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protein coding gene - ysh1 (SPAC17G6.16c) - mRNA cleavage and polyadenylation specificity factor complex endoribonuclease subunit Ysh1

Gene summary

Standard name
ysh1
Systematic ID
SPAC17G6.16c
Product
mRNA cleavage and polyadenylation specificity factor complex endoribonuclease subunit Ysh1
Organism
Schizosaccharomyces pombe (fission yeast)
UniProt ID
O13794
ORFeome ID
47/47A07
Characterisation status
biological role published
Feature type
mRNA gene
Genomic location
chromosome I: 3620761..3623710 reverse strand

Annotation

Disease association

MONDO:0859250 - neurodevelopmental disorder with microcephaly, hypotonia, nystagmus, and seizures

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GO biological process

GO:0180010 - co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway

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GO cellular component

GO:0005829 - cytosol

References:

GO:0005847 - mRNA cleavage and polyadenylation specificity factor complex

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GO:0005634 - nucleus

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GO molecular function

GO:0004534 - 5'-3' RNA exonuclease activity

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GO:0003723 - RNA binding

References:

GO:0004521 - RNA endonuclease activity

References:

Modification

MOD:00046 - O-phospho-L-serine

References:

MOD:01149 - sumoylated lysine

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MOD:01148 - ubiquitinylated lysine

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Qualitative gene expression

PomGeneEx:0000027 - ribosomal density decreased

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Quantitative gene expression

PBO:0006310 - protein level

References:

PBO:0011963 - RNA level

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Single locus phenotype

FYPO:0003412 - decreased chromatin silencing at centromere outer repeat

References:

Genotypes:

FYPO:0000313 - inviable after spore germination, without cell division, with abnormal germ tube morphology

References:

Genotypes:

FYPO:0002151 - inviable spore

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Genotypes:

FYPO:0002061 - inviable vegetative cell population

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Genotypes:

Taxonomic conservation

PBO:0011065 - conserved in eukaryotes

PBO:0011071 - conserved in eukaryotes only

PBO:0011064 - conserved in fungi

PBO:0011069 - conserved in metazoa

PBO:0011070 - conserved in vertebrates

PBO:0006222 - predominantly single copy (one to one)

Warnings

PBO:0000070 - gene structure updated

References:

Protein features

IDNameInterPro nameDB name
PF07521RMMBLRMMBLPFAM
PF11718CPSF73-100_CCPSF73-100_CPFAM
PF16661Lactamase_B_6Metallo-B-lactamasPFAM
PF10996Beta-CaspBeta_CaspPFAM
cd16292CPSF3-like_MBL-foldCDD
SM01027Beta_Casp_2Beta_CaspSMART
SM01098CPSF73_100_C_2CPSF73-100_CSMART
SM00849Lactamase_B_5aMetallo-B-lactamasSMART
G3DSA:3.60.15.10:FF:000001FUNFAM
G3DSA:3.40.50.10890:FF:000001FUNFAM
SSF56281Metallo-hydrolase/oxidoreductaseRibonucZ/Hydroxyglut_hydroSUPERFAMILY
G3DSA:3.40.50.10890GENE3D
G3DSA:3.60.15.10RibonucZ/Hydroxyglut_hydroGENE3D
PTHR11203CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR FAMILY MEMBERMBLPANTHER
mobidb-lite-Disorderdisorder_predictionMOBIDB-Disorder
mobidb-lite-Negative-Polyelectrolytedisorder_predictionMOBIDB-Negative-Polyelectrolyte
mobidb-lite-Polyampholytedisorder_predictionMOBIDB-Polyampholyte

Orthologs

References / Literature

PMID:16823372 - ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe.
Matsuyama A et al. Nat Biotechnol 2006 Jul;24(7):841-7
PMID:24713849 - Post-transcriptional regulation of meiotic genes by a nuclear RNA silencing complex.
Egan ED et al. RNA 2014 Jun;20(6):867-81
PMID:30726745 - Fission Yeast NDR/LATS Kinase Orb6 Regulates Exocytosis via Phosphorylation of the Exocyst Complex.
Tay YD et al. Cell Rep 2019 Feb 05;26(6):1654-1667.e7
PMID:32101745 - Dense Transposon Integration Reveals Essential Cleavage and Polyadenylation Factors Promote Heterochromatin Formation.
Lee SY et al. Cell Rep 2020 Feb 25;30(8):2686-2698.e8
PMID:25720772 - Quantitative phosphoproteomics reveals pathways for coordination of cell growth and division by the conserved fission yeast kinase pom1.
Kettenbach AN et al. Mol Cell Proteomics 2015 May;14(5):1275-87
PMID:37970674 - SUMOylation regulates Lem2 function in centromere clustering and silencing.
Strachan J et al. J Cell Sci 2023 Dec 01;136(23)
PMID:33823663 - A TOR (target of rapamycin) and nutritional phosphoproteome of fission yeast reveals novel targets in networks conserved in humans.
Halova L et al. Open Biol 2021 Apr;11(4):200405
PMID:24945319 - CPF-associated phosphatase activity opposes condensin-mediated chromosome condensation.
Vanoosthuyse V et al. PLoS Genet 2014 Jun;10(6):e1004415
PMID:31269446 - CPF Recruitment to Non-canonical Transcription Termination Sites Triggers Heterochromatin Assembly and Gene Silencing.
Vo TV et al. Cell Rep 2019 Jul 02;28(1):267-281.e5
PMID:28367989 - The conserved protein Seb1 drives transcription termination by binding RNA polymerase II and nascent RNA.
Wittmann S et al. Nat Commun 2017 Apr 03;8:14861
PMID:23101633 - Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells.
Marguerat S et al. Cell 2012 Oct 26;151(3):671-83
PMID:26537787 - Targeting of SUMO substrates to a Cdc48-Ufd1-Npl4 segregase and STUbL pathway in fission yeast.
Køhler JB et al. Nat Commun 2015 Nov 05;6:8827
GO_REF:0000111 - Gene Ontology annotations Inferred by Curator (IC) using at least one Inferred by Sequence Similarity (ISS) annotation to support the inference
PMID:24763107 - Absolute proteome and phosphoproteome dynamics during the cell cycle of Schizosaccharomyces pombe (Fission Yeast).
Carpy A et al. Mol Cell Proteomics 2014 Aug;13(8):1925-36
PB_REF:0000006 - Disease associations from Monarch via human-pombe orthologs
PMID:14617822 - A comparative analysis of an orthologous proteomic environment in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe.
Roguev A et al. Mol Cell Proteomics 2004 Feb;3(2):125-32
PMID:21511999 - Comparative functional genomics of the fission yeasts.
Rhind N et al. Science 2011 May 20;332(6032):930-6
PMID:26412298 - A Degenerate Cohort of Yeast Membrane Trafficking DUBs Mediates Cell Polarity and Survival.
Beckley JR et al. Mol Cell Proteomics 2015 Dec;14(12):3132-41
PMID:26404184 - High Confidence Fission Yeast SUMO Conjugates Identified by Tandem Denaturing Affinity Purification.
Nie M et al. Sci Rep 2015 Sep 25;5:14389
PMID:27401558 - The Nrd1-like protein Seb1 coordinates cotranscriptional 3' end processing and polyadenylation site selection.
Lemay JF et al. Genes Dev 2016 Jul 01;30(13):1558-72
PMID:33313903 - Ribosome profiling reveals ribosome stalling on tryptophan codons and ribosome queuing upon oxidative stress in fission yeast.
Rubio A et al. Nucleic Acids Res 2021 Jan 11;49(1):383-399
PMID:20473289 - Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe.
Kim DU et al. Nat Biotechnol 2010 Jun;28(6):617-623
GO_REF:0000033 - Annotation inferences using phylogenetic trees
PMID:23697806 - A genome-wide resource of cell cycle and cell shape genes of fission yeast.
Hayles J et al. Open Biol 2013 May 22;3(5):130053