swi6 (SPAC664.01c)


Gene Standard Nameswi6 Characterisation Statuspublished
Systematic IDSPAC664.01c Feature Typeprotein coding
Synonyms Name Descriptionswitching
ProductHP1 family chromodomain protein Swi6 Product Size328aa, 37.29 kDa
Genomic Location Chromosome I, 1704073-1702406 (1668nt); CDS:1704001-1703015 (987nt)

Ensembl Gene Location
GO Molecular Function
GO Biological Process
Term NameCount
cellular protein localization514
Annotation ExtensionEvidenceWith/FromReference
chromatin remodeling156
Annotation ExtensionEvidenceWith/FromReference
chromatin silencing at centromere60
Annotation ExtensionEvidenceWith/FromReference
chromatin silencing at centromere outer repeat region26
Annotation ExtensionEvidenceWith/FromReference
chromatin silencing at silent mating-type cassette36
Annotation ExtensionEvidenceWith/FromReference
chromatin silencing at telomere24
Annotation ExtensionEvidenceWith/FromReference
chromosome passenger complex localization to kinetochore4
Annotation ExtensionEvidenceWith/FromReference
donor selection4
Annotation ExtensionEvidenceWith/FromReference
gene conversion at mating-type locus13
Annotation ExtensionEvidenceWith/FromReference
mating type switching22
Annotation ExtensionEvidenceWith/FromReference
mitotic sister chromatid cohesion16
Annotation ExtensionEvidenceWith/FromReference
mitotic sister chromatid segregation195
Annotation ExtensionEvidenceWith/FromReference
protein localization to chromosome, centromeric region21
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
chromosome, centromeric outer repeat region12
Annotation ExtensionEvidenceWith/FromReference
condensed nuclear chromosome, centromeric region68
Annotation ExtensionEvidenceWith/FromReference
mating-type region heterochromatin28
Annotation ExtensionEvidenceWith/FromReference
mitotic spindle pole body218
Annotation ExtensionEvidenceWith/FromReference
nuclear chromatin344
nuclear heterochromatin64
Annotation ExtensionEvidenceWith/FromReference
nuclear pericentric heterochromatin42
Annotation ExtensionEvidenceWith/FromReference
nuclear subtelomeric heterochromatin21
Annotation ExtensionEvidenceWith/FromReference
nucleus2690
Annotation ExtensionEvidenceWith/FromReference
pericentric heterochromatin42
Annotation ExtensionEvidenceWith/FromReference
FYPO Single-Allele Phenotypes
Gene Deletion Viability: Viable

Population Phenotype

Term NameGenotypesCount
decreased cell population growth at low temperatureswi6::his185
decreased spore germination frequencyswi6Δ60
normal cell population growth at high temperatureswi6Δ64
normal growth on glucose carbon sourceswi6::his1263
swi6Δ
normal growth on thiabendazoleswi6+21
swi6-KR25A+SV40NLS (K143A, R144A, K145A, R146A, R149A, K151A, K152A, K156A, K161A, R163A, K164A, K169A, K172A, K177A, K184A, K187A, K191A, K217A, K222A, K241A, K242A, K243A, K251A, R256A, K261A, with SV40 NLS added at N-terminus)
swi6+SV40NLS (SV40 NLS added at N-terminus)
sensitive to 4-nitroquinoline N-oxideswi6Δ159
sensitive to 5-fluorouracilswi6Δ273
sensitive to 6-azauracilswi6Δ70
sensitive to carbendazimswi6::his123
sensitive to hydroxyureaswi6Δ547
sensitive to thiabendazoleswi6+254
swi6::his1
swi6Δ
viable vegetative cell populationswi6Δ3831

Cell Phenotype

Term NameGenotypesCount
abnormal chromatin silencing at silent mating-type cassetteswi6Δ28
abnormal mating type switching resulting in duplication or deletion in mating-type regionswi6-1153
abnormal meiotic recombination at silent mating-type cassetteswi6-1152
abnormal protein localization to heterochromatin during vegetative growth23
affecting epe1swi6Δ
abnormal sporulation resulting in formation of ascus with fewer than four sporesswi6Δ75
abolished protein localization to centromere35
affecting pds5swi6Δ
affecting hrk1swi6Δ
abolished protein localization to heterochromatin during vegetative growth7
affecting crb3swi6Δ
affecting las1swi6Δ
affecting ipi1swi6Δ
affecting rix1swi6Δ
affecting grc3swi6Δ
abolished RNA bindingswi6-shadow (1-264)10
swi6-chromo (1-74, 140-328)
decreased chromatin silencing at centromere outer repeatswi6Δ42
decreased chromatin silencing at silent mating-type cassetteswi6-11520
swi6-S115
decreased chromatin silencing at telomereswi6Δ25
decreased histone H2A phosphorylation at subtelomere during mitotic S phaseswi6Δ2
decreased histone H3-K9 dimethylation at centromereswi6Δ15
decreased histone H3-K9 dimethylation at silent mating-type cassetteswi6Δ6
decreased mating type switchingswi6 mutant14
decreased mitotic centromeric sister chromatid cohesionswi6Δ4
decreased protein level at centromere outer repeat5
affecting cut9swi6Δ
affecting cut4swi6Δ
decreased protein localization to centromere30
affecting rad21swi6Δ
decreased protein localization to heterochromatin at centromere outer repeat11
affecting dsh1swi6Δ
decreased RNA bindingswi6-KR25A (K143A, R144A, K145A, R146A, R149A, K151A, K152A, K156A, K161A, R163A, K164A, K169A, K172A, K177A, K184A, K187A, K191A, K217A, K222A, K241A, K242A, K243A, K251A, R256A, K261A)12
increased centromeric outer repeat transcript level21
increased chromatin silencing at silent mating-type cassetteswi6+2
increased level of heterochromatin-encoded proteinsswi6Δ3
increased mating type switchingswi6Δ1
swi6-115
increased meiotic DNA double-strand break formation at silent mating-type cassetteswi6-1151
increased meiotic recombination at silent mating-type cassetteswi6-1152
increased minichromosome loss during vegetative growthswi6::his164
increased protein localization to mating-type region heterochromatin1
affecting swi6swi6+
increased RNA level during vegetative growth222
affecting SO:0000286swi6Δ
lagging mitotic chromosomesswi6-11533
swi6::his1
swi6Δ
meiosis and sporulation in haploidswi6-1158
normal centromere clustering at nuclear peripheryswi6::his16
normal chromatin silencing at centromere outer repeatswi6+14
normal chromatin silencing at silent mating-type cassetteswi6-11519
normal DNA contentswi6Δ23
normal DNA double-strand break formation at mating-type locusswi6 mutant7
normal histone H2A phosphorylation at centromere outer repeatswi6Δ1
normal histone H2A phosphorylation at mating type locusswi6Δ2
normal histone H3-K9 dimethylation at centromere outer repeatswi6+2
normal histone H3-K9 dimethylation at silent mating-type cassetteswi6-KR25A+SV40NLS (K143A, R144A, K145A, R146A, R149A, K151A, K152A, K156A, K161A, R163A, K164A, K169A, K172A, K177A, K184A, K187A, K191A, K217A, K222A, K241A, K242A, K243A, K251A, R256A, K261A, with SV40 NLS added at N-terminus)3
normal histone H3-K9 dimethylation at telomereswi6-KR25A+SV40NLS (K143A, R144A, K145A, R146A, R149A, K151A, K152A, K156A, K161A, R163A, K164A, K169A, K172A, K177A, K184A, K187A, K191A, K217A, K222A, K241A, K242A, K243A, K251A, R256A, K261A, with SV40 NLS added at N-terminus)2
swi6Δ
normal meiotic telomere clusteringswi6Δ7
normal methylated histone residue bindingswi6-KR25A (K143A, R144A, K145A, R146A, R149A, K151A, K152A, K156A, K161A, R163A, K164A, K169A, K172A, K177A, K184A, K187A, K191A, K217A, K222A, K241A, K242A, K243A, K251A, R256A, K261A)1
normal RNA bindingswi6-hinge (1-139, 265-328)5
normal S-phase DNA damage checkpointswi6Δ18
normal spore morphologyswi6Δ18
normal telomere lengthswi6::his125
normal telomere tethering at nuclear peripheryswi6::his13
premature mitotic sister chromatid separationswi6Δ5
viable vegetative cell with normal cell morphologyswi6Δ3099

FYPO Multi-allele Phenotypes

Population Phenotype

Term NameGenotypes
decreased cell population growth at low temperatureswi6Δ, dis1-288
decreased cell population growth on glucose carbon sourcenda3-KM311, swi6::his1
decreased vegetative cell population growthbir1-CD (bir1 C-terminus fused to chromodomain), swi6Δ, sgo2Δ
swi6Δ, sgo2Δ
normal cell population growth at high temperaturemsc1Δ, swi6Δ, dis1-288
swi6Δ, msc1Δ
normal cell population growth at low temperatureswi6Δ, msc1Δ
swi6Δ, msc1Δ, dis1-288
normal growth on glucose carbon sourcemsc1Δ, swi6Δ, dis1-288
swi6Δ, msc1Δ
normal growth on thiabendazoleswi6+, dcr1Δ
swi6+, rdp1Δ
swi6+, ago1Δ
sensitive to thiabendazoleswi6Δ, rap1Δ
swi6+, clr4Δ
swi6Δ, poz1Δ
swi6Δ, msc1Δ

Cell Phenotype

Term NameGenotypes
abnormal chromatin silencing at silent mating-type cassetteswi6-115, clr5Δ
abolished mating type switchingswi6-115, swi3-1
decreased chromatin silencing at centromere outer repeatclr3Δ, swi6+
swi6Δ, poz1Δ
dcr1Δ, swi6+, sir2Δ
swi6+, clr4Δ
swi6+, clr3Δ, dcr1Δ
swi6Δ, rap1Δ
decreased chromatin silencing at telomeretaz1Δ, swi6+, Rap1-GBD (Rap1 fused to Gal4 DNA-binding domain)
decreased histone H3-K9 dimethylation at silent mating-type cassetteswi6Δ, cid14Δ
heterochromatin assembly beyond boundary element IRC1Repe1Δ, swi6Δ, mst2Δ
increased histone H3-K9 dimethylationepe1Δ, swi6Δ, mst2Δ
increased level of heterochromatin-encoded proteinsswi6Δ, cid14Δ
increased minichromosome loss during vegetative growthswi6::his1, nda3-KM311
meiosis and sporulation in haploidswi6-115, clr5Δ
normal chromatin silencing at centromere outer repeatswi6+, ago1Δ
swi6+, rdp1Δ
swi6+, dcr1Δ
normal chromatin silencing at telomerepoz1W209A (W209A), swi6+, Rap1-GBD (Rap1 fused to Gal4 DNA-binding domain)
taz1Δ, swi6+, Rap1-GBD (Rap1 fused to Gal4 DNA-binding domain)
normal histone H3-K9 dimethylation at telomereswi6Δ, cid14Δ
viable elongated vegetative cellswi6Δ, dis1-288
Target Of
OntologyRelationshipGeneProduct
FYPO affected by mutation in clr3 histone deacetylase (class II) Clr3
FYPO affected by mutation in clr4 histone H3 lysine methyltransferase Clr4
FYPO affected by mutation in cut4 anaphase-promoting complex, platform subcomplex scaffold subunit Apc1
FYPO affected by mutation in cut9 anaphase-promoting complex, TPR lobe subcomplex subunit Cut9/Apc6
FYPO affected by mutation in dcr1 dicer
FYPO affected by mutation in nuc2 anaphase-promoting complex TPR lobe subcomplex subunit Apc3
FYPO affected by mutation in pcf1 CAF assembly factor (CAF-1) complex large subunit Pcf1
FYPO affected by mutation in pol1 DNA polymerase alpha catalytic subunit
FYPO affected by mutation in rik1 silencing protein Rik1
FYPO affected by mutation in snu4 small nuclear RNA U4
FYPO affected by mutation in spt6 nucleosome remodeling protein Spt6
FYPO affected by mutation in stc1 LIM-like protein linking chromatin modification to RNAi, Stc1
FYPO affected by mutation in swi6 HP1 family chromodomain protein Swi6
GO localized by clr4 histone H3 lysine methyltransferase Clr4
GO localized by pob3 FACT complex subunit Pob3
GO localized by raf1 CLRC ubiquitin E3 ligase complex specificiy factor Raf1/Dos1
GO localized by raf2 Rik1-associated factor Raf2
GO localized by rdp1 RNA-directed RNA polymerase Rdp1
GO localized by rik1 silencing protein Rik1
GO localized by sir2 Sirtuin family histone deacetylase Sir2
GO localized by tas3 RITS complex subunit 3
GO substrate of hsk1 Dbf4(Dfp1)-dependent protein kinase Hsk1
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons1704073..1702406
5' UTR1704073..1704002AU011088
3' UTR1703014..1702406PMID: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
PF00385 Pfam IPR023780 Chromo domain 81 133 7
PF01393 Pfam IPR008251 Chromo shadow domain 268 324 2
SM00298 SMART IPR000953 Chromo/chromo shadow domain 80 136 9
SM00300 SMART IPR008251 Chromo shadow domain 261 327 2
PS00598 Prosite Patterns IPR023779 Chromo domain, conserved site 100 121 4
PS50013 Prosite Profiles IPR000953 Chromo/chromo shadow domain 81 143 7
PS50013 Prosite Profiles IPR000953 Chromo/chromo shadow domain 267 328 7
PTHR22812 HMMPANTHER 21 158 3
PTHR22812 HMMPANTHER 259 328 3
PTHR22812:SF95 HMMPANTHER 21 158 2
PTHR22812:SF95 HMMPANTHER 259 328 2
2.40.50.40 Gene3D Chromo/chromo shadow domain 70 135 7
2.40.50.40 Gene3D Chromo/chromo shadow domain 264 327 7
SSF54160 SuperFamily IPR016197 Chromo domain-like 74 143 9
SSF54160 SuperFamily IPR016197 Chromo domain-like 263 322 9
Coil ncoils Predicted coiled-coil protein (DUF2205) 60 80 1050

View domain organization at Pfam

Term IDTerm NameReferenceCount
PBO:0001050chromodomain proteinTemporary processing gif - replaced by AJAX with count of genes annotated with the term PBO:0001050
PBO:0012553HP1/CBX familyTemporary processing gif - replaced by AJAX with count of genes annotated with the term PBO:0012553

Protein Properties

Ave. residue weight 113.70 Da
Charge -13.50
Codon Adaptation Index 0.41
Isoelectric point 4.87
Molecular weight 37.29 kDa
Number of residues 328
Modifications

Protein Modifications

Term NameResidueCount
O-phospho-L-serine 1675
present during mitotic M phase, cellular response to thiabendazoleS18
present during mitotic M phase, cellular response to thiabendazoleS24
level fluctuates during mitotic cell cycleS212
present during mitotic M phase, cellular response to thiabendazoleS246
present during mitotic M phaseS212
S18, S159, S246
present during mitotic M phaseS203
present during mitotic M phaseS159
present during mitotic M phaseS224
Annotation ExtensionEvidenceResidueReference
experimental evidence S18 PMID:24763107
present during mitotic M phase experimental evidence S18 PMID:21712547
present during cellular response to thiabendazole IDA S18 PMID:18257517
present during mitotic M phase experimental evidence S24 PMID:21712547
present during cellular response to thiabendazole IDA S24 PMID:18257517
experimental evidence S159 PMID:24763107
present during mitotic M phase experimental evidence S159 PMID:21712547
present during mitotic M phase experimental evidence S203 PMID:21712547
level fluctuates during mitotic cell cycle experimental evidence S212 PMID:24763107
present during mitotic M phase experimental evidence S212 PMID:21712547
present during mitotic M phase experimental evidence S224 PMID:21712547
experimental evidence S246 PMID:24763107
present during cellular response to thiabendazole IDA S246 PMID:18257517
present during mitotic M phase experimental evidence S246 PMID:21712547
O-phospho-L-threonineT240 700
present during cellular response to thiabendazole, mitotic M phaseT240
present during mitotic M phaseT235
Annotation ExtensionEvidenceResidueReference
present during mitotic M phase experimental evidence T235 PMID:21712547
experimental evidence T240 PMID:24763107
present during mitotic M phase experimental evidence T240 PMID:21712547
present during cellular response to thiabendazole IDA T240 PMID:18257517
phosphorylated residue 1930
Annotation ExtensionEvidenceResidueReference
IDA PMID:19547744
Sequence
Gene Expression

Quantitative Gene Expression

View graphical display of gene expression data for swi6 (SPAC664.01c)

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
7653during GO:0000080PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
8917during GO:0000084PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
8199during GO:0000085PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
7981during GO:0000087PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
8351during GO:0072690PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
2394.42during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
3469.27during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
7during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
1.1during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
Taxonomic Conservation
DescriptionQualifierReferenceCount
no apparent S. cerevisiae ortholog599
conserved in fungi4604
conserved in eukaryotes4514
conserved in metazoa3422
conserved in vertebrates3397
conserved in eukaryotes only2504
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


External References
Database Identifier Description
NBRP SPAC664.01c Fission yeast strain database, National BioResource Project (Japan)
YOGY SPAC664.01c Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPAC664.01c BioGRID Interaction Datasets
Expression Viewer SPAC664.01c Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPAC664.01c Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPAC664.01c Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPAC664.01c Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPAC664.01c Polyadenylation Viewer (Gullerova lab)
pombeTV SPAC664.01c Transcriptome Viewer (Bähler Lab)
GEO SPAC664.01c GEO profiles
PInt SPAC664.01c Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPAC664.01c Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPAC664.01c Fission yeast phenotypic data & analysis
Cyclebase SPAC664.01c.1 Cell Cycle Data
SPD / RIKEN14/14C10Orfeome Localization Data
UniProtKB/SwissProtP40381Chromatin-associated protein swi6
ModBaseP40381Database of comparative protein structure models
STRINGP40381Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_593449chromodomain protein Swi6
RefSeq mRNANM_001018882972h- chromodomain protein Swi6 (swi6), mRNA
European Nucleotide ArchiveCU329670ENA EMBL mapping
European Nucleotide ArchiveX71783ENA EMBL mapping
ePDB1E0BThe European PDB
PDB1E0BPDB
PDBsum1E0BPDBsum
ePDB2RSOThe European PDB
PDB2RSOPDB
PDBsum2RSOPDBsum
European Nucleotide ArchiveCAA50668ENA Protein Mapping
European Nucleotide ArchiveCAB57340ENA Protein Mapping
UniParcUPI00001362A2UniProt Archive

Literature for swi6

Search: Europe PMC or PubMed

Release Version: PomBase:30_57 - 27 Jan 2016