lsd2 (SPAC23E2.02)

Gene Standard Namelsd2 Characterisation Statuspublished
Systematic IDSPAC23E2.02 Feature Typeprotein coding
Synonymssaf140, swm2 Name Description
Producthistone demethylase SWIRM2 (predicted) Product Size1273aa, 142.49 kDa
Genomic Location Chromosome I, 446491-450726 (4236nt); CDS:446491-450530 (4040nt)

Ensembl Gene Location
GO Molecular Function
Term NameCount
DNA binding381
Annotation ExtensionEvidenceWith/FromReference
histone demethylase activity (H3-monomethyl-K4 specific)2
Annotation ExtensionEvidenceWith/FromReference
nucleosome binding9
Annotation ExtensionEvidenceWith/FromReference
oxidoreductase activity286
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
Term NameCount
cellular response to heat24
Annotation ExtensionEvidenceWith/FromReference
chromatin remodeling159
Annotation ExtensionEvidenceWith/FromReference
histone H3-K4 demethylation4
Annotation ExtensionEvidenceWith/FromReference
histone H3-K9 demethylation4
Annotation ExtensionEvidenceWith/FromReference
regulation of meiotic cell cycle45
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
Annotation ExtensionEvidenceWith/FromReference
Lsd1/2 complex4
Annotation ExtensionEvidenceWith/FromReference
nuclear chromatin298
Annotation ExtensionEvidenceWith/FromReference
Annotation ExtensionEvidenceWith/FromReference
Fission Yeast Phenotype Ontology
Gene Deletion Viability: Inviable

Population Phenotype

Term NameAlleleExpressionCount
inviable vegetative cell populationlsd2ΔNull1427
not recorded (unrecorded)
normal growth on camptothecinlsd2-ao (K861A, K862A)Endogenous19
normal growth on hydroxyurealsd2-ao (K861A, K862A)Endogenous31
normal growth on methyl methanesulfonatelsd2-ao (K861A, K862A)Endogenous25
resistance to thiabendazolelsd2-ao (K861A, K862A)Endogenous10

Cell Phenotype

Term NameAlleleExpressionCount
decreased replication fork arrest at mating-type locus2
expressivity FYPO_EXT:0000003lsd2-ao (K861A, K862A)Endogenous
inviable curved septated vegetative cell10
penetrance FYPO_EXT:0000001lsd2ΔNull
normal genetic imprinting at mating-type locuslsd2-ao (K861A, K862A)Endogenous6
Target Of
FYPO affected by mutation in lsd1 histone demethylase SWIRM1 PMID:23260662
Ensembl transcript structure with UTRs, exons and introns


Exon Start End


Region Coordinates Reference
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
PF04433 Pfam IPR007526 SWIRM domain 396 481 7
PF01593 Pfam IPR002937 Amine oxidase 516 1035 3
PS50118 Prosite Profiles IPR009071 High mobility group box domain 1115 1195 9
PS50934 Prosite Profiles IPR007526 SWIRM domain 394 490 7
PTHR10742 HMMPANTHER 21 1113 3
PTHR10742:SF223 HMMPANTHER 21 1113 1 Gene3D IPR009071 High mobility group box domain 1111 1207 11 Gene3D IPR011991 Winged helix-turn-helix DNA-binding domain 393 485 46 Gene3D 503 569 29 Gene3D 606 639 29 Gene3D 993 1038 29 Gene3D 773 873 29
SSF51905 SuperFamily 603 875 26
SSF51905 SuperFamily 505 565 26
SSF51905 SuperFamily 997 1037 26
SSF46689 SuperFamily IPR009057 Homeodomain-like 392 486 25
SSF47095 SuperFamily IPR009071 High mobility group box domain 1109 1203 12
Coil ncoils Rabaptin coiled-coil domain 1085 1106 971
Coil ncoils Rabaptin coiled-coil domain 1232 1253 971

View domain organization at Pfam

Manually Curated Family or Sub-families

Term IDTerm NameReferenceCount
PBO:0000376HMG boxTemporary processing gif - replaced by AJAX with count of genes annotated with the term PBO:0000376

Protein Properties

Ave. residue weight 111.93 Da
Charge -6.00
Isoelectric point 6.21
Molecular weight 142.49 kDa
Number of residues 1273
Gene Expression

Quantitative Gene Expression

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
953during GO:0072690PECO:0000126,
single cellmass spectrometry evidencePMID:24763107
991.54during GO:0072690PECO:0000005,
population wideexperimental evidencePMID:23101633
637.39during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
population wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
1.5during GO:0072690PECO:0000005,
population wideexperimental evidencePMID:23101633
0.46during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
population wideexperimental evidencePMID:23101633
Species Distribution
no apparent S. cerevisiae ortholog597
predominantly single copy (one to one)3092
conserved in fungi4604
conserved in eukaryotes4516
conserved in metazoa3432
conserved in vertebrates3407
conserved in eukaryotes only2503

Manually curated orthologous groups


Orthologs in Compara

Physical Interactions

Source: BioGRID

View all interactions in esyN
View the HCPIN interactions in esyN

Gene Product Evidence Reference
phf1PHD finger containing protein Phf1 Affinity Capture-MSPMID:17434129
Affinity Capture-MSPMID:17371846
phf2Lsd1/2 complex PHD finger containing protein Phf2 Affinity Capture-MSPMID:17434129
Affinity Capture-MSPMID:16990277
Affinity Capture-MSPMID:17371846
cxr1mRNA processing factor Affinity Capture-MSPMID:16990277
lsd1histone demethylase SWIRM1 Affinity Capture-MSPMID:17434129
Affinity Capture-MSPMID:16990277
Affinity Capture-MSPMID:17371846
hrp1ATP-dependent DNA helicase Hrp1 Affinity Capture-MSPMID:16990277
Genetic Interactions

Source: BioGRID

View these interactions in esyN

Gene Product Evidence Reference
lsd1histone demethylase SWIRM1 Synthetic RescuePMID:23260662
External References
Database Identifier Description
NBRP SPAC23E2.02 Fission yeast strain database, National BioResource Project (Japan)
YOGY SPAC23E2.02 Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPAC23E2.02 BioGRID Interaction Datasets
Expression Viewer SPAC23E2.02 Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPAC23E2.02 Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPAC23E2.02 Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPAC23E2.02 Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPAC23E2.02 Polyadenylation Viewer (Gullerova lab)
pombeTV SPAC23E2.02 Transcriptome Viewer (Bähler Lab)
Cyclebase SPAC23E2.02 Cell Cycle Data
GEO SPAC23E2.02 GEO profiles
PInt SPAC23E2.02 Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPAC23E2.02 Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPAC23E2.02 Fission yeast phenotypic data & analysis
SPD / RIKEN48/48F11Orfeome Localization Data
UniProtKB/SwissProtQ10135Lysine-specific histone demethylase 2
ModBaseQ10135Database of comparative protein structure models
STRINGQ10135Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_592937histone demethylase SWIRM2 (predicted)
RefSeq mRNANM_001018338972h- histone demethylase SWIRM2 (predicted) (lsd2), mRNA
European Nucleotide ArchiveBAA87224.1ENA Protein Mapping
European Nucleotide ArchiveCAA93114.1ENA Protein Mapping
UniParcUPI000013A14FUniProt Archive

Literature for lsd2

Search: Europe PMC or PubMed

Release Version: PomBase:25_48 - 10 Jan 2015