Upf3b (UPF3B, regulator of nonsense mediated mRNA decay) - Rat Genome Database

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Gene: Upf3b (UPF3B, regulator of nonsense mediated mRNA decay) Rattus norvegicus
Analyze
Symbol: Upf3b
Name: UPF3B, regulator of nonsense mediated mRNA decay
RGD ID: 1560264
Description: Predicted to have mRNA binding activity. Predicted to be involved in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay and positive regulation of translation. Predicted to localize to centriolar satellite; cytosol; and nucleus. Human ortholog(s) of this gene implicated in non-syndromic X-linked intellectual disability 82 and syndromic X-linked intellectual disability 14. Orthologous to human UPF3B (UPF3B regulator of nonsense mediated mRNA decay); PARTICIPATES IN mRNA decay pathway; RNA transport pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,4-dinitrotoluene; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC313449; regulator of nonsense transcripts 3B; RGD1560264; similar to UPF3 regulator of nonsense transcripts homolog B isoform 2; UPF3 regulator of nonsense transcripts homolog B; UPF3 regulator of nonsense transcripts homolog B (yeast)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X116,335,308 - 116,353,332 (-)NCBI
Rnor_6.0 EnsemblX123,713,339 - 123,731,385 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X123,713,327 - 123,731,431 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X123,849,755 - 123,867,703 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X7,801,655 - 7,819,849 (+)NCBIRGSC3.4rn4RGSC3.4
CeleraX115,562,637 - 115,580,545 (-)NCBICelera
Cytogenetic MapXq35NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
centriolar satellite  (IEA,ISO)
cytoplasm  (IBA)
cytosol  (IEA,ISO)
exon-exon junction complex  (ISO)
nucleolus  (IBA,ISO)
nucleoplasm  (IEA,ISO)

Molecular Function
mRNA binding  (IBA,ISO)
protein binding  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:11546873   PMID:12718880   PMID:16601204   PMID:18369367   PMID:22658674   PMID:22681889  


Genomics

Comparative Map Data
Upf3b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X116,335,308 - 116,353,332 (-)NCBI
Rnor_6.0 EnsemblX123,713,339 - 123,731,385 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X123,713,327 - 123,731,431 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X123,849,755 - 123,867,703 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X7,801,655 - 7,819,849 (+)NCBIRGSC3.4rn4RGSC3.4
CeleraX115,562,637 - 115,580,545 (-)NCBICelera
Cytogenetic MapXq35NCBI
UPF3B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX119,805,311 - 119,852,998 (-)EnsemblGRCh38hg38GRCh38
GRCh38X119,805,311 - 119,853,028 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X118,967,985 - 118,986,926 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X118,852,017 - 118,870,996 (-)NCBINCBI36hg18NCBI36
Build 34X118,749,870 - 118,768,850NCBI
CeleraX119,422,616 - 119,441,635 (-)NCBI
Cytogenetic MapXq24NCBI
HuRefX108,461,263 - 108,479,939 (-)NCBIHuRef
CHM1_1X118,879,087 - 118,898,087 (-)NCBICHM1_1
Upf3b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X36,355,331 - 36,374,124 (-)NCBIGRCm39mm39
GRCm39 EnsemblX36,355,331 - 36,373,975 (-)Ensembl
GRCm38X37,091,678 - 37,110,471 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX37,091,678 - 37,110,322 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X34,631,829 - 34,650,317 (-)NCBIGRCm37mm9NCBIm37
MGSCv36X33,523,279 - 33,541,767 (-)NCBImm8
CeleraX23,815,464 - 23,833,952 (-)NCBICelera
Cytogenetic MapXA3.3NCBI
Upf3b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955534176,522 - 193,319 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955534176,553 - 193,033 (+)NCBIChiLan1.0ChiLan1.0
UPF3B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X119,292,231 - 119,311,632 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX119,292,231 - 119,311,632 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X108,897,140 - 108,916,620 (-)NCBIMhudiblu_PPA_v0panPan3
UPF3B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X91,835,845 - 91,851,755 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX91,836,727 - 91,851,640 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX77,910,224 - 77,926,190 (-)NCBI
UMICH_Zoey_3.1X91,027,322 - 91,043,287 (-)NCBI
UNSW_CanFamBas_1.0X92,787,502 - 92,803,460 (-)NCBI
UU_Cfam_GSD_1.0X92,515,688 - 92,531,655 (-)NCBI
Upf3b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X90,876,197 - 90,894,205 (-)NCBI
SpeTri2.0NW_00493647910,093,290 - 10,111,293 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
UPF3B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX98,182,269 - 98,206,097 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X98,184,646 - 98,206,135 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X113,406,198 - 113,427,250 (+)NCBISscrofa10.2Sscrofa10.2susScr3
UPF3B
(Chlorocebus sabaeus - African green monkey)
No map positions available.
Upf3b
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248953,762,087 - 3,781,662 (-)NCBI

Position Markers
RH134263  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X123,713,413 - 123,713,622NCBIRnor6.0
Rnor_5.0X123,849,841 - 123,850,050UniSTSRnor5.0
RGSC_v3.4X7,819,554 - 7,819,763UniSTSRGSC3.4
CeleraX115,562,723 - 115,562,932UniSTS
Cytogenetic MapXq12UniSTS
BE117640  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X123,717,336 - 123,717,505NCBIRnor6.0
Rnor_5.0X123,853,764 - 123,853,933UniSTSRnor5.0
RGSC_v3.4X7,815,671 - 7,815,840UniSTSRGSC3.4
CeleraX115,566,646 - 115,566,815UniSTS
Cytogenetic MapXq12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X15688119127888215Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X44320616158345622Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X70352120127888215Rat
724551Glom1Glomerulus QTL 12.80.0004kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)X82930791127930791Rat
1598872Memor14Memory QTL 144.5exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X101333032146333032Rat
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX107886746152409805Rat
1598809Memor15Memory QTL 154.4exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X110957467155957467Rat
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X110957467155957467Rat
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X118715462159970021Rat
738029Stresp2Stress response QTL 23.40.0004stress-related behavior trait (VT:0010451)defensive burying - approachX120045041143145818Rat
5685004Bss104Bone structure and strength QTL 1043.9tibia area (VT:1000281)tibia area measurement (CMO:0001382)X121442246134627946Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:368
Count of miRNA genes:231
Interacting mature miRNAs:264
Transcripts:ENSRNOT00000032618
Prediction methods:Microtar, Miranda, Pita, 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 appendage
High
Medium 3 14 31 17 19 17 2 74 27 40 11
Low 29 26 24 24 8 9 8 1 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000032618   ⟹   ENSRNOP00000029696
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX123,713,339 - 123,731,385 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092284
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX123,720,590 - 123,725,565 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092364
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX123,717,163 - 123,717,569 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092391
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX123,719,907 - 123,731,366 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092574   ⟹   ENSRNOP00000075758
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX123,714,060 - 123,731,294 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092588
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX123,713,856 - 123,715,181 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092703
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX123,729,207 - 123,730,006 (-)Ensembl
RefSeq Acc Id: NM_001135873   ⟹   NP_001129345
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X116,335,308 - 116,353,236 (-)NCBI
Rnor_6.0X123,713,327 - 123,731,403 (-)NCBI
Rnor_5.0X123,849,755 - 123,867,703 (-)NCBI
RGSC_v3.4X7,801,655 - 7,819,849 (+)RGD
CeleraX115,562,637 - 115,580,545 (-)RGD
Sequence:
RefSeq Acc Id: XM_006257455   ⟹   XP_006257517
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X116,335,315 - 116,353,332 (-)NCBI
Rnor_6.0X123,713,334 - 123,731,431 (-)NCBI
Rnor_5.0X123,849,755 - 123,867,703 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008773416   ⟹   XP_008771638
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X116,335,315 - 116,353,332 (-)NCBI
Rnor_6.0X123,713,334 - 123,731,431 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017602038   ⟹   XP_017457527
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X116,335,315 - 116,353,332 (-)NCBI
Rnor_6.0X123,713,334 - 123,731,431 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039099698   ⟹   XP_038955626
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X116,335,315 - 116,353,332 (-)NCBI
RefSeq Acc Id: XM_039099699   ⟹   XP_038955627
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X116,335,315 - 116,353,332 (-)NCBI
RefSeq Acc Id: XM_039099700   ⟹   XP_038955628
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X116,335,315 - 116,353,332 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001129345   ⟸   NM_001135873
- UniProtKB: D3ZBE8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006257517   ⟸   XM_006257455
- Peptide Label: isoform X1
- UniProtKB: A0A0U1RRP3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008771638   ⟸   XM_008773416
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017457527   ⟸   XM_017602038
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000075758   ⟸   ENSRNOT00000092574
RefSeq Acc Id: ENSRNOP00000029696   ⟸   ENSRNOT00000032618
RefSeq Acc Id: XP_038955628   ⟸   XM_039099700
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038955627   ⟸   XM_039099699
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038955626   ⟸   XM_039099698
- Peptide Label: isoform X2
Protein Domains
Smg4_UPF3

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13701990
Promoter ID:EPDNEW_R12511
Type:initiation region
Name:Upf3b_1
Description:UPF3B, regulator of nonsense mediated mRNA decay
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X123,731,333 - 123,731,393EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1560264 AgrOrtholog
Ensembl Genes ENSRNOG00000039994 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000029696 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000075758 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000032618 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000092574 UniProtKB/TrEMBL
Gene3D-CATH 3.30.70.330 UniProtKB/TrEMBL
InterPro Nonsense_mediated_decay_UPF3 UniProtKB/TrEMBL
  Nucleotide-bd_a/b_plait_sf UniProtKB/TrEMBL
  RBD_domain_sf UniProtKB/TrEMBL
  Upf3 UniProtKB/TrEMBL
  UPF3B_RRM_like_Smg4 UniProtKB/TrEMBL
KEGG Report rno:313449 UniProtKB/TrEMBL
NCBI Gene 313449 ENTREZGENE
PANTHER PTHR13112 UniProtKB/TrEMBL
Pfam Smg4_UPF3 UniProtKB/TrEMBL
PhenoGen Upf3b PhenoGen
Superfamily-SCOP SSF54928 UniProtKB/TrEMBL
UniProt A0A0U1RRP3 ENTREZGENE, UniProtKB/TrEMBL
  D3ZBE8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-05-24 Upf3b  UPF3B, regulator of nonsense mediated mRNA decay  Upf3b  UPF3 regulator of nonsense transcripts homolog B  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2017-05-18 Upf3b  UPF3 regulator of nonsense transcripts homolog B  Upf3b  UPF3 regulator of nonsense transcripts homolog B (yeast)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Upf3b  UPF3 regulator of nonsense transcripts homolog B (yeast)   Upf3b_predicted  UPF3 regulator of nonsense transcripts homolog B (yeast) (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Upf3b_predicted  UPF3 regulator of nonsense transcripts homolog B (yeast) (predicted)  RGD1560264_predicted  similar to UPF3 regulator of nonsense transcripts homolog B isoform 2 (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1560264_predicted  similar to UPF3 regulator of nonsense transcripts homolog B isoform 2 (predicted)  LOC313449  similar to UPF3 regulator of nonsense transcripts homolog B isoform 2  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC313449  similar to UPF3 regulator of nonsense transcripts homolog B isoform 2      Symbol and Name status set to provisional 70820 PROVISIONAL