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 binding379
Annotation ExtensionEvidenceWith/FromReference
histone demethylase activity (H3-monomethyl-K4 specific)2
Annotation ExtensionEvidenceWith/FromReference
nucleosome binding9
Annotation ExtensionEvidenceWith/FromReference
oxidoreductase activity277
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
Term NameCount
chromatin remodeling157
Annotation ExtensionEvidenceWith/FromReference
histone H3-K4 demethylation4
Annotation ExtensionEvidenceWith/FromReference
histone H3-K9 demethylation4
Annotation ExtensionEvidenceWith/FromReference
regulation of meiotic cell cycle39
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
cytosol2315
Annotation ExtensionEvidenceWith/FromReference
Lsd1/2 complex4
Annotation ExtensionEvidenceWith/FromReference
nuclear chromatin307
Annotation ExtensionEvidenceWith/FromReference
nucleus2696
Annotation ExtensionEvidenceWith/FromReference
Fission Yeast Phenotype Ontology
Gene Deletion Viability: Inviable

Population Phenotype

Term NameAlleleExpressionCount
inviable vegetative cell populationlsd2ΔNull1428
unnamed (unrecorded)
normal growth on camptothecinlsd2-ao (K861A, K862A)Endogenous22
normal growth on hydroxyurealsd2-ao (K861A, K862A)Endogenous36
normal growth on methyl methanesulfonatelsd2-ao (K861A, K862A)Endogenous27
resistance to thiabendazolelsd2-ao (K861A, K862A)Endogenous11

Cell Phenotype

Term NameAlleleExpressionCount
decreased replication fork arrest at mating-type locuslsd2-ao (K861A, K862A)Endogenous2
inviable curved septated vegetative celllsd2ΔNull10
normal genetic imprinting at mating-type locuslsd2-ao (K861A, K862A)Endogenous6
Target Of
OntologyRelationshipGeneProductReference
FYPO affected by mutation in lsd1 histone demethylase SWIRM1 PMID:23260662
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons446491..446513, 446679..449241, 449295..450726
Introns448080..448157
mRNA446491..450726
CDS446491..446513, 446679..449241, 449295..450530
3' UTR450531..450726PMID: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
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:SF223 HMMPANTHER 21 1113 1
PTHR10742 HMMPANTHER 21 1113 3
1.10.10.10 Gene3D IPR011991 Winged helix-turn-helix DNA-binding domain 393 485 46
3.50.50.60 Gene3D 773 873 29
3.50.50.60 Gene3D 993 1038 29
3.50.50.60 Gene3D 606 639 29
3.50.50.60 Gene3D 503 569 29
1.10.30.10 Gene3D IPR009071 High mobility group box domain 1111 1207 11
SSF46689 SuperFamily IPR009057 Homeodomain-like 392 486 25
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
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 ortholog598
predominantly single copy (one to one)3092
conserved in fungi4604
conserved in eukaryotes4516
conserved in metazoa3430
conserved in vertebrates3405
conserved in eukaryotes only2502
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

View all interactions in esyN
View the HCPIN interactions in esyN

Gene Product Evidence Reference
affinity capturescxr1mRNA processing factor Affinity Capture-MSPMID:16990277
affinity captureshrp1ATP-dependent DNA helicase Hrp1 Affinity Capture-MSPMID:16990277
affinity captured bylsd1histone demethylase SWIRM1 Affinity Capture-MSPMID:17434129
affinity captureslsd1histone demethylase SWIRM1 Affinity Capture-MSPMID:17434129
affinity captureslsd1histone demethylase SWIRM1 Affinity Capture-MSPMID:16990277
affinity captured bylsd1histone demethylase SWIRM1 Affinity Capture-MSPMID:16990277
affinity captured bylsd1histone demethylase SWIRM1 Affinity Capture-MSPMID:17371846
affinity captureslsd1histone demethylase SWIRM1 Affinity Capture-MSPMID:17371846
affinity capturesphf1PHD finger containing protein Phf1 Affinity Capture-MSPMID:17434129
affinity capturesphf1PHD finger containing protein Phf1 Affinity Capture-MSPMID:17371846
affinity capturesphf2Lsd1/2 complex PHD finger containing protein Phf2 Affinity Capture-MSPMID:17434129
affinity capturesphf2Lsd1/2 complex PHD finger containing protein Phf2 Affinity Capture-MSPMID:16990277
affinity capturesphf2Lsd1/2 complex PHD finger containing protein Phf2 Affinity Capture-MSPMID:17371846
Genetic Interactions

Source: BioGRID

View these interactions in esyN

Gene Product Evidence Reference
synthetically rescueslsd1histone 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_50 - 10 Mar 2015