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 IDTerm NameEvidenceWith/FromReferenceCount
GO:0003677DNA bindingIEAUniProtKB-KW:KW-0238GO_REF:0000037385
GO:0034649histone demethylase activity (H3-monomethyl-K4 specific)NASGO_REF:00000012
GO:0031491nucleosome binding8
contributes_toIDAPMID:17371846
GO:0016491oxidoreductase activityIEAUniProtKB-KW:KW-0560GO_REF:0000037286
GO Biological Process
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0034605cellular response to heatIEPPMID:1737184630
GO:0006338chromatin remodelingISSUniProtKB:O60341GO_REF:0000001151
GO:0034720histone H3-K4 demethylationNASGO_REF:00000014
GO:0033169histone H3-K9 demethylationIMPPMID:174341294
GO:0051445regulation of meiotic cell cycleIMPPMID:1743412946
GO Cellular Component
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0033193Lsd1/2 complexIDAPMID:174341294
GO:0005829cytosolIDAPMID:168233722319
GO:0000790nuclear chromatinICGO:0016577GO_REF:0000001278
GO:0005634nucleusIDAPMID:168233722737
IDAPMID:10759889
Fission Yeast Phenotype Ontology

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002061inviable vegetative cell populationMicroscopylsd2ΔNullPECO:0000005, PECO:0000137PMID:236978061337
Microscopynot recorded (unrecorded)PMID:16990277
Microscopylsd2ΔNullPMID:20473289
FYPO:0001690normal growth on camptothecinCell growth assaylsd2-ao (K861A, K862A)EndogenousPMID:2326066215
FYPO:0000963normal growth on hydroxyureaCell growth assaylsd2-ao (K861A, K862A)EndogenousPMID:2326066221
FYPO:0000957normal growth on methyl methanesulfonateCell growth assaylsd2-ao (K861A, K862A)EndogenousPMID:2326066219
FYPO:0000069resistance to thiabendazoleCell growth assaylsd2-ao (K861A, K862A)EndogenousPMID:232606627

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0003085decreased replication fork arrest at mating-type locus2
expressivity FYPO_EXT:0000003Gel electrophoresis evidencelsd2-ao (K861A, K862A)EndogenousPMID:23260662
FYPO:0002282inviable curved septated vegetative cell10
penetrance FYPO_EXT:0000001Microscopylsd2ΔNullPECO:0000005, PECO:0000137PMID:23697806
FYPO:0003082normal genetic imprinting at mating-type locusGel electrophoresis evidencelsd2-ao (K861A, K862A)EndogenousPMID:232606626
Target Of
OntologyRelationshipGeneProductReference
FYPO affected by mutation in lsd1 histone demethylase SWIRM1 PMID:23260662
Transcript
Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
1446491446513
2446679449241
3449295450726
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
PS50934 Prosite Profiles IPR007526 SWIRM domain 394 490 7
PS50118 Prosite Profiles IPR009071 High mobility group box domain 1115 1195 9
PTHR10742 HMMPANTHER 400 1100 3
PTHR10742:SF151 HMMPANTHER 400 1100 1
1.10.10.10 Gene3D IPR011991 Winged helix-turn-helix DNA-binding domain 393 485 46
1.10.30.10 Gene3D IPR009071 High mobility group box domain 1111 1207 11
3.50.50.60 Gene3D 773 873 29
3.50.50.60 Gene3D 503 569 29
3.50.50.60 Gene3D 993 1038 29
3.50.50.60 Gene3D 606 639 29
SSF51905 SuperFamily 997 1037 26
SSF51905 SuperFamily 505 565 26
SSF51905 SuperFamily 603 875 26
SSF47095 SuperFamily IPR009071 High mobility group box domain 1109 1203 12
SSF46689 SuperFamily IPR009057 Homeodomain-like 392 486 25
Coil ncoils Rabaptin coiled-coil domain 1085 1106 968
Coil ncoils Rabaptin coiled-coil domain 1232 1253 968

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
Sequence
Gene Expression

Quantitative Gene Expression

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
991.54during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
953during GO:0072690PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
637.39during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
1.5during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
0.46during 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
lsd1histone demethylase SWIRM1 Synthetic RescuePMID:23260662
Physical Interactions

Source: BioGRID

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
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
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:23_46 - 30 Aug 2014