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

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: UPF3B (UPF3B regulator of nonsense mediated mRNA decay) Canis lupus familiaris
Analyze
Symbol: UPF3B
Name: UPF3B regulator of nonsense mediated mRNA decay
RGD ID: 12103970
Description: ENCODES a protein that exhibits mRNA binding (inferred); nucleic acid binding (inferred); INVOLVED IN brain development (ortholog); neuron projection development (ortholog); nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (ortholog); ASSOCIATED WITH autistic disorder (ortholog); cataract (ortholog); Danon disease (ortholog); FOUND IN neuronal cell body (ortholog); nucleus (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: regulator of nonsense transcripts 3B; UPF3 regulator of nonsense transcripts homolog B; UPF3 regulator of nonsense transcripts homolog B (yeast); UPF3B, regulator of nonsense mediated mRNA decay
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
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 (-)NCBIDog10K_Boxer_Tasha
UMICH_Zoey_3.1X91,027,322 - 91,043,287 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X92,787,502 - 92,803,460 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X92,515,688 - 92,531,655 (-)NCBIUU_Cfam_GSD_1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:30032202  


Genomics

Comparative Map Data
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 (-)NCBIDog10K_Boxer_Tasha
UMICH_Zoey_3.1X91,027,322 - 91,043,287 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X92,787,502 - 92,803,460 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X92,515,688 - 92,531,655 (-)NCBIUU_Cfam_GSD_1.0
UPF3B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X119,805,311 - 119,852,963 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX119,834,022 - 119,852,998 (-)EnsemblGRCh38hg38GRCh38
GRCh37X118,967,985 - 118,986,926 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X118,852,017 - 118,870,996 (-)NCBINCBI36Build 36hg18NCBI36
Build 34X118,749,870 - 118,768,850NCBI
CeleraX119,422,616 - 119,441,635 (-)NCBICelera
Cytogenetic MapXq24NCBI
HuRefX108,461,263 - 108,479,939 (-)NCBIHuRef
CHM1_1X118,879,087 - 118,898,087 (-)NCBICHM1_1
T2T-CHM13v2.0X118,180,438 - 118,228,084 (-)NCBIT2T-CHM13v2.0
Upf3b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X36,355,331 - 36,374,124 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX36,355,331 - 36,373,975 (-)EnsemblGRCm39 Ensembl
GRCm38X37,091,678 - 37,110,471 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX37,091,678 - 37,110,322 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X34,631,829 - 34,650,317 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X33,523,279 - 33,541,767 (-)NCBIMGSCv36mm8
CeleraX23,815,464 - 23,833,952 (-)NCBICelera
Cytogenetic MapXA3.3NCBI
cM MapX21.51NCBI
Upf3b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X121,200,993 - 121,219,059 (-)NCBIGRCr8
mRatBN7.2X116,335,308 - 116,353,332 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX116,335,308 - 116,353,236 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX118,438,851 - 118,456,789 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X122,007,993 - 122,025,929 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X119,553,931 - 119,571,856 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X123,713,327 - 123,731,431 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX123,713,339 - 123,731,385 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X123,849,755 - 123,867,703 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X7,801,655 - 7,819,849 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX115,562,637 - 115,580,545 (-)NCBICelera
Cytogenetic MapXq35NCBI
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
NHGRI_mPanPan1-v2X119,241,408 - 119,260,919 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X119,245,012 - 119,264,507 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X108,897,140 - 108,916,620 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X119,292,231 - 119,311,632 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX119,292,231 - 119,311,632 (-)Ensemblpanpan1.1panPan2
Upf3b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X90,876,197 - 90,894,205 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647910,093,290 - 10,111,752 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647910,093,290 - 10,111,293 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
UPF3B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX98,182,272 - 98,206,096 (-)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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Vero_WHO_p1.0NW_02366606532,620,407 - 32,638,733 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Upf3b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248953,762,087 - 3,781,662 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in UPF3B
45 total Variants

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 reproductive system respiratory system adipose tissue
High
Medium 11 6 8 6
Low 5 5 11 6 6 6 6 6 6 4 6
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_005641742 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038451466 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038451467 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038451468 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038524217 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038524218 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038524219 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038588187 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038588188 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038588189 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038652704 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038652705 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038652706 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_846750 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_859377 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AAEX04000146 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAHUQ010000394 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAQRD010000110 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAUVH010000051 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  REHQ01000039 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSCAFT00000029261   ⟹   ENSCAFP00000027209
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 EnsemblX91,836,727 - 91,851,640 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000049933   ⟹   ENSCAFP00000036938
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 EnsemblX91,836,727 - 91,851,640 (-)Ensembl
RefSeq Acc Id: XM_005641742   ⟹   XP_005641799
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1X91,835,845 - 91,851,755 (-)NCBI
Dog10K_Boxer_TashaX77,910,224 - 77,926,190 (-)NCBI
Sequence:
RefSeq Acc Id: XM_038524217   ⟹   XP_038380145
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1X91,027,322 - 91,043,284 (-)NCBI
RefSeq Acc Id: XM_038524218   ⟹   XP_038380146
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1X91,027,322 - 91,043,287 (-)NCBI
RefSeq Acc Id: XM_038524219   ⟹   XP_038380147
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1X91,027,322 - 91,043,276 (-)NCBI
RefSeq Acc Id: XM_038588187   ⟹   XP_038444115
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0X92,515,688 - 92,531,652 (-)NCBI
RefSeq Acc Id: XM_038588188   ⟹   XP_038444116
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0X92,515,688 - 92,531,655 (-)NCBI
RefSeq Acc Id: XM_038588189   ⟹   XP_038444117
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0X92,515,688 - 92,531,644 (-)NCBI
RefSeq Acc Id: XM_038652704   ⟹   XP_038508632
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0X92,787,502 - 92,803,457 (-)NCBI
RefSeq Acc Id: XM_038652705   ⟹   XP_038508633
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0X92,787,502 - 92,803,460 (-)NCBI
RefSeq Acc Id: XM_038652706   ⟹   XP_038508634
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0X92,787,502 - 92,803,448 (-)NCBI
RefSeq Acc Id: XM_846750   ⟹   XP_851843
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1X91,835,845 - 91,851,755 (-)NCBI
Dog10K_Boxer_TashaX77,910,224 - 77,926,187 (-)NCBI
Sequence:
RefSeq Acc Id: XM_859377   ⟹   XP_864470
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1X91,835,845 - 91,851,755 (-)NCBI
Dog10K_Boxer_TashaX77,910,224 - 77,926,179 (-)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: XP_864470   ⟸   XM_859377
- Peptide Label: isoform X15
- UniProtKB: A0A8C0SRA6 (UniProtKB/TrEMBL),   A0A8P0SRY6 (UniProtKB/TrEMBL),   A0A8C0JUD2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_005641799   ⟸   XM_005641742
- Peptide Label: isoform X14
- UniProtKB: A0A8C0JUD2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_851843   ⟸   XM_846750
- Peptide Label: isoform X13
- UniProtKB: A0A8C0SRB0 (UniProtKB/TrEMBL),   A0A8P0NJM4 (UniProtKB/TrEMBL),   A0A8C0JUD2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000027209   ⟸   ENSCAFT00000029261
RefSeq Acc Id: ENSCAFP00000036938   ⟸   ENSCAFT00000049933
RefSeq Acc Id: XP_038380146   ⟸   XM_038524218
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038380145   ⟸   XM_038524217
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038380147   ⟸   XM_038524219
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038508633   ⟸   XM_038652705
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038508632   ⟸   XM_038652704
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038508634   ⟸   XM_038652706
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038444116   ⟸   XM_038588188
- Peptide Label: isoform X11
- UniProtKB: A0A8C0JUD2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038444115   ⟸   XM_038588187
- Peptide Label: isoform X10
- UniProtKB: A0A8C0JUD2 (UniProtKB/TrEMBL),   A0A8C0SRB0 (UniProtKB/TrEMBL),   A0A8P0NJM4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038444117   ⟸   XM_038588189
- Peptide Label: isoform X12
- UniProtKB: A0A8C0JUD2 (UniProtKB/TrEMBL),   A0A8C0SRA6 (UniProtKB/TrEMBL),   A0A8P0SRY6 (UniProtKB/TrEMBL)
Protein Domains
UPF3

Promoters
RGD ID:13689416
Promoter ID:EPDNEW_C7484
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:
Dog AssemblyChrPosition (strand)Source
CanFam3.1X91,851,653 - 91,851,713EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000018426 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00040015219 UniProtKB/TrEMBL
  ENSCAFG00845025251 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000029261.5 UniProtKB/TrEMBL
  ENSCAFT00000049933.4 UniProtKB/TrEMBL
  ENSCAFT00040028000.1 UniProtKB/TrEMBL
  ENSCAFT00040028079.1 UniProtKB/TrEMBL
  ENSCAFT00845044533 ENTREZGENE
  ENSCAFT00845044533.1 UniProtKB/TrEMBL
  ENSCAFT00845044594 ENTREZGENE
  ENSCAFT00845044594.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.70.330 UniProtKB/TrEMBL
InterPro Nucleotide-bd_a/b_plait_sf UniProtKB/TrEMBL
  RBD_domain_sf UniProtKB/TrEMBL
  Upf3 UniProtKB/TrEMBL
  UPF3_dom UniProtKB/TrEMBL
  UPF3B_RRM-like UniProtKB/TrEMBL
NCBI Gene UPF3B ENTREZGENE
PANTHER PTHR13112 UniProtKB/TrEMBL
  REGULATOR OF NONSENSE TRANSCRIPTS 3B UniProtKB/TrEMBL
Pfam Smg4_UPF3 UniProtKB/TrEMBL
Superfamily-SCOP SSF54928 UniProtKB/TrEMBL
UniProt A0A8C0JUD2 ENTREZGENE
  A0A8C0SRA6 ENTREZGENE, UniProtKB/TrEMBL
  A0A8C0SRB0 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3PTW8 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3S570 ENTREZGENE, UniProtKB/TrEMBL
  A0A8P0NJM4 ENTREZGENE
  A0A8P0SRY6 ENTREZGENE
UniProt Secondary A0A8P0NJM4 UniProtKB/TrEMBL
  A0A8P0SRY6 UniProtKB/TrEMBL
VGNC ID VGNC:48153 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-01-30 UPF3B  UPF3B regulator of nonsense mediated mRNA decay    UPF3B, regulator of nonsense mediated mRNA decay  Symbol and/or name change 5135510 APPROVED
2017-05-23 UPF3B  UPF3B, regulator of nonsense mediated mRNA decay    UPF3 regulator of nonsense transcripts homolog B  Symbol and/or name change 5135510 APPROVED
2017-05-16 UPF3B  UPF3 regulator of nonsense transcripts homolog B    UPF3 regulator of nonsense transcripts homolog B (yeast)  Symbol and/or name change 5135510 APPROVED