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 bindingISSPS51011GO_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:000000212
GO:0019787small conjugating protein ligase activityISMIPR001965GO_REF:0000024105
GO:0008270zinc ion bindingIEAIPR001841GO_REF:0000002248
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:189572027
GO:0034721histone H3-K4 demethylation, trimethyl-H3-K4-specificIDAPMID:189572022
GO:0051567histone H3-K9 methylationIMPPMID:189572022
GO:0000070mitotic sister chromatid segregationIMPPMID:18957202133
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 centromeric heterochromatinIDAPMID:1895720219
GO:0005634nucleusIDAPMID:189572022730
IDAPMID:16823372
Fission Yeast Phenotype Ontology

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002061inviable vegetative cell populationMicroscopylid2ΔNullPMID:204732891309
Microscopylid2ΔNullPECO:0000005, PECO:0000137PMID:23697806
FYPO:0000091sensitive to thiabendazoleno_namePMID:1895720292

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0000160DNA fragmentationno_namePMID:1895720219
FYPO:0000059abnormal mitotic cell cycleMicroscopylid2ΔNullPECO:0000004, PECO:0000137PMID:23697806564
FYPO:0001122elongated vegetative cellno_namePMID:18957202624
FYPO:0001490inviable elongated vegetative cellMicroscopylid2ΔNullPECO:0000005, PECO:0000137PMID:23697806368
penetrance FYPO_EXT:0000003
FYPO:0001511inviable vegetative cell, abnormal cell shape, normal cell sizeMicroscopylid2ΔNullPECO:0000137, PECO:0000005PMID:23697806198
expressivity FYPO_EXT:0000003
penetrance FYPO_EXT:0000001
FYPO:0000283mitotic chromosome fragmentation upon segregationno_namePMID:189572022
FYPO:0003087normal chromatin binding at mating-type region replication fork barrierChromatin immunoprecipitation experimentlid2-jNot specifiedPMID:232606622
affecting lsd1
Transcript
Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
128637842868411

UTRs

Region Start End Reference
five_prime_UTR28637842863814PMID:21511999
three_prime_UTR28683572868411PMID: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
PF00628 Pfam IPR019787 Zinc finger, PHD-finger 271 317 16
PF00628 Pfam IPR019787 Zinc finger, PHD-finger 1098 1143 16
PF02373 Pfam IPR003347 JmjC domain 442 557 6
PF01388 Pfam IPR001606 ARID/BRIGHT DNA-binding domain 122 208 3
PF08429 Pfam IPR013637 Lysine-specific demethylase-like domain 709 1048 2
PF02928 Pfam IPR004198 Zinc finger, C5HC2-type 646 697 3
SM01014 SMART 118 208 4
SM00558 SMART IPR003347 JmjC domain 408 574 7
SM00249 SMART IPR001965 Zinc finger, PHD-type 1098 1143 19
SM00249 SMART IPR001965 Zinc finger, PHD-type 270 316 19
SM00249 SMART IPR001965 Zinc finger, PHD-type 1354 1401 19
SM00184 SMART IPR001841 Zinc finger, RING-type 1096 1142 51
SM00184 SMART IPR001841 Zinc finger, RING-type 1354 1400 51
PS51184 Prosite Profiles IPR003347 JmjC domain 408 574 7
PS51011 Prosite Profiles IPR001606 ARID/BRIGHT DNA-binding domain 121 212 4
PS50016 Prosite Profiles IPR019787 Zinc finger, PHD-finger 1352 1403 15
PS50016 Prosite Profiles IPR019787 Zinc finger, PHD-finger 268 318 15
PS50016 Prosite Profiles IPR019787 Zinc finger, PHD-finger 1093 1145 15
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 57 1247 4
PTHR10694:SF6 HMMPANTHER 57 1247 1
G3DSA:3.30.40.10 Gene3D IPR013083 1094 1144 84
G3DSA:3.30.40.10 Gene3D IPR013083 269 316 84
G3DSA:3.30.40.10 Gene3D IPR013083 1350 1404 84
G3DSA:1.10.150.60 Gene3D IPR001606 123 218 4
SSF57903 SuperFamily IPR011011 1353 1413 25
SSF57903 SuperFamily IPR011011 262 318 25
SSF57903 SuperFamily IPR011011 1095 1143 25
SSF46774 SuperFamily IPR001606 103 209 4
SSF51197 SuperFamily 468 568 13
Low complexity (SEG) seg 209 228
Low complexity (SEG) seg 773 785
Low complexity (SEG) seg 1287 1315

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
Sequence
Gene Expression

Quantitative Gene Expression

Protein Level

Molecules/Cell (average)DuringConditionScaleEvidenceReference
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)DuringConditionScaleEvidenceReference
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
cancer141
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
SPAC227.17cconserved protein Positive GeneticPMID:22681890
Physical Interactions

Source: BioGRID

Gene Product Evidence Reference
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)
SPD / RIKEN49/49H05Orfeome Localization Data
EntrezGene2541299Lid2 complex subunit, with PHD finger and jmjC domain, Lid2
WikiGene2541299Lid2 complex subunit, with PHD finger and jmjC domain, Lid2
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, with PHD finger and jmjC domain, Lid2
RefSeq mRNANM_001022094972h- Lid2 complex subunit, with PHD finger and jmjC domain, Lid2 (lid2), mRNA
European Nucleotide ArchiveCAC19756ENA Protein Mapping
UniParcUPI0000069D9AUniProt Archive

Literature for lid2

Search: Europe PMC or PubMed

Release Version: PomBase:21_41 - 24 Feb 2014