lid2 (SPBP19A11.06)


Gene Standard Namelid2 Characterisation Statuspublished
Systematic IDSPBP19A11.06 Feature Typeprotein coding
SynonymsSPBP4H10.01 Name Description
ProductLid2 complex subunit, predicted histone demethylase Lid2 Product Size1513aa, 172.26 kDa
Genomic Location Chromosome II, 2863784-2868411 (4628nt); CDS:2863815-2868356 (4542nt)

Ensembl Gene Location
GO Molecular Function
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0003677DNA bindingISSwithGO_REF:0000001385
GO:0034647histone demethylase activity (H3-trimethyl-K4 specific)IDAPMID:189572022
GO:0016706oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donorsIEAIPR013637GO_REF:000000211
GO:0019787small conjugating protein ligase activityISMIPR001965GO_REF:000002423
GO:0008270zinc ion bindingIEAIPR001841GO_REF:0000002249
GO Biological Process
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0034630RITS complex localizationIMPPMID:189572022
GO:0030702chromatin silencing at centromereIMPPMID:1895720253
GO:0030466chromatin silencing at silent mating-type cassetteIMPPMID:1895720232
GO:0031507heterochromatin assemblyIMPPMID:189572028
GO:0034721histone H3-K4 demethylation, trimethyl-H3-K4-specificIDAPMID:189572022
GO:0051567histone H3-K9 methylationIMPPMID:189572022
GO:0000070mitotic sister chromatid segregationIMPPMID:18957202131
GO:0051572negative regulation of histone H3-K4 methylationIMPPMID:189572025
GO Cellular Component
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0048189Lid2 complexIDAPMID:124884475
GO:0031934mating-type region heterochromatinIDAPMID:1895720225
GO:0031618nuclear pericentric heterochromatinIDAPMID:1895720238
GO:0005634nucleusIDAPMID:189572022737
IDAPMID:16823372
Fission Yeast Phenotype Ontology

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002061inviable vegetative cell populationMicroscopylid2ΔNullPMID:204732891337
Microscopylid2ΔNullPECO:0000005, PECO:0000137PMID:23697806
FYPO:0000091sensitive to thiabendazoleCell growth assaynot recorded (unrecorded)PMID:18957202175

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0000160DNA fragmentationnot recorded (unrecorded)PMID:1895720220
FYPO:0000059abnormal mitotic cell cycleMicroscopylid2ΔNullPECO:0000004, PECO:0000137PMID:23697806640
FYPO:0001122elongated vegetative cellMicroscopynot recorded (unrecorded)PMID:18957202663
FYPO:0001490inviable elongated vegetative cell389
penetrance FYPO_EXT:0000003Microscopylid2ΔNullPECO:0000005, PECO:0000137PMID:23697806
FYPO:0001511inviable vegetative cell, abnormal cell shape, normal cell size199
expressivity FYPO_EXT:0000003
penetrance FYPO_EXT:0000001
Microscopylid2ΔNullPECO:0000137, PECO:0000005PMID:23697806
FYPO:0000283mitotic chromosome fragmentation upon segregationnot recorded (unrecorded)PMID:189572024
FYPO:0003087normal chromatin binding at mating-type region replication fork barrier2
affecting lsd1Chromatin immunoprecipitation experimentlid2-jNot specifiedPMID:23260662
Transcript
Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
128637842868411
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
PF00628 Pfam IPR019787 Zinc finger, PHD-finger 1098 1143 15
PF00628 Pfam IPR019787 Zinc finger, PHD-finger 271 317 15
PF02928 Pfam IPR004198 Zinc finger, C5HC2-type 646 697 3
PF02373 Pfam IPR003347 JmjC domain 442 557 6
PF08429 Pfam IPR013637 Lysine-specific demethylase-like domain 709 1048 2
PF01388 Pfam IPR001606 ARID/BRIGHT DNA-binding domain 122 208 3
SM00249 SMART IPR001965 Zinc finger, PHD-type 1098 1143 17
SM00249 SMART IPR001965 Zinc finger, PHD-type 270 316 17
SM00249 SMART IPR001965 Zinc finger, PHD-type 1354 1401 17
SM00558 SMART IPR003347 JmjC domain 408 574 7
SM01014 SMART 118 208 4
PS01359 Prosite Patterns IPR019786 Zinc finger, PHD-type, conserved site 271 315 19
PS01359 Prosite Patterns IPR019786 Zinc finger, PHD-type, conserved site 1096 1142 19
PS01359 Prosite Patterns IPR019786 Zinc finger, PHD-type, conserved site 1355 1400 19
PS51011 Prosite Profiles IPR001606 ARID/BRIGHT DNA-binding domain 121 212 4
PS50016 Prosite Profiles IPR019787 Zinc finger, PHD-finger 1093 1145 15
PS51184 Prosite Profiles IPR003347 JmjC domain 408 574 7
PS50016 Prosite Profiles IPR019787 Zinc finger, PHD-finger 268 318 15
PS50016 Prosite Profiles IPR019787 Zinc finger, PHD-finger 1352 1403 15
PTHR10694:SF6 HMMPANTHER 57 1247 1
PTHR10694 HMMPANTHER 57 1247 4
3.30.40.10 Gene3D IPR013083 Zinc finger, RING/FYVE/PHD-type 1350 1404 86
3.30.40.10 Gene3D IPR013083 Zinc finger, RING/FYVE/PHD-type 1094 1144 86
3.30.40.10 Gene3D IPR013083 Zinc finger, RING/FYVE/PHD-type 269 316 86
1.10.150.60 Gene3D IPR001606 ARID/BRIGHT DNA-binding domain 123 218 4
SSF57903 SuperFamily IPR011011 Zinc finger, FYVE/PHD-type 262 318 25
SSF51197 SuperFamily 468 568 13
SSF57903 SuperFamily IPR011011 Zinc finger, FYVE/PHD-type 1353 1413 25
SSF57903 SuperFamily IPR011011 Zinc finger, FYVE/PHD-type 1095 1143 25
SSF46774 SuperFamily IPR001606 ARID/BRIGHT DNA-binding domain 103 209 4

View domain organization at Pfam

Manually Curated Family or Sub-families

Term IDTerm NameReferenceCount
PBO:0000137zinc finger proteinTemporary processing gif - replaced by AJAX with count of genes annotated with the term PBO:0000137
PBO:0000447zf-PHD fingerTemporary processing gif - replaced by AJAX with count of genes annotated with the term PBO:0000447
PBO:0001099zf-C5HC2 typeTemporary processing gif - replaced by AJAX with count of genes annotated with the term PBO:0001099
PBO:0001100jmjC domainTemporary processing gif - replaced by AJAX with count of genes annotated with the term PBO:0001100
PBO:0001101jmjN domainTemporary processing gif - replaced by AJAX with count of genes annotated with the term PBO:0001101
PBO:0001189ARID domainTemporary processing gif - replaced by AJAX with count of genes annotated with the term PBO:0001189

Protein Properties

Ave. residue weight 113.85 Da
Charge 22.00
Isoelectric point 7.85
Molecular weight 172.26 kDa
Number of residues 1513
Modifications

Protein Modifications

Term IDTerm NameEvidenceResidueReferenceCount
MOD:00046O-phospho-L-serineS1458PMID:247631071670
Sequence
Gene Expression

Quantitative Gene Expression

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
566during GO:0000080PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
932during GO:0000084PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
678during GO:0000085PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
560during GO:0000087PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
654during GO:0072690PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
472.15during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
NDduring cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
2during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
0.73during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633
Disease Association
DescriptionQualifierReferenceCount
cancer142
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
SPAC227.17cconserved protein Positive GeneticPMID:22681890
Physical Interactions

Source: BioGRID

Gene Product Evidence Reference
lid2Lid2 complex subunit, predicted histone demethylase Lid2 Affinity Capture-MSPMID:14617822
jmj3Lid2 complex subunit, histone demethylase H3-K36 specific Jmj3 Affinity Capture-MSPMID:14617822
sdc1Dpy-30 domain protein Sdc1 Affinity Capture-MSPMID:14617822
snt2Lid2 complex subunit Snt2 Affinity Capture-MSPMID:14617822
ash2Ash2-trithorax family protein Affinity Capture-MSPMID:14617822
External References
Database Identifier Description
NBRP SPBP19A11.06 Fission yeast strain database, National BioResource Project (Japan)
YOGY SPBP19A11.06 Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPBP19A11.06 BioGRID Interaction Datasets
Expression Viewer SPBP19A11.06 Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPBP19A11.06 Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPBP19A11.06 Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPBP19A11.06 Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPBP19A11.06 Polyadenylation Viewer (Gullerova lab)
pombeTV SPBP19A11.06 Transcriptome Viewer (Bähler Lab)
Cyclebase SPBP19A11.06 Cell Cycle Data
GEO SPBP19A11.06 GEO profiles
PInt SPBP19A11.06 Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPBP19A11.06 Peptides identified in tandem mass spectrometry proteomics experiments
SPD / RIKEN49/49H05Orfeome Localization Data
UniProtKB/SwissProtQ9HDV4Lid2 complex component lid2
ModBaseQ9HDV4Database of comparative protein structure models
STRINGQ9HDV4Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_596174Lid2 complex subunit, predicted histone demethylase Lid2
RefSeq mRNANM_001022094972h- Lid2 complex subunit, predicted histone demethylase Lid2 (lid2), mRNA
European Nucleotide ArchiveCAC19756.1ENA Protein Mapping
UniParcUPI0000069D9AUniProt Archive

Literature for lid2

Search: Europe PMC or PubMed

Release Version: PomBase:23_46 - 30 Aug 2014