lcb2 (SPAC21E11.08)


Gene Standard Namelcb2 Characterisation Statusbiological_role_inferred
Systematic IDSPAC21E11.08 Feature Typeprotein coding
SynonymsSPAC2C4.02 Name Description
Productserine palmitoyltransferase Lcb2 (predicted) Product Size603aa, 67.52 kDa
Genomic Location Chromosome I, 4261533-4263964 (2432nt); CDS:4261888-4263699 (1812nt)

Ensembl Gene Location
GO Molecular Function
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0004758serine C-palmitoyltransferase activityISOSGD:S000002469GO_REF:00000242
GO Biological Process
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0030148sphingolipid biosynthetic processISOSGD:S000002469GO_REF:000002420
GO Cellular Component
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0005783endoplasmic reticulumIDAPMID:16823372594
GO:0016021integral component of membraneIEAUniProtKB-KW:KW-0812GO_REF:00000371018
GO:0017059serine C-palmitoyltransferase complexISOSGD:S000002469GO_REF:00000243
Fission Yeast Phenotype Ontology
Gene Deletion Viability: Inviable

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002061inviable vegetative cell populationMicroscopylcb2ΔNullPMID:204732891338
Microscopylcb2ΔNullPECO:0000005, PECO:0000137PMID:23697806

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0001122elongated vegetative cell685
penetrance FYPO_EXT:0000003Microscopylcb2ΔNullPECO:0000005, PECO:0000137PMID:23697806
FYPO:0002451inviable vegetative cell with abnormal cell shapeMicroscopylcb2ΔNullPECO:0000005, PECO:0000137PMID:23697806460
FYPO:0000647vegetative cell lysis80
penetrance FYPO_EXT:0000003Microscopylcb2ΔNullPECO:0000005, PECO:0000137PMID:23697806
Transcript
Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
142615334263964

UTRs

Region Coordinates Reference
five_prime_UTR4261533..4261887PMID:21511999
three_prime_UTR4263700..4263964PMID: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
PF00155 Pfam IPR004839 Aminotransferase, class I/classII 190 546 11
TMhelix TMHMM 90 109 959
PS00599 Prosite Patterns IPR001917 Aminotransferase, class-II, pyridoxal-phosphate binding site 395 404 3
PTHR13693 HMMPANTHER 28 589 3
PTHR13693:SF3 HMMPANTHER 28 589 1
3.90.1150.10 Gene3D IPR015422 Pyridoxal phosphate-dependent transferase, major region, subdomain 2 431 552 25
3.40.640.10 Gene3D IPR015421 Pyridoxal phosphate-dependent transferase, major region, subdomain 1 210 430 31
SSF53383 SuperFamily IPR015424 Pyridoxal phosphate-dependent transferase 136 554 31
Coil ncoils Rabaptin coiled-coil domain 34 55 968

View domain organization at Pfam

Sequence Ontology

Term IDTerm NameReferenceCount
SO:0001812transmembrane_helix465

Protein Properties

Ave. residue weight 111.97 Da
Charge 8.50
Isoelectric point 7.45
Molecular weight 67.52 kDa
Number of residues 603
Modifications

Protein Modifications

Term IDTerm NameEvidenceResidueReferenceCount
MOD:00046O-phospho-L-serineexperimental evidenceS35PMID:217125471670
present during mitotic M phase
experimental evidenceS35PMID:24763107
present during mitotic M phaseexperimental evidenceS38PMID:21712547
MOD:00047O-phospho-L-threonineexperimental evidenceT36PMID:21712547692
present during mitotic M phase
experimental evidenceT36PMID:24763107
Sequence
Gene Expression

Quantitative Gene Expression

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
40771during GO:0000080PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
45162during GO:0000084PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
39114during GO:0000085PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
41079during GO:0000087PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
17468.94during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
41248during GO:0072690PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
4512.4during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
8.7during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
1.6during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633
Species Distribution
DescriptionQualifierReferenceCount
predominantly single copy (one to one)3092
conserved in fungi4600
conserved in eukaryotes4514
conserved in metazoa3425
conserved in vertebrates3400
conserved in eukaryotes only2497
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

Gene Product Evidence Reference
far8SIP/FAR complex striatin subunit, Far8/Csc3 Affinity Capture-MSPMID:22119525
hhp2serine/threonine protein kinase Hhp2 Affinity Capture-MSPMID:24055157
hhp1serine/threonine protein kinase Hhp1 Affinity Capture-MSPMID:24055157
tea1cell end marker Tea1 Affinity Capture-MSPMID:21652630
paa1protein phosphatase regulatory subunit Paa1 Affinity Capture-MSPMID:22119525
External References
Database Identifier Description
NBRP SPAC21E11.08 Fission yeast strain database, National BioResource Project (Japan)
YOGY SPAC21E11.08 Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPAC21E11.08 BioGRID Interaction Datasets
Expression Viewer SPAC21E11.08 Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPAC21E11.08 Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPAC21E11.08 Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPAC21E11.08 Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPAC21E11.08 Polyadenylation Viewer (Gullerova lab)
pombeTV SPAC21E11.08 Transcriptome Viewer (Bähler Lab)
Cyclebase SPAC21E11.08 Cell Cycle Data
GEO SPAC21E11.08 GEO profiles
PInt SPAC21E11.08 Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPAC21E11.08 Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPAC21E11.08 Fission yeast phenotypic data & analysis
SPD / RIKEN33/33D10Orfeome Localization Data
IntEnz2.3.1.50Integrated relational Enzyme database
Rhea2.3.1.50Annotated reactions database
UniProtKB/SwissProtQ09925Serine palmitoyltransferase 2
ModBaseQ09925Database of comparative protein structure models
STRINGQ09925Network display of known and predicted interactions and functional associations
RefSeq mRNAXM_001713051972h- serine palmitoyltransferase Lcb2 (predicted) (lcb2), mRNA
RefSeq PeptideXP_001713103serine palmitoyltransferase Lcb2 (predicted)
European Nucleotide ArchiveAAC49534.1ENA Protein Mapping
European Nucleotide ArchiveCAA91967.2ENA Protein Mapping
UniParcUPI000012E27FUniProt Archive

Literature for lcb2

Search: Europe PMC or PubMed

Release Version: PomBase:23_47 - 27 Oct 2014