Upf3a (UPF3A, regulator of nonsense mediated mRNA decay) - Rat Genome Database

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Gene: Upf3a (UPF3A, regulator of nonsense mediated mRNA decay) Rattus norvegicus
Analyze
Symbol: Upf3a
Name: UPF3A, regulator of nonsense mediated mRNA decay
RGD ID: 1308778
Description: Predicted to enable mRNA binding activity and telomeric DNA binding activity. Predicted to be involved in negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay and positive regulation of translation. Predicted to act upstream of or within positive regulation of mRNA cis splicing, via spliceosome and random inactivation of X chromosome. Predicted to be located in neuron projection. Predicted to be part of exon-exon junction complex. Predicted to be active in cytoplasm and nucleolus. Orthologous to human UPF3A (UPF3A regulator of nonsense mediated mRNA decay); PARTICIPATES IN mRNA decay pathway; RNA transport pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC361176; regulator of nonsense transcripts 3A; UPF3 regulator of nonsense transcripts homolog A; UPF3 regulator of nonsense transcripts homolog A (yeast)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81682,459,651 - 82,470,686 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1682,459,906 - 82,470,686 (-)EnsemblGRCr8
mRatBN7.21675,757,442 - 75,768,478 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1675,757,441 - 75,769,345 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1681,038,094 - 81,049,129 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01684,491,624 - 84,502,061 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01679,741,309 - 79,752,356 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01681,521,084 - 81,532,512 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1681,521,073 - 81,532,520 (+)Ensemblrn6Rnor6.0
Rnor_5.01681,009,176 - 81,020,604 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41680,612,505 - 80,623,540 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1673,566,324 - 73,577,359 (-)NCBICelera
RGSC_v3.11680,612,769 - 80,623,805 (-)NCBI
Cytogenetic Map16q12.5NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:16601204   PMID:17916692  


Genomics

Comparative Map Data
Upf3a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81682,459,651 - 82,470,686 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1682,459,906 - 82,470,686 (-)EnsemblGRCr8
mRatBN7.21675,757,442 - 75,768,478 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1675,757,441 - 75,769,345 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1681,038,094 - 81,049,129 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01684,491,624 - 84,502,061 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01679,741,309 - 79,752,356 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01681,521,084 - 81,532,512 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1681,521,073 - 81,532,520 (+)Ensemblrn6Rnor6.0
Rnor_5.01681,009,176 - 81,020,604 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41680,612,505 - 80,623,540 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1673,566,324 - 73,577,359 (-)NCBICelera
RGSC_v3.11680,612,769 - 80,623,805 (-)NCBI
Cytogenetic Map16q12.5NCBI
UPF3A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3813114,281,601 - 114,305,817 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl13114,281,568 - 114,305,817 (+)Ensemblhg38GRCh38
GRCh3713115,047,076 - 115,071,292 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3613114,065,180 - 114,089,385 (+)NCBIBuild 36Build 36hg18NCBI36
Build 3413114,065,179 - 114,089,383NCBI
Celera1395,719,450 - 95,743,911 (+)NCBICelera
Cytogenetic Map13q34NCBI
HuRef1395,309,726 - 95,333,660 (+)NCBIHuRef
CHM1_113115,015,732 - 115,039,962 (+)NCBICHM1_1
T2T-CHM13v2.013113,490,661 - 113,514,877 (+)NCBIT2T-CHM13v2.0
Upf3a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39813,834,636 - 13,848,723 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl813,835,615 - 13,849,193 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38813,785,055 - 13,798,723 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl813,785,615 - 13,799,193 (+)Ensemblmm10GRCm38
MGSCv37813,785,615 - 13,798,538 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36813,785,609 - 13,799,165 (+)NCBIMGSCv36mm8
Celera813,951,656 - 13,964,579 (+)NCBICelera
Cytogenetic Map8A1.1NCBI
cM Map86.38NCBI
Upf3a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495540425,556 - 36,730 (-)NCBIChiLan1.0ChiLan1.0
UPF3A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v214115,777,762 - 115,802,131 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan113114,458,047 - 114,482,606 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01395,349,449 - 95,373,984 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.113114,416,454 - 114,439,586 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl13114,415,784 - 114,438,692 (+)EnsemblpanPan2panpan1.1
UPF3A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12261,320,575 - 61,373,082 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2261,320,451 - 61,345,839 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2261,032,216 - 61,084,507 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02262,007,564 - 62,059,865 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2262,008,456 - 62,032,911 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12261,445,161 - 61,478,456 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02261,453,315 - 61,503,788 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02261,480,547 - 61,514,061 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Upf3a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945196,196,490 - 196,210,608 (+)NCBIHiC_Itri_2
SpeTri2.0NW_004937030243,104 - 258,355 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
UPF3A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1179,118,603 - 79,136,222 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11179,117,708 - 79,137,083 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
UPF3A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1392,066,229 - 92,089,868 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl392,066,248 - 92,088,976 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604649,360,990 - 49,384,490 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Upf3a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624793136,642 - 151,692 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_004624793134,607 - 151,730 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Upf3a
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11369,928,008 - 69,938,548 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Upf3a
51 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:39
Count of miRNA genes:36
Interacting mature miRNAs:38
Transcripts:ENSRNOT00000066521
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)164445512389455123Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165942871491442908Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)164199206486992064Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)164445512389455123Rat
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165942871491442908Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165942871491442908Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164909919691442908Rat

Markers in Region
BE099587  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21675,767,257 - 75,767,416 (-)MAPPERmRatBN7.2
Rnor_6.01681,522,146 - 81,522,304NCBIRnor6.0
Rnor_5.01681,010,238 - 81,010,396UniSTSRnor5.0
RGSC_v3.41680,622,320 - 80,622,478UniSTSRGSC3.4
Celera1673,576,139 - 73,576,297UniSTS
RH 3.4 Map16744.4UniSTS
Cytogenetic Map16q12.5UniSTS
RH136670  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21675,757,503 - 75,757,719 (-)MAPPERmRatBN7.2
Rnor_6.01681,532,235 - 81,532,450NCBIRnor6.0
Rnor_5.01681,020,327 - 81,020,542UniSTSRnor5.0
RGSC_v3.41680,612,567 - 80,612,782UniSTSRGSC3.4
Celera1673,566,386 - 73,566,601UniSTS
RH 3.4 Map16742.6UniSTS
Cytogenetic Map16q12.5UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 164 91 90 59 92 59 6 356 192 11 143 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000066521   ⟹   ENSRNOP00000060194
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1682,459,906 - 82,470,686 (-)Ensembl
mRatBN7.2 Ensembl1675,757,441 - 75,769,345 (-)Ensembl
Rnor_6.0 Ensembl1681,521,073 - 81,532,520 (+)Ensembl
RefSeq Acc Id: NM_001012159   ⟹   NP_001012159
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81682,459,651 - 82,470,686 (-)NCBI
mRatBN7.21675,757,442 - 75,768,478 (-)NCBI
Rnor_6.01681,521,084 - 81,532,512 (+)NCBI
Rnor_5.01681,009,176 - 81,020,604 (+)NCBI
RGSC_v3.41680,612,505 - 80,623,540 (-)RGD
Celera1673,566,324 - 73,577,359 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001012159 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH88463 (Get FASTA)   NCBI Sequence Viewer  
  EDM08913 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000060194
  ENSRNOP00000060194.3
RefSeq Acc Id: NP_001012159   ⟸   NM_001012159
- UniProtKB: Q5I0C8 (UniProtKB/TrEMBL),   F7F115 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000060194   ⟸   ENSRNOT00000066521
Protein Domains
UPF3

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5I0C8-F1-model_v2 AlphaFold Q5I0C8 1-405 view protein structure

Transcriptome

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

Promoters
RGD ID:13700228
Promoter ID:EPDNEW_R10752
Type:multiple initiation site
Name:Upf3a_1
Description:UPF3A, 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_6.01681,521,077 - 81,521,137EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308778 AgrOrtholog
BioCyc Gene G2FUF-10736 BioCyc
Ensembl Genes ENSRNOG00000017397 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000066521 ENTREZGENE
  ENSRNOT00000066521.5 UniProtKB/TrEMBL
Gene3D-CATH 3.30.70.330 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7127783 IMAGE-MGC_LOAD
InterPro Nonsense_mediated_decay_UPF3 UniProtKB/TrEMBL
  Nucleotide-bd_a/b_plait_sf UniProtKB/TrEMBL
  RBD_domain_sf UniProtKB/TrEMBL
  Upf3 UniProtKB/TrEMBL
KEGG Report rno:361176 UniProtKB/TrEMBL
MGC_CLONE MGC:95118 IMAGE-MGC_LOAD
NCBI Gene 361176 ENTREZGENE
PANTHER PTHR13112 UniProtKB/TrEMBL
  PTHR13112:SF2 UniProtKB/TrEMBL
Pfam Smg4_UPF3 UniProtKB/TrEMBL
PhenoGen Upf3a PhenoGen
RatGTEx ENSRNOG00000017397 RatGTEx
Superfamily-SCOP SSF54928 UniProtKB/TrEMBL
UniProt F7F115 ENTREZGENE, UniProtKB/TrEMBL
  Q5I0C8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-05-24 Upf3a  UPF3A, regulator of nonsense mediated mRNA decay  Upf3a  UPF3 regulator of nonsense transcripts homolog A (yeast)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Upf3a  UPF3 regulator of nonsense transcripts homolog A (yeast)  Upf3a_predicted  UPF3 regulator of nonsense transcripts homolog A (yeast) (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Upf3a_predicted  UPF3 regulator of nonsense transcripts homolog A (yeast) (predicted)      Symbol and Name status set to approved 70820 APPROVED