Upf1 (UPF1 regulator of nonsense transcripts homolog (yeast)) - Rat Genome Database
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Gene: Upf1 (UPF1 regulator of nonsense transcripts homolog (yeast)) Mus musculus
Analyze
Symbol: Upf1
Name: UPF1 regulator of nonsense transcripts homolog (yeast)
RGD ID: 1313947
MGI Page MGI
Description: Predicted to have RNA helicase activity; chromatin binding activity; and nucleic acid binding activity. Involved in dosage compensation by inactivation of X chromosome. Predicted to localize to chromatin; cytoplasm; and nucleus. Is expressed in cerebral cortex ventricular layer; embryo; and oocyte. Orthologous to human UPF1 (UPF1 RNA helicase and ATPase); PARTICIPATES IN mRNA decay pathway; INTERACTS WITH 1,2-dimethylhydrazine; 17alpha-ethynylestradiol; 2,3',4,4',5-Pentachlorobiphenyl.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: ATP-dependent helicase RENT1; B430202H16Rik; mUpf1; nonsense mRNA reducing factor 1; NORF1; PNO; PNORF-1; regulator of nonsense transcripts 1; Regulator of nonsense transcripts 1 (Nonsense mRNA reducing factor 1) (NORF1) (Up-frameshift suppressor 1 homolog); Ren; Rent1; up-frameshift suppressor 1 homolog; Upflp
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39870,784,143 - 70,806,418 (-)NCBIGRCm39mm39
GRCm38870,331,493 - 70,353,423 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl870,331,525 - 70,353,278 (-)EnsemblGRCm38mm10GRCm38
MGSCv37872,855,421 - 72,877,172 (-)NCBIGRCm37mm9NCBIm37
MGSCv36873,260,514 - 73,282,268 (-)NCBImm8
Celera872,887,999 - 72,909,735 (-)NCBICelera
Cytogenetic Map8B3.3NCBI
cM Map834.15NCBI
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

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

Additional References at PubMed
PMID:8855285   PMID:8889548   PMID:10349636   PMID:11042159   PMID:11076861   PMID:11152657   PMID:11217851   PMID:11353399   PMID:12466851   PMID:12477932   PMID:12520002   PMID:12904583  
PMID:15489334   PMID:15782199   PMID:16141072   PMID:16141073   PMID:16789828   PMID:17000771   PMID:21670277   PMID:21873635   PMID:22083510   PMID:22503102   PMID:23202588   PMID:23766421  
PMID:23821644   PMID:24457600   PMID:25770585   PMID:26265008   PMID:27149095   PMID:28128343   PMID:28378742   PMID:28634551   PMID:28671696   PMID:29581509   PMID:29959727   PMID:30333137  
PMID:30457570   PMID:30584064   PMID:31040226   PMID:31138677   PMID:31276534   PMID:31329944   PMID:32098917   PMID:32124941   PMID:32325033   PMID:32581705   PMID:32620797   PMID:32968282  


Genomics

Comparative Map Data
Upf1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39870,784,143 - 70,806,418 (-)NCBIGRCm39mm39
GRCm38870,331,493 - 70,353,423 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl870,331,525 - 70,353,278 (-)EnsemblGRCm38mm10GRCm38
MGSCv37872,855,421 - 72,877,172 (-)NCBIGRCm37mm9NCBIm37
MGSCv36873,260,514 - 73,282,268 (-)NCBImm8
Celera872,887,999 - 72,909,735 (-)NCBICelera
Cytogenetic Map8B3.3NCBI
cM Map834.15NCBI
UPF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1918,831,938 - 18,868,236 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl1918,831,959 - 18,868,230 (+)EnsemblGRCh38hg38GRCh38
GRCh381918,831,405 - 18,868,230 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371918,942,744 - 18,979,039 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361918,803,744 - 18,840,039 (+)NCBINCBI36hg18NCBI36
Build 341918,803,787 - 18,840,038NCBI
Celera1918,847,541 - 18,883,840 (+)NCBI
Cytogenetic Map19p13.11NCBI
HuRef1918,507,089 - 18,543,390 (+)NCBIHuRef
CHM1_11918,942,555 - 18,978,850 (+)NCBICHM1_1
Upf1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01620,824,888 - 20,845,632 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1620,824,864 - 20,845,243 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01620,677,403 - 20,698,177 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1619,266,888 - 19,287,629 (+)NCBICelera
Cytogenetic Map16p14NCBI
Upf1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555242,798,336 - 2,913,176 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555242,798,336 - 2,814,063 (-)NCBIChiLan1.0ChiLan1.0
UPF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11919,293,020 - 19,315,295 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1919,292,725 - 19,313,224 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01918,269,878 - 18,306,199 (+)NCBIMhudiblu_PPA_v0panPan3
UPF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2044,236,264 - 44,270,916 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12044,234,411 - 44,271,129 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Upf1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365962,469,444 - 2,505,688 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
UPF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl258,975,015 - 59,013,495 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1258,975,013 - 59,013,546 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2258,558,438 - 58,561,969 (+)NCBISscrofa10.2Sscrofa10.2susScr3
UPF1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1617,291,189 - 17,328,768 (+)NCBI
ChlSab1.1 Ensembl617,291,175 - 17,330,193 (+)Ensembl
Upf1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046249081,909,995 - 1,935,370 (+)NCBI

Position Markers
Gdf1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38870,331,381 - 70,331,527UniSTSGRCm38
MGSCv37872,855,280 - 72,855,426UniSTSGRCm37
Celera872,887,858 - 72,888,004UniSTS
Cytogenetic Map8B3.3UniSTS
cM Map8 UniSTS
AI385651  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38870,331,438 - 70,331,536UniSTSGRCm38
MGSCv37872,855,337 - 72,855,435UniSTSGRCm37
Celera872,887,915 - 72,888,013UniSTS
Cytogenetic Map8B3.3UniSTS
Whitehead/MRC_RH8743.32UniSTS
UniSTS:235917  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38870,331,749 - 70,331,854UniSTSGRCm38
MGSCv37872,855,648 - 72,855,753UniSTSGRCm37
Celera872,888,226 - 72,888,331UniSTS
Cytogenetic Map8B3.3UniSTS
RH139099  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38870,331,392 - 70,331,538UniSTSGRCm38
MGSCv37872,855,291 - 72,855,437UniSTSGRCm37
Celera872,887,869 - 72,888,015UniSTS
Cytogenetic Map8B3.3UniSTS
Rent1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38870,343,343 - 70,344,358UniSTSGRCm38
MGSCv37872,867,242 - 72,868,257UniSTSGRCm37
Celera872,899,809 - 72,900,824UniSTS
Cytogenetic Map8B3.3UniSTS
cM Map833.5UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1558870Eae36_mexperimental allergic encephalomyelitis susceptibility 36 (mouse)Not determined81472316071045600Mouse
1357811Orq3_movulation rate QTL 3 (mouse)Not determined83201654471287993Mouse
4141437W10q14_mweight 10 weeks QTL 14 (mouse)Not determined3201654471287993Mouse
4141172W6q9_mweight 6 weeks QTL 9 (mouse)Not determined3201654471287993Mouse
4140966Egq12_mearly growth QTL 12 (mouse)Not determined3201654471287993Mouse
4140967Bmd39_mbone mineral density 39 (mouse)Not determined832016544117238700Mouse
1558875Eae31_mexperimental allergic encephalomyelitis susceptibility 31 (mouse)Not determined834642776114837007Mouse
1301013Capsq4_mcapsaicin sensitivity related QTL 4 (mouse)Not determined83616300092728652Mouse
27226754Femd6_mfemur midshaft diameter 6, 10 week (mouse)837400000109600000Mouse
12904744Carcdq1_mcardiac collagen deposition QTL 1 (mouse)83970925694689598Mouse
1301544Iba3_minduction of brown adipocytes 3 (mouse)Not determined84429488078295025Mouse
1301717Adip4_madiposity 4 (mouse)Not determined84763703081637146Mouse
10766453Char11_mP. chabaudi malaria resistance QTL 11 (mouse)84763703081637146Mouse
1301441Skull11_mskull morphology 11 (mouse)Not determined84773713481737254Mouse
1357715Alaa3_malopecia areata 3 (mouse)Not determined84879293982793021Mouse
14746987Manh64_mmandible shape 64 (mouse)85005330684053306Mouse
14747005Mancz7_mmandible centroid size 7 (mouse)85005330684053306Mouse
14700686Civq3_mcerebral infarct volume QTL 3 (mouse)85188219185882191Mouse
1301506Aevm1_mautoimmune extremity vasculitis in MRL mice 1 (mouse)Not determined85428781788287993Mouse
1301952Im3_mimmunoregulatory 3 (mouse)Not determined85470661488706763Mouse
10412287Carg3_mCandida albicans resistance gene 3 (mouse)Not determined85554502889545028Mouse
11353828Gf7_mgonadal fat pad weight 7 (mouse)85820147992201479Mouse
10043975Obq31_mobesity QTL 31 (mouse)Not determined85840977692409776Mouse
1301688Orch6_mautoimmune orchitis resistance 6 (mouse)Not determined86078685094786976Mouse
4141285Tgq18_mtriglyceride QTL 18 (mouse)Not determined6346010797460107Mouse
4141797Skmw16_mskeletal muscle weight 16 (mouse)Not determined86393954797939696Mouse
1357787Vtbt5_mvertebral trabecular bone trait 5 (mouse)Not determined86535776899357920Mouse
10043992Hbnr11_mHeligmosomoides bakeri nematode resistance 11 (mouse)Not determined86560020799600347Mouse
10766466Char12_mP. chabaudi malaria resistance QTL 12 (mouse)86826982782600347Mouse
1301767Fcsa2_mfemoral cross-sectional area 2 (mouse)Not determined870305375104305495Mouse
4142283Imraq2_mimmune response to AAV2 QTL 2 (mouse)Not determined870305375104305495Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:387
Count of miRNA genes:262
Interacting mature miRNAs:304
Transcripts:ENSMUST00000075666
Prediction methods:Miranda, Rnahybrid, Targetscan
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


Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001122829 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_030680 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006509604 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006509605 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC158553 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF182947 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF322655 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AH013841 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK052517 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK148196 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK200037 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK205237 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK205256 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC030916 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC052149 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC056442 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BE456815 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BQ771453 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH466569 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSMUST00000075666   ⟹   ENSMUSP00000075089
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl870,331,525 - 70,353,278 (-)Ensembl
RefSeq Acc Id: ENSMUST00000215817   ⟹   ENSMUSP00000148927
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl870,331,525 - 70,353,211 (-)Ensembl
RefSeq Acc Id: NM_001122829   ⟹   NP_001116301
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39870,784,143 - 70,805,929 (-)NCBI
GRCm38870,331,493 - 70,353,279 (-)NCBI
MGSCv37872,855,421 - 72,877,172 (-)RGD
Celera872,887,999 - 72,909,735 (-)RGD
cM Map8 ENTREZGENE
Sequence:
RefSeq Acc Id: NM_030680   ⟹   NP_109605
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39870,784,143 - 70,805,929 (-)NCBI
GRCm38870,331,493 - 70,353,279 (-)NCBI
MGSCv37872,855,421 - 72,877,172 (-)RGD
Celera872,887,999 - 72,909,735 (-)RGD
cM Map8 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006509604   ⟹   XP_006509667
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39870,784,172 - 70,806,418 (-)NCBI
GRCm38870,331,522 - 70,353,423 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006509605   ⟹   XP_006509668
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39870,784,389 - 70,806,418 (-)NCBI
GRCm38870,331,522 - 70,353,423 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_109605   ⟸   NM_030680
- Peptide Label: isoform b
- UniProtKB: Q9EPU0 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001116301   ⟸   NM_001122829
- Peptide Label: isoform a
- UniProtKB: Q9EPU0 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006509668   ⟸   XM_006509605
- Peptide Label: isoform X1
- UniProtKB: Q9EPU0 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006509667   ⟸   XM_006509604
- Peptide Label: isoform X1
- UniProtKB: Q9EPU0 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSMUSP00000075089   ⟸   ENSMUST00000075666
RefSeq Acc Id: ENSMUSP00000148927   ⟸   ENSMUST00000215817

Promoters
RGD ID:8667303
Promoter ID:EPDNEW_M11682
Type:initiation region
Name:Upf1_1
Description:Mus musculus UPF1 regulator of nonsense transcripts homolog ,transcript variant 2, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38870,353,300 - 70,353,360EPDNEW
RGD ID:6843862
Promoter ID:MM_KWN:54699
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:ENSMUST00000075666,   NM_030680,   UC009MAC.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36872,877,069 - 72,877,569 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:107995 AgrOrtholog
Ensembl Genes ENSMUSG00000058301 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSMUSP00000075089 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUSP00000148927 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000075666 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUST00000215817 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro DNA2/NAM7-like_AAA UniProtKB/Swiss-Prot
  DNA2/NAM7_AAA_11 UniProtKB/Swiss-Prot
  DUF5599 UniProtKB/Swiss-Prot
  Helicase/UvrB_N UniProtKB/Swiss-Prot
  P-loop_NTPase UniProtKB/Swiss-Prot
  RNA-helicase_UPF1_UPF2-interct UniProtKB/Swiss-Prot
KEGG Report mmu:19704 UniProtKB/Swiss-Prot
MGD MGI:107995 ENTREZGENE
NCBI Gene 19704 ENTREZGENE
Pfam AAA_11 UniProtKB/Swiss-Prot
  AAA_12 UniProtKB/Swiss-Prot
  DUF5599 UniProtKB/Swiss-Prot
  ResIII UniProtKB/Swiss-Prot
  UPF1_Zn_bind UniProtKB/Swiss-Prot
PhenoGen Upf1 PhenoGen
Superfamily-SCOP SSF52540 UniProtKB/Swiss-Prot
UniGene Mm.258280 ENTREZGENE
  Mm.390048 ENTREZGENE
UniProt Q9EPU0 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q3UG00 UniProtKB/Swiss-Prot
  Q6GYP5 UniProtKB/Swiss-Prot
  Q6PHQ5 UniProtKB/Swiss-Prot
  Q8K0N4 UniProtKB/Swiss-Prot
  Q99PR4 UniProtKB/Swiss-Prot