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

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Gene: UPF3A (UPF3A regulator of nonsense mediated mRNA decay) Pan paniscus
Analyze
Symbol: UPF3A
Name: UPF3A regulator of nonsense mediated mRNA decay
RGD ID: 11752104
Description: ENCODES a protein that exhibits mRNA binding (inferred); nucleic acid binding (inferred); telomeric DNA binding (inferred); INVOLVED IN in utero embryonic development (ortholog); nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (ortholog); positive regulation of mRNA cis splicing, via spliceosome (ortholog); ASSOCIATED WITH factor X deficiency (ortholog); genetic disease (ortholog); FOUND IN cytoplasm (inferred); cytosol (inferred); exon-exon junction complex (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: regulator of nonsense transcripts 3A; UPF3 regulator of nonsense transcripts homolog A; UPF3 regulator of nonsense transcripts homolog A (yeast); UPF3A, regulator of nonsense mediated mRNA decay
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Mhudiblu_PPA_v0 - Bonobo Mhudiblu_PPA_v0 Assembly
Position:
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 (+)Ensemblpanpan1.1panPan2
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

References
Additional References at PubMed
PMID:30032202  


Genomics

Comparative Map Data
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 (+)Ensemblpanpan1.1panPan2
UPF3A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3813114,281,601 - 114,305,817 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl13114,281,601 - 114,305,817 (+)EnsemblGRCh38hg38GRCh38
GRCh3713115,047,076 - 115,071,292 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3613114,065,180 - 114,089,385 (+)NCBINCBI36Build 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 Ensembl
GRCm38813,785,055 - 13,798,723 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl813,785,615 - 13,799,193 (+)EnsemblGRCm38mm10GRCm38
MGSCv37813,785,615 - 13,798,538 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36813,785,609 - 13,799,165 (+)NCBIMGSCv36mm8
Celera813,951,656 - 13,964,579 (+)NCBICelera
Cytogenetic Map8A1.1NCBI
cM Map86.38NCBI
Upf3a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81682,459,651 - 82,470,686 (-)NCBIGRCr8
mRatBN7.21675,757,442 - 75,768,478 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1675,757,441 - 75,769,345 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1681,038,094 - 81,049,129 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01684,491,624 - 84,502,061 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01679,741,309 - 79,752,356 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01681,521,084 - 81,532,512 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1681,521,073 - 81,532,520 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01681,009,176 - 81,020,604 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41680,612,505 - 80,623,540 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11680,612,769 - 80,623,805 (-)NCBI
Celera1673,566,324 - 73,577,359 (-)NCBICelera
Cytogenetic Map16q12.5NCBI
Upf3a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495540425,556 - 36,730 (-)NCBIChiLan1.0ChiLan1.0
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 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2261,032,216 - 61,084,507 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02262,007,564 - 62,059,865 (+)NCBIROS_Cfam_1.0
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_1.0
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 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624793134,607 - 151,730 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts XM_024925275 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_024925276 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_034937095 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_034937096 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_034937100 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_034937101 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_034937104 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_055097075 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_055097077 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_055097078 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_055097079 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063595999 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063596000 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_003025561 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_004666043 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_004666044 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_004666045 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JARIFH020000014 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSPPAT00000062013   ⟹   ENSPPAP00000039104
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
PanPan1.1 Ensembl13114,415,784 - 114,438,692 (+)Ensembl
RefSeq Acc Id: XM_024925275   ⟹   XP_024781043
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v214115,777,762 - 115,802,131 (+)NCBI
NHGRI_mPanPan113114,458,204 - 114,482,606 (+)NCBI
Mhudiblu_PPA_v01395,349,601 - 95,373,984 (+)NCBI
PanPan1.113114,416,454 - 114,439,586 (+)NCBI
Sequence:
RefSeq Acc Id: XM_034937095   ⟹   XP_034792986
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v214115,777,762 - 115,795,219 (+)NCBI
NHGRI_mPanPan113114,458,068 - 114,475,692 (+)NCBI
Mhudiblu_PPA_v01395,349,471 - 95,360,883 (+)NCBI
RefSeq Acc Id: XM_034937096   ⟹   XP_034792987
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v214115,777,762 - 115,802,131 (+)NCBI
NHGRI_mPanPan113114,458,209 - 114,482,606 (+)NCBI
Mhudiblu_PPA_v01395,349,601 - 95,373,984 (+)NCBI
RefSeq Acc Id: XM_034937100   ⟹   XP_034792991
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v214115,777,762 - 115,798,255 (+)NCBI
NHGRI_mPanPan113114,458,203 - 114,478,728 (+)NCBI
Mhudiblu_PPA_v01395,349,595 - 95,369,932 (+)NCBI
RefSeq Acc Id: XM_034937101   ⟹   XP_034792992
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v214115,777,767 - 115,795,219 (+)NCBI
NHGRI_mPanPan113114,458,204 - 114,475,692 (+)NCBI
Mhudiblu_PPA_v01395,349,595 - 95,367,069 (+)NCBI
RefSeq Acc Id: XM_034937104   ⟹   XP_034792995
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v214115,777,772 - 115,785,931 (+)NCBI
NHGRI_mPanPan113114,458,047 - 114,466,231 (+)NCBI
Mhudiblu_PPA_v01395,349,449 - 95,355,715 (+)NCBI
RefSeq Acc Id: XM_055097075   ⟹   XP_054953050
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v214115,777,763 - 115,785,931 (+)NCBI
NHGRI_mPanPan113114,458,084 - 114,466,231 (+)NCBI
RefSeq Acc Id: XM_055097077   ⟹   XP_054953052
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v214115,777,767 - 115,798,255 (+)NCBI
NHGRI_mPanPan113114,458,203 - 114,478,728 (+)NCBI
RefSeq Acc Id: XM_055097078   ⟹   XP_054953053
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v214115,777,767 - 115,798,255 (+)NCBI
NHGRI_mPanPan113114,458,203 - 114,478,728 (+)NCBI
RefSeq Acc Id: XM_055097079   ⟹   XP_054953054
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v214115,777,767 - 115,788,202 (+)NCBI
NHGRI_mPanPan113114,458,194 - 114,468,502 (+)NCBI
RefSeq Acc Id: XM_063595999   ⟹   XP_063452069
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v214115,777,762 - 115,795,219 (+)NCBI
RefSeq Acc Id: XM_063596000   ⟹   XP_063452070
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v214115,779,236 - 115,795,219 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: XP_024781043   ⟸   XM_024925275
- Peptide Label: isoform X3
- UniProtKB: A0A2R9CB47 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_034792995   ⟸   XM_034937104
- Peptide Label: isoform X9
RefSeq Acc Id: XP_034792986   ⟸   XM_034937095
- Peptide Label: isoform X1
RefSeq Acc Id: XP_034792991   ⟸   XM_034937100
- Peptide Label: isoform X6
RefSeq Acc Id: XP_034792992   ⟸   XM_034937101
- Peptide Label: isoform X8
RefSeq Acc Id: XP_034792987   ⟸   XM_034937096
- Peptide Label: isoform X4
- UniProtKB: A0A2R9CB47 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSPPAP00000039104   ⟸   ENSPPAT00000062013
RefSeq Acc Id: XP_054953050   ⟸   XM_055097075
- Peptide Label: isoform X7
RefSeq Acc Id: XP_054953054   ⟸   XM_055097079
- Peptide Label: isoform X11
RefSeq Acc Id: XP_054953052   ⟸   XM_055097077
- Peptide Label: isoform X8
RefSeq Acc Id: XP_054953053   ⟸   XM_055097078
- Peptide Label: isoform X10
RefSeq Acc Id: XP_063452069   ⟸   XM_063595999
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063452070   ⟸   XM_063596000
- Peptide Label: isoform X5
Protein Domains
UPF3


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSPPAG00000042267 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSPPAT00000062013.1 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
NCBI Gene UPF3A ENTREZGENE
PANTHER PTHR13112 UniProtKB/TrEMBL
  PTHR13112:SF2 UniProtKB/TrEMBL
Pfam Smg4_UPF3 UniProtKB/TrEMBL
Superfamily-SCOP SSF54928 UniProtKB/TrEMBL
UniProt A0A2R9CB47 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-01-29 UPF3A  UPF3A regulator of nonsense mediated mRNA decay    UPF3A, regulator of nonsense mediated mRNA decay  Symbol and/or name change 5135510 APPROVED
2017-05-23 UPF3A  UPF3A, regulator of nonsense mediated mRNA decay    UPF3 regulator of nonsense transcripts homolog A (yeast)  Symbol and/or name change 5135510 APPROVED