lsd2 (SPAC23E2.02)

Gene Standard Namelsd2 ChromosomeI
Systematic IDSPAC23E2.02 Gene Start446491
Synonymssaf140, swm2 Gene End450726
Producthistone demethylase SWIRM2 (predicted) Gene Length4236
Feature Typeprotein coding CDS Start446491
Name Description CDS End450530
Characterisation Statuspublished CDS Length4040

Ensembl Gene Location
  1. fep1
  2. SPATRNAVAL.01
  3. SPNCRNA.649
  4. lsd2
  5. ste7
  6. SPNCRNA.650
Fission Yeast Phenotype Ontology

Ontology Graph

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Term IDTerm NameEvidenceAlleleAllele TypeExpressionConditionReference
FYPO:0001489inviable vegetative cellMicroscopylsd2delta (deletion)deletionPMID:20473289
no_name (unrecorded)unrecordedPMID:16990277
GO Molecular Function

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Term IDTerm NameEvidenceWith/FromReference
GO:0003677DNA bindingIEAUniProtKB:KW-0238GO_REF:0000037
GO:0003714transcription corepressor activityISSUniProtKB:O60341GO_REF:0000001
GO:0016491oxidoreductase activityIEAUniProtKB:KW-0560GO_REF:0000037
GO:0031491nucleosome binding
contributes_toIDAPMID:17371846
GO:0034649histone demethylase activity (H3-monomethyl-K4 specific)NASGO_REF:0000001
GO Biological Process

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Term IDTerm NameEvidenceWith/FromReference
GO:0006338chromatin remodelingISSUniProtKB:O60341GO_REF:0000001
GO:0033169histone H3-K9 demethylationIMPPMID:17434129
GO:0034605cellular response to heatIEPPMID:17371846
GO:0040020regulation of meiosisIMPPMID:17434129
GO:0045892negative regulation of transcription, DNA-dependentICGO:0003714GO_REF:0000001
GO:0045893positive regulation of transcription, DNA-dependentIMPPMID:16990277
GO Cellular Component

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Term IDTerm NameEvidenceWith/FromReference
GO:0000790nuclear chromatinICGO:0016577GO_REF:0000001
GO:0005634nucleusIDAPMID:16823372
IDAPMID:10759889
GO:0005829cytosolIDAPMID:16823372
GO:0033193Lsd1/2 complexIDAPMID:17434129
Transcript
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Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
1446491446513
2446679449241
3449295450726

References

Region Start End Reference
three_prime_UTR450531450726PMID:21511999
Protein Features
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Graphical View

Ensembl protein image with mapped locations of structural domains

Protein Families and Domains

Feature ID InterPro Database Description Start End All Genes
PF01593 IPR002937 Pfam Amine oxidase 516 1035 3
PF04433 IPR007526 Pfam SWIRM domain 396 481 7
SM00398 IPR009071 SMART High mobility group (HMG) box domain 1114 1196 10
PS50934 IPR007526 Prosite Profiles SWIRM domain 394 490 7
PS50118 IPR009071 Prosite Profiles High mobility group (HMG) box domain 1115 1195 9
G3DSA:1.10.30.10 IPR009071 Gene3D 1111 1207 11
G3DSA:1.10.10.10 IPR011991 Gene3D 393 485 43
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 IPR009071 SuperFamily 1109 1203 12
SSF51905 SuperFamily 997 1037 26
SSF51905 SuperFamily 505 565 26
SSF51905 SuperFamily 603 875 26
SSF46689 IPR009057 SuperFamily 392 486 25
Coil ncoils Rabaptin coiled-coil domain 1085 1106 974
Coil ncoils Rabaptin coiled-coil domain 1232 1253 974
PTHR10742:SF151 hmmpanther 100 1211 1
PTHR10742 hmmpanther 100 1211 3

View domain organization at Pfam

Manually Curated Family or Sub-families

Term IDTerm NameReferenceAll Genes
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
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Gene Expression
DescriptionEvidenceDuringConditionRangeAverage per CellReference
protein levelexperimental evidencecell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005		population_wide637.39PMID:23101633
experimental evidencevegetative growth of a single-celled organismPECO:0000014,
PECO:0000005		population_wide991.54PMID:23101633
RNA levelexperimental evidencecell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005		population_wide0.46PMID:23101633
experimental evidencevegetative growth of a single-celled organismPECO:0000014,
PECO:0000005		population_wide1.5PMID:23101633
Species Distribution
DescriptionQualifierReference
no apparent S. cerevisiae ortholog
predominantly single copy (one to one)
conserved in fungi
conserved in eukaryotes
conserved in metazoa
conserved in vertebrates
conserved in eukaryotes only
Manually curated orthologous groups
SpeciesGeneDescription

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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:17371846
Affinity Capture-MSPMID:17434129
SPBC23E6.01cmRNA processing factor (predicted) Affinity Capture-MSPMID:16990277
lsd1histone demethylase SWIRM1 Affinity Capture-MSPMID:16990277
Affinity Capture-MSPMID:17371846
Affinity Capture-MSPMID:17434129
phf2Lsd1/2 complex PHD finger containing protein Phf2 Affinity Capture-MSPMID:16990277
Affinity Capture-MSPMID:17434129
Affinity Capture-MSPMID:17371846
hrp1ATP-dependent DNA helicase Hrp1 Affinity Capture-MSPMID:16990277
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External References
Database Identifier Description
NBRP SPAC23E2.02 Fission yeast strain database, National BioResource Project (Japan)
YOGY SPAC23E2.02 Retrieval of eukaryotic orthologs
BioGrid SPAC23E2.02 BioGRID Interaction Datasets
Bähler Lab SPAC23E2.02 Cell Cycle Expression Profile
Bähler Lab SPAC23E2.02 Meiosis/Sporulation Expression Profies
Bähler Lab SPAC23E2.02 Pheromone response/mating expression profiles
Bähler Lab SPAC23E2.02 Environmental stress expression profiles
Bähler Lab SPAC23E2.02 Bähler Lab Transcriptome Viewer
Cyclebase SPAC23E2.02 Cell Cycle Data
PInt SPAC23E2.02 Bähler Lab Protein-Protein Interaction Predictor
Entrez Gene SPAC23E2.02 Entrez Gene
WikiGene2541832histone demethylase SWIRM2 (predicted)
Uniprot_genenameLSD2
EntrezGene2541832histone demethylase SWIRM2 (predicted)
SPD / RIKEN48/48F11Orfeome Localization Data
UniProtKB/SwissProtQ10135Lysine-specific histone demethylase 2
ModBaseQ10135Database of comparative protein structure models
Pfam Protein DomainsQ10135Pfam Domain Arrangement
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
SPD / RIKEN48/48F11Orfeome Localization Data

Literature for lsd2
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Search: UK PMC or PubMed

Release Version: PomBase:18.34 - 04 Apr 2013