upf2 (SPAC19A8.08)


Gene Standard Nameupf2 Characterisation Statuspublished
Systematic IDSPAC19A8.08 Feature Typeprotein coding
Synonyms Name Description
Productnonsense-mediated decay protein Upf2 Product Size1049aa, 122.10 kDa
Genomic Location Chromosome I, 2472061-2468576 (3486nt); CDS:2471943-2468794 (3150nt)

Ensembl Gene Location
GO Molecular Function
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0003723RNA bindingIEAIPR003890GO_REF:0000002627
GO Biological Process
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0000184nuclear-transcribed mRNA catabolic process, nonsense-mediated decay25
requiredIMPPMID:11073994
GO Cellular Component
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0005737cytoplasmISOSGD:S000001119GO_REF:00000244198
GO:0005829cytosolIDAPMID:168233722317
Fission Yeast Phenotype Ontology

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002060viable vegetative cell populationMicroscopyupf2ΔNullPECO:0000005, PECO:0000137PMID:236978063755
Microscopyupf2ΔNullPMID:20473289

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002177viable vegetative cell with normal cell morphologyMicroscopyupf2ΔNullPECO:0000005, PECO:0000137PMID:236978063078
penetrance FYPO_EXT:0000001
Transcript
Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
124720612468576

UTRs

Region Start End Reference
five_prime_UTR24720612471944PMID:21511999
Protein Features

Graphical View

Ensembl protein image with mapped locations of structural domains

Protein Families and Domains

Feature ID Database InterPro Description Start End Count
PF02854 Pfam IPR003890 MIF4G-like, type 3 41 292 5
PF02854 Pfam IPR003890 MIF4G-like, type 3 456 633 5
PF02854 Pfam IPR003890 MIF4G-like, type 3 653 852 5
PF04050 Pfam IPR007193 Up-frameshift suppressor 2 876 1047 1
SM00543 SMART IPR003890 MIF4G-like, type 3 446 634 5
SM00543 SMART IPR003890 MIF4G-like, type 3 649 855 5
SM00543 SMART IPR003890 MIF4G-like, type 3 41 282 5
PTHR12839 HMMPANTHER 4 1049 1
PTHR12839:SF7 HMMPANTHER 4 1049 1
G3DSA:1.25.40.180 Gene3D IPR016021 908 919 7
G3DSA:1.25.40.180 Gene3D IPR016021 445 634 7
G3DSA:1.25.40.180 Gene3D IPR016021 648 869 7
SSF48371 SuperFamily IPR016024 444 634 130
SSF48371 SuperFamily IPR016024 648 883 130
Coil ncoils Rabaptin coiled-coil domain 859 880 975
Coil ncoils Rabaptin coiled-coil domain 929 957 975
Low complexity (SEG) seg 908 937
Low complexity (SEG) seg 696 708

View domain organization at Pfam

Protein Properties

Ave. residue weight 116.39 Da
Charge -18.00
Isoelectric point 5.22
Molecular weight 122.10 kDa
Number of residues 1049
Sequence
Gene Expression

Quantitative Gene Expression

Protein Level

Molecules/Cell (average)DuringConditionScaleEvidenceReference
1249.34during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
NDduring cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)DuringConditionScaleEvidenceReference
2during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
0.78during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633
Species Distribution
DescriptionQualifierReferenceCount
predominantly single copy (one to one)3080
conserved in fungi4564
conserved in eukaryotes4482
conserved in metazoa3419
conserved in vertebrates3394
conserved in eukaryotes only2485
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


External References
Database Identifier Description
NBRP SPAC19A8.08 Fission yeast strain database, National BioResource Project (Japan)
YOGY SPAC19A8.08 Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPAC19A8.08 BioGRID Interaction Datasets
Expression Viewer SPAC19A8.08 Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPAC19A8.08 Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPAC19A8.08 Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPAC19A8.08 Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPAC19A8.08 Polyadenylation Viewer (Gullerova lab)
pombeTV SPAC19A8.08 Transcriptome Viewer (Bähler Lab)
Cyclebase SPAC19A8.08 Cell Cycle Data
GEO SPAC19A8.08 GEO profiles
PInt SPAC19A8.08 Protein-Protein Interaction Predictor (Bähler Lab)
WikiGene2542147nonsense-mediated decay protein Upf2
EntrezGene2542147nonsense-mediated decay protein Upf2
SPD / RIKEN30/30B05Orfeome Localization Data
UniProtKB/SwissProtO13824Nonsense-mediated mRNA decay protein 2
ModBaseO13824Database of comparative protein structure models
StringO13824Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_593784nonsense-mediated decay protein Upf2
RefSeq mRNANM_001019213972h- nonsense-mediated decay protein Upf2 (upf2), mRNA
European Nucleotide ArchiveAAG33226ENA Protein Mapping
European Nucleotide ArchiveCAB11644ENA Protein Mapping
UniParcUPI0000130269UniProt Archive

Literature for upf2

Search: Europe PMC or PubMed

Release Version: PomBase:21_41 - 24 Feb 2014