lcb4 (SPAC4A8.07c)


Gene Standard Namelcb4 Characterisation Statusbiological role inferred
Systematic IDSPAC4A8.07c Feature Typeprotein coding
Synonyms Name Description
Productsphingoid long chain base kinase (predicted) Product Size458aa, 51.29 kDa
Genomic Location Chromosome I, 2558444-2556600 (1845nt); CDS:2558297-2556773 (1525nt)

Ensembl Gene Location
GO Molecular Function
Term NameCount
ATP binding559
Annotation ExtensionEvidenceWith/FromReference
D-erythro-sphingosine kinase activity1
Annotation ExtensionEvidenceWith/FromReference
diacylglycerol kinase activity1
Annotation ExtensionEvidenceWith/FromReference
sphinganine kinase activity1
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
Term NameCount
calcium-mediated signaling10
Annotation ExtensionEvidenceWith/FromReference
sphingoid biosynthetic process2
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
endoplasmic reticulum596
Annotation ExtensionEvidenceWith/FromReference
Golgi apparatus357
Annotation ExtensionEvidenceWith/FromReference
late endosome membrane8
Annotation ExtensionEvidenceWith/FromReference
plasma membrane255
Annotation ExtensionEvidenceWith/FromReference
FYPO Single-Allele Phenotypes
Gene Deletion Viability: Viable

Population Phenotype

Term NameGenotypesCount
viable vegetative cell populationlcb4Δ3840

Cell Phenotype

Term NameGenotypesCount
viable vegetative cell with normal cell morphologylcb4Δ3100
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons2558444..2558183, 2558123..2557938, 2557848..2556600
Intron2558182..2558124, 2557937..2557849
mRNA2558444..2556600
5' UTR2558444..2558298PMID:21511999
CDS2558297..2558183, 2558123..2557938, 2557848..2556773
3' UTR2556772..2556600PMID: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
PF00781 Pfam IPR001206 Diacylglycerol kinase, catalytic domain 108 236 1
SM00046 SMART IPR001206 Diacylglycerol kinase, catalytic domain 107 265 1
PS50146 Prosite Profiles IPR001206 Diacylglycerol kinase, catalytic domain 103 241 1
PTHR12358:SF31 HMMPANTHER 85 449 1
PTHR12358 HMMPANTHER 85 449 2
SSF111331 SuperFamily IPR016064 NAD kinase/diacylglycerol kinase-like domain 331 449 5
SSF111331 SuperFamily IPR016064 NAD kinase/diacylglycerol kinase-like domain 105 293 5

View domain organization at Pfam

Protein Properties

Ave. residue weight 111.98 Da
Charge 3.50
Codon Adaptation Index 0.44
Isoelectric point 7.06
Molecular weight 51.29 kDa
Number of residues 458
Sequence
Gene Expression

Quantitative Gene Expression

View graphical display of gene expression data for lcb4 (SPAC4A8.07c)

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
13263during GO:0000080PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
12517during GO:0000084PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
13242during GO:0000085PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
12856during GO:0000087PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
3541.23during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
13051during GO:0072690PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
2767.91during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
1.8during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
0.57during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
Taxonomic Conservation
DescriptionQualifierReferenceCount
conserved in fungi4606
conserved in eukaryotes4516
conserved in bacteria1001
conserved in metazoa3424
conserved in vertebrates3399
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


External References
Database Identifier Description
NBRP SPAC4A8.07c Fission yeast strain database, National BioResource Project (Japan)
YOGY SPAC4A8.07c Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPAC4A8.07c BioGRID Interaction Datasets
Expression Viewer SPAC4A8.07c Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPAC4A8.07c Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPAC4A8.07c Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPAC4A8.07c Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPAC4A8.07c Polyadenylation Viewer (Gullerova lab)
pombeTV SPAC4A8.07c Transcriptome Viewer (Bähler Lab)
GEO SPAC4A8.07c GEO profiles
PInt SPAC4A8.07c Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPAC4A8.07c Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPAC4A8.07c Fission yeast phenotypic data & analysis
Cyclebase SPAC4A8.07c.1 Cell Cycle Data
SPD / RIKEN24/24G05Orfeome Localization Data
IntEnz2.7.1.107Integrated relational Enzyme database
Rhea2.7.1.107Annotated reactions database
UniProtKB/SwissProtO14159Sphingoid long chain base kinase 4
ModBaseO14159Database of comparative protein structure models
STRINGO14159Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_593818sphingoid long chain base kinase (predicted)
RefSeq mRNANM_001019248972h- sphingoid long chain base kinase (predicted) (SPAC4A8.07c), mRNA

Literature for lcb4

Search: Europe PMC or PubMed

Release Version: PomBase:30_59 - 12 Apr 2016