lcb1 (SPBC18E5.02c)


Gene Standard Namelcb1 Characterisation Statusbiological role inferred
Systematic IDSPBC18E5.02c Feature Typeprotein coding
SynonymsSPBC29A3.20c Name Description
Productserine palmitoyltransferase complex subunit (predicted) Product Size509aa, 57.47 kDa
Genomic Location Chromosome II, 2079050-2076986 (2065nt); CDS:2078859-2077163 (1697nt)

Ensembl Gene Location
GO Molecular Function
Term NameCount
serine C-palmitoyltransferase activity2
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
Term NameCount
sphingolipid biosynthetic process21
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
endoplasmic reticulum599
Annotation ExtensionEvidenceWith/FromReference
integral component of membrane966
Annotation ExtensionEvidenceWith/FromReference
serine C-palmitoyltransferase complex4
Annotation ExtensionEvidenceWith/FromReference
FYPO Single-Allele Phenotypes
Gene Deletion Viability: Inviable

Population Phenotype

Term NameGenotypesCount
inviable vegetative cell populationlcb1Δ1455

Cell Phenotype

Term NameGenotypesCount
inviable after spore germination with normal, unseptated germ tube morphologylcb1Δ237
inviable sporelcb1Δ476
Target Of
OntologyRelationshipGeneProduct
GO substrate of ubp5 ubiquitin C-terminal hydrolase Ubp5
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons2079050..2078614, 2078555..2078455, 2078398..2077408, 2077354..2076986
Intron2078613..2078556, 2078454..2078399, 2077407..2077355
mRNA2079050..2076986
5' UTR2079050..2078860PMID:21511999
CDS2078859..2078614, 2078555..2078455, 2078398..2077408, 2077354..2077163
3' UTR2077162..2076986PMID: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 128 489 11
PTHR13693 HMMPANTHER 1 509 3
PTHR13693:SF2 HMMPANTHER 1 509 1
3.40.640.10 Gene3D IPR015421 Pyridoxal phosphate-dependent transferase, major region, subdomain 1 146 383 31
SSF53383 SuperFamily IPR015424 Pyridoxal phosphate-dependent transferase 87 494 31

View domain organization at Pfam

Protein Properties

Ave. residue weight 112.91 Da
Charge 0.50
Codon Adaptation Index 0.49
Isoelectric point 6.58
Molecular weight 57.47 kDa
Number of residues 509
Modifications

Protein Modifications

Term NameResidueCount
O-phospho-L-serineS183 2289
Annotation ExtensionEvidenceResidueReference
IDA S183 PMID:25720772
Sequence
Gene Expression

Quantitative Gene Expression

View graphical display of gene expression data for lcb1 (SPBC18E5.02c)

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
27174during GO:0000080PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
27021during GO:0000084PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
27111during GO:0000085PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
25206during GO:0000087PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
16262.98during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
27606during GO:0072690PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
7132.53during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
4.5during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
0.96during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
Taxonomic Conservation
DescriptionQualifierReferenceCount
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 SPBC18E5.02c into the Query Builder
View all interactions in esyN
View the HCPIN interactions in esyN

Gene Product Evidence Reference
affinity captured bypaa1protein phosphatase regulatory subunit Paa1 Affinity Capture-MSPMID:22119525
External References
Database Identifier Description
NBRP SPBC18E5.02c Fission yeast strain database, National BioResource Project (Japan)
YOGY SPBC18E5.02c Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPBC18E5.02c BioGRID Interaction Datasets
Expression Viewer SPBC18E5.02c Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPBC18E5.02c Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPBC18E5.02c Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPBC18E5.02c Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPBC18E5.02c Polyadenylation Viewer (Gullerova lab)
pombeTV SPBC18E5.02c Transcriptome Viewer (Bähler Lab)
GEO SPBC18E5.02c GEO profiles
PInt SPBC18E5.02c Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPBC18E5.02c Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPBC18E5.02c Fission yeast phenotypic data & analysis
Cyclebase SPBC18E5.02c.1 Cell Cycle Data
IntEnz2.3.1.50Integrated relational Enzyme database
Rhea2.3.1.50Annotated reactions database
SPD / RIKEN35/35D03Orfeome Localization Data
UniProtKB/SwissProtO59682Serine palmitoyltransferase 1
ModBaseO59682Database of comparative protein structure models
STRINGO59682Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_595848serine palmitoyltransferase complex subunit (predicted)
RefSeq mRNANM_001021752972h- serine palmitoyltransferase complex subunit (predicted) (SPBC18E5.02c), mRNA
European Nucleotide ArchiveCAA18397.1ENA Protein Mapping
UniParcUPI000006C847UniProt Archive

Literature for lcb1

Search: Europe PMC or PubMed

Release Version: PomBase:30_61 - 12 Sep 2016