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protein coding gene - rad16 (SPCC970.01) - DNA repair endonuclease XPF

Gene summary

Standard name
rad16
Systematic ID
SPCC970.01
Product
DNA repair endonuclease XPF
Organism
Schizosaccharomyces pombe (fission yeast)
Synonyms
rad10, rad20, swi9
UniProt ID
P36617
ORFeome ID
47/47F11
Characterisation status
biological role published
Feature type
mRNA gene
Genomic location
chromosome III: 514796..518097 reverse strand

Annotation

PBO:0001164 - 3.1.-.-

Disease association

MONDO:0014108 - Fanconi anemia complementation group Q

References:

MONDO:0010215 - xeroderma pigmentosum group F

References:

MONDO:0012590 - XFE progeroid syndrome

References:

GO biological process

GO:0000724 - double-strand break repair via homologous recombination

References:

GO:0045002 - double-strand break repair via single-strand annealing

References:

GO:0000736 - double-strand break repair via single-strand annealing, removal of nonhomologous ends

References:

GO:0007534 - gene conversion at mating-type locus

References:

GO:0007533 - mating type switching

References:

GO:0006289 - nucleotide-excision repair

References:

GO:1901255 - nucleotide-excision repair involved in interstrand cross-link repair

References:

GO:0007131 - reciprocal meiotic recombination

References:

GO:0000712 - resolution of meiotic recombination intermediates

References:

GO cellular component

GO:0044732 - mitotic spindle pole body

References:

GO:0000110 - nucleotide-excision repair factor 1 complex

References:

GO:0005634 - nucleus

References:

GO molecular function

GO:1990599 - 3' overhang single-stranded DNA endodeoxyribonuclease activity

References:

GO:0003684 - damaged DNA binding

References:

GO:0005515 - protein binding

References:

GO:0003697 - single-stranded DNA binding

References:

Modification

MOD:00046 - O-phospho-L-serine

References:

Multi-locus phenotype

FYPO:0005433 - decreased meiotic recombination at hotspot

References:

Genotypes:

FYPO:0001355 - decreased vegetative cell population growth

References:

Genotypes:

FYPO:0005434 - globally decreased meiotic recombination

References:

Genotypes:

FYPO:0005775 - sensitive to acetaldehyde

References:

Genotypes:

FYPO:0000085 - sensitive to camptothecin

References:

Genotypes:

FYPO:0000102 - sensitive to cisplatin

References:

Genotypes:

FYPO:0002167 - sensitive to ethyl methanesulfonate

References:

Genotypes:

FYPO:0007330 - sensitive to formaldehyde

References:

Genotypes:

FYPO:0000088 - sensitive to hydroxyurea

References:

Genotypes:

FYPO:0000267 - sensitive to ionizing radiation during vegetative growth

References:

Genotypes:

FYPO:0000089 - sensitive to methyl methanesulfonate

References:

Genotypes:

FYPO:0001813 - sensitive to N-methyl-N'-nitro-N-nitrosoguanidine

References:

Genotypes:

FYPO:0000268 - sensitive to UV during vegetative growth

References:

Genotypes:

Quantitative gene expression

PBO:0006310 - protein level

References:

PBO:0011963 - RNA level

References:

Single locus phenotype

FYPO:0000777 - abnormal double-strand break repair during vegetative growth

References:

Genotypes:

FYPO:0003659 - abnormal mating type switching resulting in duplication or deletion in mating-type region

References:

Genotypes:

FYPO:0003164 - abolished nuclease activity

References:

Genotypes:

FYPO:0003352 - decreased DNA double-strand break formation at mating-type locus

References:

Genotypes:

FYPO:0003912 - decreased double-strand break repair via homologous recombination

References:

Genotypes:

FYPO:0000185 - decreased gene conversion during vegetative growth

References:

Genotypes:

FYPO:0003179 - decreased intragenic meiotic recombination

References:

Genotypes:

FYPO:0000470 - decreased mating type switching

References:

Genotypes:

FYPO:0005433 - decreased meiotic recombination at hotspot

References:

Genotypes:

FYPO:0009077 - increased cell population growth on ethanol carbon source

References:

Genotypes:

FYPO:0009072 - increased cell population growth on lysine nitrogen source

References:

Genotypes:

FYPO:0001840 - increased minichromosome loss during vegetative growth

References:

Genotypes:

FYPO:0005777 - increased number of Rad52 foci during cellular response to acetaldehyde

References:

Genotypes:

FYPO:0000972 - increased number of Rad52 foci during vegetative growth

References:

Genotypes:

FYPO:0006518 - loss of viability in G0

References:

Genotypes:

FYPO:0000245 - loss of viability in stationary phase

References:

Genotypes:

FYPO:0003353 - normal DNA double-strand break formation at mating-type locus

References:

Genotypes:

FYPO:0005945 - normal frequency of break-induced loss of heterozygosity

References:

Genotypes:

FYPO:0007553 - normal G1 to G0 transition

References:

Genotypes:

FYPO:0001690 - normal growth on camptothecin

References:

Genotypes:

FYPO:0001164 - normal growth on glucose carbon source

References:

Genotypes:

FYPO:0004404 - normal growth on JM216

References:

Genotypes:

FYPO:0004406 - normal growth on JM335

References:

Genotypes:

FYPO:0004410 - normal growth on tetraplatin

References:

Genotypes:

FYPO:0004408 - normal growth on triplatin tetranitrate

References:

Genotypes:

FYPO:0009031 - resistance to bleomycin

References:

Genotypes:

FYPO:0000067 - resistance to brefeldin A

References:

Genotypes:

FYPO:0000763 - resistance to cadmium

References:

Genotypes:

FYPO:0004403 - resistance to JM216

References:

Genotypes:

FYPO:0001583 - resistance to lithium

References:

Genotypes:

FYPO:0001034 - resistance to tunicamycin

References:

Genotypes:

FYPO:0001098 - sensitive to 4-nitroquinoline N-oxide

References:

Genotypes:

FYPO:0005775 - sensitive to acetaldehyde

References:

Genotypes:

FYPO:0001097 - sensitive to amitrole

References:

Genotypes:

FYPO:0007921 - sensitive to benzamidine

References:

Genotypes:

FYPO:0003384 - sensitive to chromium

References:

Genotypes:

FYPO:0000102 - sensitive to cisplatin

References:

Genotypes:

FYPO:0000104 - sensitive to cycloheximide

References:

Genotypes:

FYPO:0000799 - sensitive to diamide

References:

Genotypes:

FYPO:0007931 - sensitive to egtazic acid

References:

Genotypes:

FYPO:0000842 - sensitive to ethanol during vegetative growth

References:

Genotypes:

FYPO:0007928 - sensitive to ethylenediaminetetraacetic acid

References:

Genotypes:

FYPO:0007330 - sensitive to formaldehyde

References:

Genotypes:

FYPO:0000785 - sensitive to formamide

References:

Genotypes:

FYPO:0000087 - sensitive to hydrogen peroxide

References:

Genotypes:

FYPO:0000088 - sensitive to hydroxyurea

References:

Genotypes:

FYPO:0000267 - sensitive to ionizing radiation during vegetative growth

References:

Genotypes:

FYPO:0009071 - sensitive to itraconazole

References:

Genotypes:

FYPO:0004402 - sensitive to JM216

References:

Genotypes:

FYPO:0004405 - sensitive to JM335

References:

Genotypes:

FYPO:0009084 - sensitive to lithium chloride and methyl methanesulfonate

References:

Genotypes:

FYPO:0006836 - sensitive to magnesium chloride

References:

Genotypes:

FYPO:0000089 - sensitive to methyl methanesulfonate

References:

Genotypes:

FYPO:0002345 - sensitive to oxaliplatin

References:

Genotypes:

FYPO:0009082 - sensitive to potassium chloride and methyl methanesulfonate

References:

Genotypes:

FYPO:0007924 - sensitive to potassium chloride and sodium dodecyl sulfate

References:

Genotypes:

FYPO:0000797 - sensitive to tert-butyl hydroperoxide

References:

Genotypes:

FYPO:0004409 - sensitive to tetraplatin

References:

Genotypes:

FYPO:0000268 - sensitive to UV during vegetative growth

References:

Genotypes:

FYPO:0003656 - sensitive to vanadate

References:

Genotypes:

FYPO:0009064 - sensitive to X-rays and rapamycin during vegetative growth.

References:

Genotypes:

FYPO:0009063 - sensitive to X-rays during vegetative growth

References:

Genotypes:

FYPO:0003612 - viable spore population

References:

Genotypes:

FYPO:0001491 - viable vegetative cell

References:

Genotypes:

FYPO:0002060 - viable vegetative cell population

References:

Genotypes:

FYPO:0002177 - viable vegetative cell with normal cell morphology

References:

Genotypes:

Subunit composition

PBO:0015221 - heteromeric(2)

References:

Taxonomic conservation

PBO:0011072 - conserved in archaea

PBO:0011067 - conserved in bacteria

PBO:0011065 - conserved in eukaryotes

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
PF02732ERCC4ERCC4_domainPFAM
cd20078XPF_nuclease_XPF_eukXPF_nucleaseCDD
SM00891ERCC4_2ERCC4_domainSMART
G3DSA:3.40.50.10130:FF:000002FUNFAM
SSF52980Restriction endonuclease-likeRestrct_endonuc-II-likeSUPERFAMILY
SSF47781RuvA domain 2-likeRuvA_2-likeSUPERFAMILY
G3DSA:3.40.50.10130GENE3D
G3DSA:1.10.150.20GENE3D
PTHR10150DNA REPAIR ENDONUCLEASE XPFPANTHER
mobidb-lite-Disorderdisorder_predictionMOBIDB-Disorder
mobidb-lite-Polardisorder_predictionMOBIDB-Polar
mobidb-lite-Polyampholytedisorder_predictionMOBIDB-Polyampholyte
TIGR00596rad1XPFNCBIFAM

Orthologs

References / Literature

PMID:22365419 - The Schizosaccharomyces pombe AlkB homolog Abh1 exhibits AP lyase activity but no demethylase activity.
Korvald H et al. DNA Repair (Amst) 2012 May 01;11(5):453-62
PMID:15654094 - A novel recombination pathway initiated by the Mre11/Rad50/Nbs1 complex eliminates palindromes during meiosis in Schizosaccharomyces pombe.
Farah JA et al. Genetics 2005 Mar;169(3):1261-74
PMID:19470480 - Ctp1 and Exonuclease 1, alternative nucleases regulated by the MRN complex, are required for efficient meiotic recombination.
Farah JA et al. Proc Natl Acad Sci U S A 2009 Jun 09;106(23):9356-61
PMID:6587363 - Genes required for initiation and resolution steps of mating-type switching in fission yeast.
Egel R et al. Proc Natl Acad Sci U S A 1984 Jun;81(11):3481-5
PMID:25203555 - Fission yeast Pxd1 promotes proper DNA repair by activating Rad16XPF and inhibiting Dna2.
Zhang JM et al. PLoS Biol 2014 Sep;12(9):e1001946
PMID:29852001 - New insights into donor directionality of mating-type switching in Schizosaccharomyces pombe.
Maki T et al. PLoS Genet 2018 May;14(5):e1007424
PMID:2598273 - Some of the swi genes of Schizosaccharomyces pombe also have a function in the repair of radiation damage.
Schmidt H et al. Curr Genet 1989 Aug;16(2):89-94
PMID:8114734 - The rad16 gene of Schizosaccharomyces pombe: a homolog of the RAD1 gene of Saccharomyces cerevisiae.
Carr AM et al. Mol Cell Biol 1994 Mar;14(3):2029-40
PMID:32034465 - Genetic investigation of formaldehyde-induced DNA damage response in Schizosaccharomyces pombe.
Anandarajan V et al. Curr Genet 2020 Jun;66(3):593-605
PMID:8709952 - The genetics of the repair of 5-azacytidine-mediated DNA damage in the fission yeast Schizosaccharomyces pombe.
Hegde V et al. Mol Gen Genet 1996 Jun 24;251(4):483-92
PMID:21511999 - Comparative functional genomics of the fission yeasts.
Rhind N et al. Science 2011 May 20;332(6032):930-6
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
PMID:28281664 - Genetic interactions and functional analyses of the fission yeast gsk3 and amk2 single and double mutants defective in TORC1-dependent processes.
Rallis C et al. Sci Rep 2017 Mar 10;7:44257
PMID:11719193 - Mus81-Eme1 are essential components of a Holliday junction resolvase.
Boddy MN et al. Cell 2001 Nov 16;107(4):537-48
GO_REF:0000033 - Annotation inferences using phylogenetic trees
PMID:32692737 - CRL4Cdt2 ubiquitin ligase regulates Dna2 and Rad16 (XPF) nucleases by targeting Pxd1 for degradation.
Zhang JM et al. PLoS Genet 2020 Jul;16(7):e1008933
PMID:22064477 - The RecQ4 orthologue Hrq1 is critical for DNA interstrand cross-link repair and genome stability in fission yeast.
Groocock LM et al. Mol Cell Biol 2012 Jan;32(2):276-87
PMID:25293972 - Increased meiotic crossovers and reduced genome stability in absence of Schizosaccharomyces pombe Rad16 (XPF).
Mastro TL et al. Genetics 2014 Dec;198(4):1457-72
PMID:18270439 - Involvement of 3-methyladenine DNA glycosylases Mag1p and Mag2p in base excision repair of methyl methanesulfonate-damaged DNA in the fission yeast Schizosaccharomyces pombe.
Kanamitsu K et al. Genes Genet Syst 2007 Dec;82(6):489-94
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:166019 - Genetic control of radiation sensitivity in Schizosaccharomyces pombe.
Nasim A et al. Genetics 1975 Apr;79(4):573-82
PMID:33260998 - High-Throughput Flow Cytometry Combined with Genetic Analysis Brings New Insights into the Understanding of Chromatin Regulation of Cellular Quiescence.
Zahedi Y et al. Int J Mol Sci 2020 Nov 27;21(23)
PMID:21670547 - Fission yeast homologs of human XPC and CSB, rhp41 and rhp26, are involved in transcription-coupled repair of methyl methanesulfonate-induced DNA damage.
Kanamitsu K et al. Genes Genet Syst 2011;86(2):83-91
PMID:23335786 - Spontaneous telomere to telomere fusions occur in unperturbed fission yeast cells.
Almeida H et al. Nucleic Acids Res 2013 Mar 01;41(5):3056-67
PMID:27168121 - Discovery of genes involved in mitosis, cell division, cell wall integrity and chromosome segregation through construction of Schizosaccharomyces pombe deletion strains.
Chen JS et al. Yeast 2016 Sep;33(9):507-17
PMID:30148840 - Tdp1 processes chromate-induced single-strand DNA breaks that collapse replication forks.
Ganguly A et al. PLoS Genet 2018 Aug;14(8):e1007595
PMID:22665798 - Induction of a G1-S checkpoint in fission yeast.
Bøe CA et al. Proc Natl Acad Sci U S A 2012 Jun 19;109(25):9911-6
PMID:34250083 - Barcode sequencing and a high-throughput assay for chronological lifespan uncover ageing-associated genes in fission yeast.
Romila CA et al. Microb Cell 2021 Jul 05;8(7):146-160
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:19798055 - Failed gene conversion leads to extensive end processing and chromosomal rearrangements in fission yeast.
Tinline-Purvis H et al. EMBO J 2009 Nov 04;28(21):3400-12
PMID:15485909 - Rad62 protein functionally and physically associates with the smc5/smc6 protein complex and is required for chromosome integrity and recombination repair in fission yeast.
Morikawa H et al. Mol Cell Biol 2004 Nov;24(21):9401-13
PMID:27687866 - Genetic controls of DNA damage avoidance in response to acetaldehyde in fission yeast.
Noguchi C et al. Cell Cycle 2017 Jan 02;16(1):45-58
PMID:9658208 - Sensitivity to cisplatin and platinum-containing compounds of Schizosaccharomyces pombe rad mutants.
Perego P et al. Mol Pharmacol 1998 Jul;54(1):213-9
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
PMID:25777942 - A novel protein, Rsf1/Pxd1, is critical for the single-strand annealing pathway of double-strand break repair in Schizosaccharomyces pombe.
Wang H et al. Mol Microbiol 2015 Jun;96(6):1211-25
PMID:7254221 - Spontaneous and UV-induced recombination in radiation-sensitive mutants of Schizosaccharomyces pombe.
Grossenbacher-Grunder AM et al. Mutat Res 1981 Mar;81(1):37-48
PMID:37787768 - Broad functional profiling of fission yeast proteins using phenomics and machine learning.
Rodríguez-López M et al. Elife 2023 Oct 03;12
PMID:36408920 - UniProt: the Universal Protein Knowledgebase in 2023.
UniProt Consortium Nucleic Acids Res 2023 Jan 06;51(D1):D523-D531
PMID:12628934 - Pathway utilization in response to a site-specific DNA double-strand break in fission yeast.
Prudden J et al. EMBO J 2003 Mar 17;22(6):1419-30
PMID:24192486 - The conserved Fanconi anemia nuclease Fan1 and the SUMO E3 ligase Pli1 act in two novel Pso2-independent pathways of DNA interstrand crosslink repair in yeast.
Fontebasso Y et al. DNA Repair (Amst) 2013 Dec;12(12):1011-23
PMID:24719968 - Switching genes in Schizosaccharomyces pombe.
Gutz H et al. Curr Genet 1985;9(5):325-31
PMID:24861625 - Hyperactive Cdc2 kinase interferes with the response to broken replication forks by trapping S.pombe Crb2 in its mitotic T215 phosphorylated state.
Mahyous Saeyd SA et al. Nucleic Acids Res 2014 Jul;42(12):7734-47
PMID:23188080 - The fission yeast MRN complex tethers dysfunctional telomeres for NHEJ repair.
Reis CC et al. EMBO J 2012 Dec 12;31(24):4576-86
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
PB_REF:0000006 - Disease associations from Monarch via human-pombe orthologs