lid2 (SPBP19A11.06)

Gene Standard Namelid2 ChromosomeII
Systematic IDSPBP19A11.06 Gene Start2863784
SynonymsSPBP4H10.01 Gene End2868411
ProductLid2 complex subunit, predicted histone demethylase Lid2 Gene Length4628
Feature Typeprotein coding CDS Start2863815
Name Description CDS End2868356
Characterisation Statuspublished CDS Length4542

Ensembl Gene Location
  1. mor2
  2. mrp7
  3. SPNCRNA.1555
  4. SPNCRNA.1556
  5. lid2
  6. SPNCRNA.1557
  7. SPBP19A11.07c
  8. oxa102
Fission Yeast Phenotype Ontology

Ontology Graph

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Term IDTerm NameEvidenceAlleleAllele TypeExpressionConditionReference
FYPO:0000091sensitive to thiabendazoleno_name (unrecorded)unrecordedPMID:18957202
FYPO:0000160DNA fragmentationno_name (unrecorded)unrecordedPMID:18957202
FYPO:0000283mitotic chromosome fragmentation upon segregationno_name (unrecorded)unrecordedPMID:18957202
FYPO:0002061inviable vegetative cell populationMicroscopylid2delta (deletion)deletionPMID:20473289
GO Molecular Function

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Term IDTerm NameEvidenceWith/FromReference
GO:0003677DNA bindingISSPS51011GO_REF:0000001
GO:0008270zinc ion bindingIEAIPR001841, IPR001965GO_REF:0000002
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:0000002
GO:0019787small conjugating protein ligase activityISMIPR001965GO_REF:0000024
GO:0034647histone demethylase activity (H3-trimethyl-K4 specific)IDAPMID:18957202
GO Biological Process

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Term IDTerm NameEvidenceWith/FromReference
GO:0000070mitotic sister chromatid segregationIMPPMID:18957202
GO:0006338chromatin remodelingICGO:0048189GO_REF:0000001
GO:0030466chromatin silencing at silent mating-type cassetteIMPPMID:18957202
GO:0030702chromatin silencing at centromereIMPPMID:18957202
GO:0031507heterochromatin assemblyIMPPMID:18957202
GO:0034630RITS complex localizationIMPPMID:18957202
GO:0051567histone H3-K9 methylationIMPPMID:18957202
GO:0051572negative regulation of histone H3-K4 methylationIMPPMID:18957202
GO Cellular Component

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Term IDTerm NameEvidenceWith/FromReference
GO:0005634nucleusIDAPMID:16823372
IDAPMID:18957202
GO:0031618nuclear centromeric heterochromatinIDAPMID:18957202
GO:0031934mating-type region heterochromatinIDAPMID:18957202
GO:0048189Lid2 complexIDAPMID:12488447
Transcript
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Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
128637842868411

References

Region Start End Reference
three_prime_UTR28683572868411PMID:21511999
five_prime_UTR28637842863814PMID:21511999
three_prime_UTR28683572868411PMID: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
PF08429 IPR013637 Pfam Lysine-specific demethylase-like domain 709 1048 2
PF02928 IPR004198 Pfam Zinc finger, C5HC2-type 646 697 3
PF02373 IPR003347 Pfam JmjC domain 442 557 6
PF00628 IPR019787 Pfam Zinc finger, PHD-finger 271 317 15
PF00628 IPR019787 Pfam Zinc finger, PHD-finger 1098 1143 15
PF01388 IPR001606 Pfam ARID/BRIGHT DNA-binding domain 122 208 3
SM01014 SMART 118 208 4
SM00558 IPR003347 SMART JmjC domain 408 574 7
SM00249 IPR001965 SMART Zinc finger, PHD-type 1098 1143 19
SM00249 IPR001965 SMART Zinc finger, PHD-type 270 316 19
SM00249 IPR001965 SMART Zinc finger, PHD-type 1354 1401 19
SM00184 IPR001841 SMART Zinc finger, RING-type 1096 1142 50
SM00184 IPR001841 SMART Zinc finger, RING-type 1354 1400 50
PS51184 IPR003347 Prosite Profiles JmjC domain 408 574 7
PS51011 IPR001606 Prosite Profiles ARID/BRIGHT DNA-binding domain 121 212 4
PS50016 IPR019787 Prosite Profiles Zinc finger, PHD-finger 1352 1403 15
PS50016 IPR019787 Prosite Profiles Zinc finger, PHD-finger 268 318 15
PS50016 IPR019787 Prosite Profiles Zinc finger, PHD-finger 1093 1145 15
PS01359 IPR019786 Prosite Patterns Zinc finger, PHD-type, conserved site 1096 1142 19
PS01359 IPR019786 Prosite Patterns Zinc finger, PHD-type, conserved site 271 315 19
PS01359 IPR019786 Prosite Patterns Zinc finger, PHD-type, conserved site 1355 1400 19
G3DSA:3.30.40.10 IPR013083 Gene3D 1094 1144 84
G3DSA:3.30.40.10 IPR013083 Gene3D 269 316 84
G3DSA:3.30.40.10 IPR013083 Gene3D 1350 1404 84
G3DSA:1.10.150.60 IPR001606 Gene3D 123 218 4
SSF57903 IPR011011 SuperFamily 1353 1413 25
SSF57903 IPR011011 SuperFamily 262 318 25
SSF57903 IPR011011 SuperFamily 1095 1143 25
SSF46774 IPR001606 SuperFamily 103 209 4
SSF51197 SuperFamily 468 568 12
PTHR10694 hmmpanther 59 1411 4
PTHR10694:SF6 hmmpanther 59 1411 1

View domain organization at Pfam

Manually Curated Family or Sub-families

Term IDTerm NameReferenceAll Genes
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
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Gene Expression
DescriptionEvidenceDuringConditionRangeAverage per CellReference
protein levelexperimental evidencesingle-celled organism vegetative growth phasePECO:0000014,
PECO:0000005		population_wide472.15PMID:23101633
experimental evidencecell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127		population_widePMID:23101633
RNA levelexperimental evidencecell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005		population_wide0.73PMID:23101633
experimental evidencesingle-celled organism vegetative growth phasePECO:0000014,
PECO:0000005		population_wide2PMID:23101633
Disease Association
DescriptionQualifierReference
cancer
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
SPAC227.17cconserved protein Positive GeneticPMID:22681890
Physical Interactions

Source: BioGRID

Gene Product Evidence Reference
snt2Lid2 complex subunit Snt2 Affinity Capture-MSPMID:14617822
jmj3Lid2 complex subunit, histone demethylase H3-K36 specific Jmj3 Affinity Capture-MSPMID:14617822
ash2Ash2-trithorax family protein Affinity Capture-MSPMID:14617822
sdc1Dpy-30 domain protein Sdc1 Affinity Capture-MSPMID:14617822
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External References
Database Identifier Description
NBRP SPBP19A11.06 Fission yeast strain database, National BioResource Project (Japan)
YOGY SPBP19A11.06 Retrieval of eukaryotic orthologs
BioGrid SPBP19A11.06 BioGRID Interaction Datasets
Bähler Lab SPBP19A11.06 Cell Cycle Expression Profile
Bähler Lab SPBP19A11.06 Meiosis/Sporulation Expression Profies
Bähler Lab SPBP19A11.06 Pheromone response/mating expression profiles
Bähler Lab SPBP19A11.06 Environmental stress expression profiles
Bähler Lab SPBP19A11.06 Bähler Lab Transcriptome Viewer
Cyclebase SPBP19A11.06 Cell Cycle Data
PInt SPBP19A11.06 Bähler Lab Protein-Protein Interaction Predictor
Entrez Gene SPBP19A11.06 Entrez Gene
SPD / RIKEN49/49H05Orfeome Localization Data
EntrezGene2541299Lid2 complex subunit, with PHD finger and jmjC domain, Lid2
Uniprot_genenameLID2
WikiGene2541299Lid2 complex subunit, with PHD finger and jmjC domain, Lid2
UniProtKB/SwissProtQ9HDV4Lid2 complex component lid2
ModBaseQ9HDV4Database of comparative protein structure models
Pfam Protein DomainsQ9HDV4Pfam Domain Arrangement
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
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Search: UK PMC or PubMed

Release Version: PomBase:18_35 - 11 May 2013