determined2277525257594076Mouse
11522747Eae41_mexperimental allergic encephalomyelitis susceptibility 41 (mouse)164039913478015472Mouse
27226785Feml12_mfemur length 12, 5 week (mouse)16331786464620363Mouse
26884376Skwq4_mskull length QTL 4, 5 week (mouse)16841786490896888Mouse
1300534Bmd15_mbone mineral density 15 (mouse)Not determined162193838355938574Mouse
4142187Arrd3_mage-related retinal degeneration 3 (mouse)Not determined3252290965466552Mouse

Markers in Region
UniSTS:237521  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381650,726,767 - 50,726,900UniSTSGRCm38
MGSCv371650,726,880 - 50,727,013UniSTSGRCm37
Celera1651,074,065 - 51,074,198UniSTS
Cytogenetic Map16B5UniSTS
px-31f3  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map11B5UniSTS
Cytogenetic Map7A1UniSTS
Cytogenetic Map16C3.3UniSTS
Cytogenetic Map10A4UniSTS
Cytogenetic Map10A3-A4UniSTS
Cytogenetic Map18B3UniSTS
Cytogenetic Map7CUniSTS
Cytogenetic Map9E3.1UniSTS
Cytogenetic Map10A1UniSTS
Cytogenetic Map17CUniSTS
Cytogenetic Map15F1UniSTS
Cytogenetic Map7F3UniSTS
Cytogenetic Map16B5UniSTS
Cytogenetic Map15D3UniSTS
Cytogenetic Map7F1UniSTS
Cytogenetic Map10C3UniSTS
Cytogenetic Map3F1UniSTS
Cytogenetic Map14BUniSTS
Cytogenetic Map5C3.1UniSTS
Cytogenetic Map10B5.1UniSTS
Cytogenetic Map18E4UniSTS
Cytogenetic Map1A2UniSTS
Cytogenetic Map18D1UniSTS
Cytogenetic Map8A2UniSTS
Cytogenetic Map5A3UniSTS
Cytogenetic Map2A3UniSTS
Cytogenetic Map14D2UniSTS
Cytogenetic Map3F2.2UniSTS
Cytogenetic Map13C1UniSTS
Cytogenetic Map5G2UniSTS
Cytogenetic Map10C1UniSTS
Cytogenetic Map11CUniSTS
Cytogenetic Map17B3UniSTS
Cytogenetic Map12C2UniSTS
Cytogenetic Map13B2UniSTS
Cytogenetic Map15A1UniSTS
Cytogenetic Map11E1UniSTS
Cytogenetic Map5B1UniSTS
Cytogenetic Map10D1UniSTS
Cytogenetic Map13D1UniSTS
Cytogenetic Map4C3UniSTS
Cytogenetic MapXDUniSTS
Cytogenetic Map18D3UniSTS
cM Map1060.0UniSTS
cM Map154.6UniSTS
cM Map439.4UniSTS
cM Map1170.0UniSTS
cM Map1336.0UniSTS
cM Map518.2UniSTS
cM Map1229.0UniSTS
cM MapX42.0UniSTS
cM Map1347.01UniSTS
px-38e3  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map4D1UniSTS
Cytogenetic Map18B3UniSTS
Cytogenetic Map18D3UniSTS
Cytogenetic Map5B3UniSTS
Cytogenetic Map17B3UniSTS
Cytogenetic Map4C7UniSTS
Cytogenetic Map13C1UniSTS
Cytogenetic Map16B5UniSTS
Cytogenetic Map4D2.3UniSTS
Cytogenetic Map8B3.3UniSTS
Cytogenetic Map1H4UniSTS
Cytogenetic Map7F2UniSTS
Cytogenetic Map10D2UniSTS
Cytogenetic Map2G3UniSTS
Cytogenetic Map14BUniSTS
Cytogenetic Map11B5UniSTS
Cytogenetic MapYA1UniSTS
Cytogenetic Map11A3.2UniSTS
Cytogenetic Map3A1UniSTS
Cytogenetic Map13C3UniSTS
Cytogenetic Map1H6UniSTS
Cytogenetic Map5B2UniSTS
Cytogenetic Map19C3UniSTS
Cytogenetic Map10D1UniSTS
Cytogenetic Map10A1UniSTS
cM Map1060.0UniSTS
cM Map1106.6UniSTS
cM Map1936.5UniSTS
cM Map520.0UniSTS
cM Map1340.0UniSTS


Expression


Sequence


RefSeq Acc Id: ENSMUST00000169791
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1650,547,114 - 50,553,136 (-)Ensembl
GRCm38.p6 Ensembl1650,727,436 - 50,732,688 (-)Ensembl
RefSeq Acc Id: ENSMUST00000186535
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1650,545,988 - 50,553,136 (-)Ensembl
GRCm38.p6 Ensembl1650,725,625 - 50,732,728 (-)Ensembl
RefSeq Acc Id: ENSMUST00000186806
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1650,546,751 - 50,553,136 (-)Ensembl
GRCm38.p6 Ensembl1650,726,751 - 50,732,737 (-)Ensembl
RefSeq Acc Id: ENSMUST00000186944
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1650,539,657 - 50,553,136 (-)Ensembl
GRCm38.p6 Ensembl1650,719,294 - 50,732,773 (-)Ensembl
RefSeq Acc Id: ENSMUST00000191079
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1650,539,662 - 50,553,046 (-)Ensembl
GRCm38.p6 Ensembl1650,719,299 - 50,732,683 (-)Ensembl
RefSeq Acc Id: ENSMUST00000241647
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1650,547,798 - 50,553,125 (-)Ensembl
RefSeq Acc Id: ENSMUST00000242044
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1650,550,182 - 50,553,159 (-)Ensembl
RefSeq Acc Id: ENSMUST00000243162
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1650,539,655 - 50,553,136 (-)Ensembl
RefSeq Acc Id: ENSMUST00000243192
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1650,551,759 - 50,553,100 (-)Ensembl
RefSeq Acc Id: ENSMUST00000243362
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1650,530,732 - 50,553,136 (-)Ensembl
RefSeq Acc Id: ENSMUST00000243372
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1650,547,804 - 50,553,091 (-)Ensembl
RefSeq Acc Id: ENSMUST00000246984
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1650,539,659 - 50,553,117 (-)Ensembl
RefSeq Acc Id: NR_028300
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391650,547,114 - 50,553,136 (-)NCBI
GRCm381650,726,751 - 50,732,773 (-)ENTREZGENE
MGSCv371650,726,864 - 50,732,886 (-)RGD
Celera1651,074,049 - 51,080,080 (-)RGD
cM Map16 ENTREZGENE
Sequence:
Promoters
RGD ID:8686354
Promoter ID:EPDNEW_M21207
Type:initiation region
Name:Dubr_2
Description:Mus musculus Dppa2 upstream binding RNA , long non-coding RNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M21208  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381650,722,879 - 50,722,939EPDNEW
RGD ID:6826786
Promoter ID:MM_KWN:21206
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:AK035047_5330426P16RIK,   UC007ZKY.1,   UC007ZKZ.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361650,732,636 - 50,733,136 (-)MPROMDB
RGD ID:15094702
Promoter ID:EPDNEWNC_M2605
Type:initiation region
Name:Dubr_1
Description:Dppa2 upstream binding RNA [Source:MGISymbol;Acc:MGI:1915440]
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
GRCm381650,732,728 - 50,732,788EPDNEWNC
RGD ID:8686356
Promoter ID:EPDNEW_M21208
Type:initiation region
Name:Dubr_1
Description:Mus musculus Dppa2 upstream binding RNA , long non-coding RNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M21207  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381650,732,737 - 50,732,797EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1915440 AgrOrtholog
Ensembl Genes ENSMUSG00000022639 Ensembl
MGD MGI:1915440 ENTREZGENE
NCBI Gene 68190 ENTREZGENE
PhenoGen Dubr PhenoGen
RNAcentral URS000075D69E RNACentral
UniProt Q3UVR5_MOUSE UniProtKB/TrEMBL
  Q8BR36_MOUSE UniProtKB/TrEMBL
  Q8BT49_MOUSE UniProtKB/TrEMBL
  Q8C744_MOUSE UniProtKB/TrEMBL
  Q9CTC3_MOUSE UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-09-29 Dubr  Dppa2 upstream binding RNA  5330426P16Rik  RIKEN cDNA 5330426P16 gene  Symbol and/or name change 5135510 APPROVED