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:0000037283
GO:0003714transcription corepressor activityISSUniProtKB:O60341GO_REF:000000113
GO Biological Process
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0034605cellular response to heatIEPPMID:1737184643
GO:0006338chromatin remodelingISSUniProtKB:O60341GO_REF:0000001156
GO:0034720histone H3-K4 demethylationNASGO_REF:00000014
GO:0033169histone H3-K9 demethylationIMPPMID:174341294
GO:0045892negative regulation of transcription, DNA-templatedICGO:0003714GO_REF:0000001161
GO:0045893positive regulation of transcription, DNA-templatedIMPPMID:1699027798
GO:2001141regulation of RNA biosynthetic processISSUniProtKB:O60341GO_REF:0000001419
GO:0040020regulation of meiosisIMPPMID:1743412937
GO Cellular Component
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0033193Lsd1/2 complexIDAPMID:174341294
GO:0005829cytosolIDAPMID:168233722317
GO:0000790nuclear chromatinICGO:0016577GO_REF:0000001247
GO:0005634nucleusIDAPMID:107598892730
IDAPMID:16823372
Fission Yeast Phenotype Ontology

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002061inviable vegetative cell populationno_namePMID:169902771309
Microscopylsd2ΔNullPECO:0000005, PECO:0000137PMID:23697806
Microscopylsd2ΔNullPMID:20473289
FYPO:0001690normal cell population growth on camptothecinCell growth assaylsd2-ao (K861A,K862A)EndogenousPMID:2326066210
FYPO:0000963normal cell population growth on hydroxyureaCell growth assaylsd2-ao (K861A,K862A)EndogenousPMID:2326066216
FYPO:0000957normal cell population growth on methyl methanesulfonateCell growth assaylsd2-ao (K861A,K862A)EndogenousPMID:2326066214
FYPO:0000069resistance to thiabendazoleCell growth assaylsd2-ao (K861A,K862A)EndogenousPMID:232606626

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0003085decreased replication fork arrest at mating-type locusGel electrophoresis evidencelsd2-ao (K861A,K862A)EndogenousPMID:232606622
expressivity FYPO_EXT:0000003
FYPO:0002282inviable curved septated vegetative cellMicroscopylsd2ΔNullPECO:0000005, PECO:0000137PMID:2369780610
penetrance FYPO_EXT:0000001
FYPO:0003082normal genetic imprinting at mating-type locusGel electrophoresis evidencelsd2-ao (K861A,K862A)EndogenousPMID:232606626
Transcript
Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
1446491446513
2446679449241
3449295450726

UTRs

Region Start End Reference
three_prime_UTR450531450726PMID: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
PF01593 Pfam IPR002937 Amine oxidase 516 1035 3
PF04433 Pfam IPR007526 SWIRM domain 396 481 7
SM00398 SMART IPR009071 High mobility group box domain 1114 1196 10
PS50934 Prosite Profiles IPR007526 SWIRM domain 394 490 7
PS50118 Prosite Profiles IPR009071 High mobility group box domain 1115 1195 9
PTHR10742:SF151 HMMPANTHER 400 1100 1
PTHR10742 HMMPANTHER 400 1100 3
G3DSA:1.10.30.10 Gene3D IPR009071 1111 1207 11
G3DSA:1.10.10.10 Gene3D IPR011991 393 485 44
G3DSA:3.50.50.60 Gene3D 503 569 29
G3DSA:3.50.50.60 Gene3D 993 1038 29
G3DSA:3.50.50.60 Gene3D 606 639 29
G3DSA:3.50.50.60 Gene3D 773 873 29
SSF47095 SuperFamily IPR009071 1109 1203 12
SSF51905 SuperFamily 997 1037 26
SSF51905 SuperFamily 505 565 26
SSF51905 SuperFamily 603 875 26
SSF46689 SuperFamily IPR009057 392 486 25
Coil ncoils Rabaptin coiled-coil domain 1085 1106 975
Coil ncoils Rabaptin coiled-coil domain 1232 1253 975
Low complexity (SEG) seg 574 590
Low complexity (SEG) seg 488 504
Low complexity (SEG) seg 310 324
Low complexity (SEG) seg 85 94
Low complexity (SEG) seg 63 74

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)DuringConditionScaleEvidenceReference
637.39during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633
991.54during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)DuringConditionScaleEvidenceReference
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 ortholog579
predominantly single copy (one to one)3080
conserved in fungi4564
conserved in eukaryotes4482
conserved in metazoa3419
conserved in vertebrates3394
conserved in eukaryotes only2485
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
cxr1mRNA processing factor Affinity Capture-MSPMID:16990277
lsd1histone demethylase SWIRM1 Affinity Capture-MSPMID:17434129
Affinity Capture-MSPMID:16990277
Affinity Capture-MSPMID:17371846
phf2Lsd1/2 complex PHD finger containing protein Phf2 Affinity Capture-MSPMID:17434129
Affinity Capture-MSPMID:16990277
Affinity Capture-MSPMID:17371846
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)
WikiGene2541832histone demethylase SWIRM2 (predicted)
EntrezGene2541832histone demethylase SWIRM2 (predicted)
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 ArchiveBAA87224ENA Protein Mapping
European Nucleotide ArchiveCAA93114ENA Protein Mapping
UniParcUPI000013A14FUniProt Archive

Literature for lsd2

Search: Europe PMC or PubMed

Release Version: PomBase:21_41 - 24 Feb 2014