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Upf3a Gene Detail
Summary
  • Symbol
    Upf3a
  • Name
    UPF3 regulator of nonsense transcripts homolog A (yeast)
  • Synonyms
    2600001C03Rik, 4930546M19Rik, RENT3A, UPF3
  • Feature Type
    protein coding gene
  • IDs
    MGI:1914281
    NCBI Gene: 67031
  • Gene Overview
    MyGene.info: UPF3A
  • Alliance
  • Transcription Start Sites
    1 TSS
Location &
Maps
more
  • Sequence Map
    Chr8:13785233-13798538 bp, + strand
  • From NCBI annotation of GRCm38

    View this region in JBrowse

  • Genome Browsers
  • Genetic Map
    Chromosome 8, 6.38 cM, cytoband A2
  • Mapping Data
    2 experiments
Strain
Comparison
more
  • SNPs within 2kb
    224 from dbSNP Build 142
  • Strain Annotations
    18
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_1914281
protein coding gene Chr8:13785233-13799193 (.)
129S1/SvImJ MGP_129S1SvImJ_G0033387
protein coding gene Chr8:11152846-11166670 (+)
A/J MGP_AJ_G0033367
protein coding gene Chr8:10741346-10754075 (+)
AKR/J MGP_AKRJ_G0033298
protein coding gene Chr8:11027211-11039955 (+)
BALB/cJ MGP_BALBcJ_G0033368
protein coding gene Chr8:10871156-10883901 (+)
C3H/HeJ MGP_C3HHeJ_G0033081
protein coding gene Chr8:11249158-11261888 (+)
C57BL/6NJ MGP_C57BL6NJ_G0033880
protein coding gene Chr8:11518882-11531624 (+)
CAROLI/EiJ MGP_CAROLIEiJ_G0030848
protein coding gene Chr8:10238548-10251710 (+)
CAST/EiJ MGP_CASTEiJ_G0032403
protein coding gene Chr8:11016830-11030337 (+)
CBA/J MGP_CBAJ_G0033054
protein coding gene Chr8:12022255-12035532 (+)
DBA/2J MGP_DBA2J_G0033207
protein coding gene Chr8:10685582-10698929 (+)
FVB/NJ MGP_FVBNJ_G0033156
protein coding gene Chr8:10705883-10718565 (+)
LP/J MGP_LPJ_G0033301
protein coding gene Chr8:11076841-11091445 (+)
NOD/ShiLtJ MGP_NODShiLtJ_G0033190
protein coding gene Chr8:12238132-12250973 (+)
NZO/HlLtJ MGP_NZOHlLtJ_G0033897
protein coding gene Chr8:11101493-11114236 (+)
PWK/PhJ MGP_PWKPhJ_G0032116
protein coding gene Chr8:10745277-10759271 (+)
SPRET/EiJ MGP_SPRETEiJ_G0031958
protein coding gene Chr8:10988750-11001902 (+)
WSB/EiJ MGP_WSBEiJ_G0032519
protein coding gene Chr8:11123968-11136858 (+)



Homology
more
  • Human Ortholog
    UPF3A, UPF3A, regulator of nonsense mediated mRNA decay
  • Vertebrate Orthologs
    9
  • Human Ortholog
    UPF3A, UPF3A, regulator of nonsense mediated mRNA decay
    Orthology source: HomoloGene, HGNC
  • Synonyms
    HUPF3A, RENT3A, UPF3
  • Links
    NCBI Gene ID: 65110
    neXtProt AC: NX_Q9H1J1
    UniProt: Q9H1J1

  • Chr Location
    13q34; chr13:114281584-114305817 (+)  GRCh38.p7

Mutations,
Alleles, and
Phenotypes
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  • Phenotype Summary
    14 phenotypes from 2 alleles in 3 genetic backgrounds
    2 phenotype references
Phenotype Overview

adipose tissue
behavior/neurological
cardiovascular system
cellular
craniofacial
digestive/alimentary system
embryo
endocrine/exocrine glands
growth/size/body
hearing/vestibular/ear
hematopoietic system
homeostasis/metabolism
immune system
integument
limbs/digits/tail
liver/biliary system
mortality/aging
muscle
neoplasm
nervous system
pigmentation
renal/urinary system
reproductive system
respiratory system
skeleton
taste/olfaction
vision/eye

Click cells to view annotations.
The gene product protects against mRNA transcript degradation. Homozygous constitutive KO is embryonic lethal. Homozygous conditional KO in testes leads to reduced male fertility.
Gene Ontology
(GO)
Classifications
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  • All GO Annotations
  • GO References
Molecular Function

carbohydrate derivative binding
cytoskeletal protein binding
DNA binding
enzyme regulator
hydrolase
ligase
lipid binding
oxidoreductase
RNA binding
signaling receptor activity
signaling receptor binding
transcription
transferase
transporter
Biological Process

carbohydrate derivative metabolism
cell death
cell differentiation
cell proliferation
cellular component organization
establishment of localization
homeostatic process
immune system process
lipid metabolic process
nucleic acid-templated transcription
protein metabolic process
response to stimulus
signaling
system development
Cellular Component

cell projection
cytoplasmic vesicle
cytoskeleton
cytosol
endoplasmic reticulum
endosome
extracellular region
Golgi apparatus
mitochondrion
non-membrane-bounded organelle
nucleus
organelle envelope
organelle lumen
plasma membrane
synapse
vacuole
Click cells to view annotations.
Expression
less
Expression Overview

early conceptus
embryo ectoderm
embryo endoderm
embryo mesoderm
embryo mesenchyme
extraembryonic component
alimentary system
auditory system
branchial arches
cardiovascular system
connective tissue
endocrine system
exocrine system
hemolymphoid system
integumental system
limbs
liver and biliary system
musculoskeletal system
nervous system
olfactory system
reproductive system
respiratory system
urinary system
visual system
Click cells to view annotations.


  • Assay Results
  • Tissues
  • cDNA Data
  • Literature Summary
  • Comparison Matrix
  • Interactions
    less
    Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic 67031 NCBI Gene Model | MGI Sequence Detail 13306 C57BL/6J ±  kb
    transcript NM_025924 RefSeq | MGI Sequence Detail 1402 Not Specified  
    polypeptide NP_080200 RefSeq | MGI Sequence Detail 422 Not Specified  
    For the selected sequence
    Protein
    Information
    less
    • UniProt
      3 Sequences
    • InterPro Domains
      IPR012677 Nucleotide-binding alpha-beta plait domain superfamily
      IPR034978 Regulator of nonsense transcripts 3A
      IPR035979 RNA-binding domain superfamily
      IPR005120 UPF3 domain
    Molecular
    Reagents
    less
    • All nucleic 48
      cDNA 45
      Primer pair 3

      Microarray probesets 4
    Other
    Accession IDs
    less
    MGI:1922480
    References
    more
    • Summaries
      All 27
      Developmental Gene Expression 2
      Gene Ontology 4
      Phenotypes 2
    • Earliest
      J:65060 Kawai J, et al., Functional annotation of a full-length mouse cDNA collection. Nature. 2001 Feb 8;409(6821):685-90
    • Latest
      J:234504 Shum EY, et al., The Antagonistic Gene Paralogs Upf3a and Upf3b Govern Nonsense-Mediated RNA Decay. Cell. 2016 Apr 7;165(2):382-95

    Contributing Projects:
    Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Tumor Biology (MTB), Gene Ontology (GO), MouseCyc
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    last database update
    11/13/2018
    MGI 6.13
    The Jackson Laboratory