lid2 (SPBP19A11.06)


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

Ensembl Gene Location
GO Molecular Function
GO Biological Process
Term NameCount
chromatin remodeling154
Annotation ExtensionEvidenceWith/FromReference
chromatin silencing at centromere58
Annotation ExtensionEvidenceWith/FromReference
chromatin silencing at silent mating-type cassette36
Annotation ExtensionEvidenceWith/FromReference
heterochromatin assembly34
Annotation ExtensionEvidenceWith/FromReference
histone H3-K9 methylation13
Annotation ExtensionEvidenceWith/FromReference
mitotic sister chromatid segregation187
Annotation ExtensionEvidenceWith/FromReference
negative regulation of histone H3-K4 methylation5
Annotation ExtensionEvidenceWith/FromReference
RITS complex localization2
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
Lid2 complex5
Annotation ExtensionEvidenceWith/FromReference
mating-type region heterochromatin29
Annotation ExtensionEvidenceWith/FromReference
nuclear pericentric heterochromatin42
Annotation ExtensionEvidenceWith/FromReference
nucleus2700
Annotation ExtensionEvidenceWith/FromReference
FYPO Single-Allele Phenotypes
Gene Deletion Viability: Inviable

Population Phenotype

Term NameGenotypesCount
inviable vegetative cell populationlid2Δ1455
sensitive to thiabendazole329

Cell Phenotype

Term NameGenotypesCount
abnormal mitotic cell cyclelid2Δ894
elongated vegetative cell802
fragmented DNA26
inviable elongated vegetative celllid2Δ420
inviable vegetative cell, abnormal cell shape, normal cell sizelid2Δ199
mitotic chromosome fragmentation upon segregation5
normal chromatin binding at mating-type region replication fork barrier2
affecting lsd1lid2-j
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons2863784..2868411
mRNA2863784..2868411
5' UTR2863784..2863814PMID:21511999
CDS2863815..2868356
3' UTR2868357..2868411PMID: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
PF08429 Pfam IPR013637 Lysine-specific demethylase-like domain 710 1048 2
PF00628 Pfam IPR019787 Zinc finger, PHD-finger 271 317 13
PF02928 Pfam IPR004198 Zinc finger, C5HC2-type 646 697 3
PF01388 Pfam IPR001606 ARID DNA-binding domain 126 208 3
PF02373 Pfam IPR003347 JmjC domain 442 557 6
SM00558 SMART IPR003347 JmjC domain 408 574 7
SM01014 SMART 118 208 4
SM00249 SMART IPR001965 Zinc finger, PHD-type 1354 1401 17
SM00249 SMART IPR001965 Zinc finger, PHD-type 1098 1143 17
SM00249 SMART IPR001965 Zinc finger, PHD-type 270 316 17
PS50016 Prosite Profiles IPR019787 Zinc finger, PHD-finger 1352 1403 15
PS50016 Prosite Profiles IPR019787 Zinc finger, PHD-finger 1093 1145 15
PS50016 Prosite Profiles IPR019787 Zinc finger, PHD-finger 268 318 15
PS51011 Prosite Profiles IPR001606 ARID DNA-binding domain 121 212 4
PS51184 Prosite Profiles IPR003347 JmjC domain 408 574 7
PS01359 Prosite Patterns IPR019786 Zinc finger, PHD-type, conserved site 1355 1400 19
PS01359 Prosite Patterns IPR019786 Zinc finger, PHD-type, conserved site 1096 1142 19
PS01359 Prosite Patterns IPR019786 Zinc finger, PHD-type, conserved site 271 315 19
PTHR10694 HMMPANTHER 82 242 4
PTHR10694 HMMPANTHER 306 1294 4
PTHR10694 HMMPANTHER 1353 1370 4
PTHR10694:SF8 HMMPANTHER 82 242 3
PTHR10694:SF8 HMMPANTHER 306 1294 3
PTHR10694:SF8 HMMPANTHER 1353 1370 3
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 1350 1404 86
1.10.150.60 Gene3D IPR001606 ARID DNA-binding domain 123 218 4
3.30.40.10 Gene3D IPR013083 Zinc finger, RING/FYVE/PHD-type 269 316 86
SSF57903 SuperFamily IPR011011 Zinc finger, FYVE/PHD-type 1353 1413 25
SSF46774 SuperFamily IPR001606 ARID DNA-binding domain 103 209 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 1095 1143 25

View domain organization at Pfam

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
Codon Adaptation Index 0.39
Isoelectric point 7.85
Molecular weight 172.26 kDa
Number of residues 1513
Modifications

Protein Modifications

Term NameResidueCount
O-phospho-L-serineS1341, S1458 2289
Annotation ExtensionEvidenceResidueReference
IDA S1341 PMID:25720772
IDA S1458 PMID:25720772
experimental evidence S1458 PMID:24763107
O-phosphorylated residueS1077,S1081, S1077,T1080 2457
Annotation ExtensionEvidenceResidueReference
IDA S1077,S1081 PMID:25720772
IDA S1077,T1080 PMID:25720772
Sequence
Gene Expression

Quantitative Gene Expression

View graphical display of gene expression data for lid2 (SPBP19A11.06)

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
566during GO:0000080PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
932during GO:0000084PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
678during GO:0000085PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
560during GO:0000087PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
654during GO:0072690PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
472.15during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
2during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
0.73during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
Disease Association
DescriptionQualifierReferenceCount
cancer148
Taxonomic Conservation
DescriptionQualifierReferenceCount
no apparent S. cerevisiae ortholog600
predominantly single copy (one to one)3093
conserved in fungi4607
conserved in eukaryotes4517
conserved in metazoa3427
conserved in vertebrates3402
conserved in eukaryotes only2502
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

Load genes that interact physically with SPBP19A11.06 into the Query Builder
View all interactions in esyN
View the HCPIN interactions in esyN

Gene Product Evidence Reference
affinity captured bysnt2Lid2 complex PHD finger subunit Snt2 Affinity Capture-MSPMID:14617822
affinity captured byash2Ash2-trithorax family protein Affinity Capture-MSPMID:14617822
affinity captured bysdc1Dpy-30 domain protein Sdc1 Affinity Capture-MSPMID:14617822
affinity capturessnt2Lid2 complex PHD finger subunit Snt2 Affinity Capture-MSPMID:14617822
affinity captureslid2Lid2 complex PHD finger and jmjC subunit Lid2 Affinity Capture-MSPMID:14617822
affinity capturesash2Ash2-trithorax family protein Affinity Capture-MSPMID:14617822
affinity capturesjmj3Lid2 complex subunit, histone demethylase H3-K36 specific Jmj3 Affinity Capture-MSPMID:14617822
Genetic Interactions

Source: BioGRID

Load genes that interact genetically with SPBP19A11.06 into the Query Builder
View these interactions in esyN

Gene Product Evidence Reference
positive genetic interaction withSPAC227.17cconserved eukaryotic protein, DUF3128, human c22orf39 ortholog Positive GeneticPMID:22681890
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)
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
SYSGRO SPBP19A11.06 Fission yeast phenotypic data & analysis
Cyclebase SPBP19A11.06.1 Cell Cycle Data
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:30_61 - 12 Sep 2016