tri1 (SPBC29A10.09c)


Gene Standard Nametri1 Characterisation Statuspublished
Systematic IDSPBC29A10.09c Feature Typeprotein coding
Synonyms Name Description
Producttriman, ribonuclease involved in priRNA formation Tri1 Product Size427aa, 49.01 kDa
Genomic Location Chromosome II, 2557200-2554177 (3024nt); CDS:2556947-2555664 (1284nt)

Ensembl Gene Location
GO Molecular Function
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:00001753'-5'-exoribonuclease activity16
has substrate regional_centromere_outer_repeat_transcriptIDAPMID:24095277
activated by magnesium(2+)IDAPMID:24095277
has substrate polyadenylated_mRNAIDAPMID:24095277
GO:0003723RNA bindingICGO:0004540, GO:0003676GO_REF:0000001648
GO Biological Process
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0090503RNA phosphodiester bond hydrolysis, exonucleolyticIDAPMID:2409527721
GO:0070924heterochromatin assembly involved in chromatin silencing by small RNAIMPPMID:240952772
GO:0043628ncRNA 3'-end processingIMPPMID:2409527730
GO Cellular Component
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0005634nucleusIEAIPR006941GO_REF:00000022737
Fission Yeast Phenotype Ontology

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002060viable vegetative cell populationMicroscopytri1ΔNullPECO:0000005, PECO:0000137PMID:236978063751
Microscopytri1ΔNullPMID:20473289

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0003098abnormal heterochromatin assembly at centromere outer repeatCell growth assaytri1ΔNullPMID:240952771
FYPO:0002064abolished 3'-5'-exoribonuclease activityEnzyme assay dataD28A (D28A)Not specifiedPMID:240952773
FYPO:0002134decreased RNA binding9
affecting ago1Gel electrophoresis evidencetri1ΔNullPMID:24095277
FYPO:0003094decreased centromeric outer repeat transcript levelTranscript expression level evidencetri1ΔNullPMID:240952778
FYPO:0003101decreased heterochromatin assembly at protein coding gene2
affecting mcp5Chromatin immunoprecipitation experimenttri1ΔNullPMID:24095277
affecting SPAC8C9.04Chromatin immunoprecipitation experimenttri1ΔNullPMID:24095277
FYPO:0003096decreased histone H3-K9 methylation at centromere outer repeatChromatin immunoprecipitation experimenttri1ΔNullPMID:240952777
FYPO:0003103decreased mRNA-derived small RNA level1
affecting SPAC8C9.04Transcript expression level evidencetri1ΔNullPMID:24095277
affecting mcp5Transcript expression level evidencetri1ΔNullPMID:24095277
FYPO:0003093increased Argonaute-associated RNA lengthGel electrophoresis evidencetri1ΔNullPMID:240952771
FYPO:0003100normal heterochromatin assembly at protein coding gene1
affecting mei4Chromatin immunoprecipitation experimenttri1ΔNullPMID:24095277
FYPO:0002177viable vegetative cell with normal cell morphology3088
penetrance FYPO_EXT:0000001Microscopytri1ΔNullPECO:0000005, PECO:0000137PMID:23697806
Transcript
Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
125572002554177
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
PF04857 Pfam IPR006941 Ribonuclease CAF1 1 396 2
PTHR15092 HMMPANTHER 1 416 1
PTHR15092:SF9 HMMPANTHER 1 416 1
3.30.420.10 Gene3D 257 407 32
3.30.420.10 Gene3D 2 128 32
SSF53098 SuperFamily IPR012337 Ribonuclease H-like domain 259 350 34
SSF53098 SuperFamily IPR012337 Ribonuclease H-like domain 378 410 34
SSF53098 SuperFamily IPR012337 Ribonuclease H-like domain 1 130 34

View domain organization at Pfam

Protein Properties

Ave. residue weight 114.77 Da
Charge 8.50
Isoelectric point 8.14
Molecular weight 49.01 kDa
Number of residues 427
Sequence
Gene Expression

Quantitative Gene Expression

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
NDduring 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)ExtensionConditionScaleEvidenceReference
0.19during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
0.18during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633
Species Distribution
DescriptionQualifierReferenceCount
no apparent S. cerevisiae ortholog601
predominantly single copy (one to one)3092
conserved in fungi4599
conserved in eukaryotes4514
conserved in metazoa3428
conserved in vertebrates3402
conserved in eukaryotes only2498
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Genetic Interactions

Source: BioGRID

Gene Product Evidence Reference
rrp6exosome 3'-5' exoribonuclease subunit Rrp6 (predicted) Phenotypic SuppressionPMID:24095277
vph2endoplasmic reticulum membrane protein involved in assembly of the V-ATPase (predicted) Positive GeneticPMID:22681890
swd3WD repeat protein Swd3 Negative GeneticPMID:22681890
dcr1dicer Phenotypic EnhancementPMID:24095277
Phenotypic Suppression
hrr1Helicase Required for RNAi-mediated heterochromatin assembly Hrr1 Negative GeneticPMID:22681890
Physical Interactions

Source: BioGRID

Gene Product Evidence Reference
ago1argonaute Affinity Capture-MSPMID:24095277
Reconstituted Complex
External References
Database Identifier Description
NBRP SPBC29A10.09c Fission yeast strain database, National BioResource Project (Japan)
YOGY SPBC29A10.09c Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPBC29A10.09c BioGRID Interaction Datasets
Expression Viewer SPBC29A10.09c Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPBC29A10.09c Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPBC29A10.09c Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPBC29A10.09c Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPBC29A10.09c Polyadenylation Viewer (Gullerova lab)
pombeTV SPBC29A10.09c Transcriptome Viewer (Bähler Lab)
Cyclebase SPBC29A10.09c Cell Cycle Data
GEO SPBC29A10.09c GEO profiles
PInt SPBC29A10.09c Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPBC29A10.09c Peptides identified in tandem mass spectrometry proteomics experiments
SPD / RIKEN51/51D05Orfeome Localization Data
UniProtKB/SwissProtO94386Uncharacterized protein C29A10.09c
ModBaseO94386Database of comparative protein structure models
STRINGO94386Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_596054CAF1 family ribonuclease (predicted)
RefSeq mRNANM_001021965972h- CAF1 family ribonuclease (predicted) (SPBC29A10.09c), mRNA
European Nucleotide ArchiveCAA22437.1ENA Protein Mapping
UniParcUPI000006A184UniProt Archive

Literature for tri1

Search: Europe PMC or PubMed

Release Version: PomBase:23_46 - 30 Aug 2014