cdc5 (SPAC644.12)


Gene Standard Namecdc5 Characterisation Statuspublished
Systematic IDSPAC644.12 Feature Typeprotein coding
Synonyms Name DescriptionCell Division Cycle
Productsplicing factor, Prp19 complex subunit Cdc5 Product Size757aa, 86.84 kDa
Genomic Location Chromosome I, 2694717-2697430 (2714nt); CDS:2694758-2697334 (2577nt)

Ensembl Gene Location
GO Molecular Function
Term NameCount
DNA binding373
Annotation ExtensionEvidenceWith/FromReference
protein binding862
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
Term NameCount
mRNA cis splicing, via spliceosome120
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
FYPO Single-Allele Phenotypes
Gene Deletion Viability: Inviable

Population Phenotype

Term NameGenotypesCount
inviable vegetative cell populationcdc5-1201450
cdc5Δ

Cell Phenotype

Term NameGenotypesCount
abnormal mitotic cell cyclecdc5Δ849
abnormal mitotic cell cycle arrest with replicated DNAcdc5Δ43
cdc5-120
abnormal mitotic sister chromatid segregationcdc5Δ259
abolished premeiotic DNA replicationcdc5-12015
cell cycle arrest in mitotic G2 phasecdc5-12035
decreased mRNA splicing, via spliceosome36
affecting taf111cdc5+
decreased snRNA splicing15
affecting snu6cdc5+
inviable after spore germinationcdc5Δ809
inviable after spore germination with elongated germ tubecdc5Δ164
inviable elongated mononucleate aseptate cellcdc5-12040
cdc5Δ
inviable swollen elongated vegetative cellcdc5-12028
mitotic cell cycle arrest before cell separationcdc5Δ13
normal sporulationcdc5-12051

FYPO Multi-allele Phenotypes

Population Phenotype

Term NameGenotypes
decreased vegetative cell population growthcdc5-120, prp5-1
inviable vegetative cell populationcdc5-120, prp5-1
Target Of
OntologyRelationshipGeneProduct
FYPO affected by mutation in iss10 Mmi1-driven selective elimination factor Iss10
FYPO affected by mutation in mtl1 TRAMP complex ATP-dependent RNA helicase (predicted)
FYPO affected by mutation in rmn1 RNA-binding protein
FYPO affected by mutation in smn1 SMN family protein Smn1
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons2694717..2694776, 2694817..2694836, 2694903..2694917, 2694982..2695101, 2695171..2695619, 2695684..2697430
Intron2694777..2694816, 2694837..2694902, 2694918..2694981, 2695102..2695170, 2695620..2695683
5' UTR2694717..2694757SPCDC
3' UTR2697335..2697430SPCDC
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
PF11831 Pfam IPR021786 Pre-mRNA splicing factor component Cdc5p/Cef1 416 612 1
PF13921 Pfam 9 69 3
SM00717 SMART IPR001005 SANT/Myb domain 5 54 15
SM00717 SMART IPR001005 SANT/Myb domain 57 104 15
PS51294 Prosite Profiles IPR017930 Myb domain 57 106 5
PS51294 Prosite Profiles IPR017930 Myb domain 1 56 5
PTHR10641 HMMPANTHER 135 196 3
PTHR10641 HMMPANTHER 735 749 3
PTHR10641:SF559 HMMPANTHER 1 104 1
PTHR10641:SF559 HMMPANTHER 135 196 1
PTHR10641:SF559 HMMPANTHER 735 749 1
PTHR10641 HMMPANTHER 1 104 3
1.10.10.60 Gene3D IPR009057 Homeodomain-like 56 103 24
1.10.10.60 Gene3D IPR009057 Homeodomain-like 4 55 24
SSF46689 SuperFamily IPR009057 Homeodomain-like 36 108 25
SSF46689 SuperFamily IPR009057 Homeodomain-like 5 49 25
Coil ncoils Predicted coiled-coil protein (DUF2205) 289 309 1050
Coil ncoils Predicted coiled-coil protein (DUF2205) 658 678 1050
Coil ncoils Predicted coiled-coil protein (DUF2205) 91 115 1050

View domain organization at Pfam

Term IDTerm NameReferenceCount
PBO:0001260Myb familyTemporary processing gif - replaced by AJAX with count of genes annotated with the term PBO:0001260

Protein Properties

Ave. residue weight 114.72 Da
Charge 5.00
Codon Adaptation Index 0.37
Isoelectric point 8.14
Molecular weight 86.84 kDa
Number of residues 757
Modifications

Protein Modifications

Term NameResidueCount
phosphorylated residue 1930
Annotation ExtensionEvidenceResidueReference
IDA PMID:19547744
Sequence
Gene Expression

Quantitative Gene Expression

View graphical display of gene expression data for cdc5 (SPAC644.12)

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
1369during GO:0000080PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
1086during GO:0000084PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
1128during GO:0000085PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
1400during GO:0000087PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
2623.94during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
1275during GO:0072690PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
4297.63during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
2.8during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
0.95during 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)3090
conserved in fungi4604
conserved in eukaryotes4514
conserved in metazoa3422
conserved in vertebrates3397
conserved in eukaryotes only2504
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

Load gene that interact physically with SPAC644.12 into the Query Builder
View all interactions in esyN
View the HCPIN interactions in esyN

Gene Product Evidence Reference
binds DNA-binding domain construct withman1LEM domain protein Man1, Sad1 interacting factor Two-hybridPMID:23695164
binds DNA-binding domain construct withyip5Rab GTPase binding Yip5 (predicted) Two-hybridPMID:23695164
Genetic Interactions

Source: BioGRID

Load gene that interact genetically with SPAC644.12 into the Query Builder
View these interactions in esyN

Gene Product Evidence Reference
negative genetic interaction withatg6autophagy associated beclin family protein Atg6 Negative GeneticPMID:22681890
negative genetic interaction withelp2elongator complex subunit Elp2 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withSPBC16H5.13WD repeat protein, human WDR7 ortholog Negative GeneticPMID:22681890
negative genetic interaction withubp4ubiquitin C-terminal hydrolase Ubp4 Negative GeneticPMID:22681890
negative genetic interaction withvps35retromer complex subunit Vps35 Negative GeneticPMID:22681890
negative genetic interaction withvps17retromer complex subunit Vps17 Negative GeneticPMID:22681890
negative genetic interaction withSPBC651.04Schizosaccharomyces specific protein Negative GeneticPMID:22681890
negative genetic interaction withcho1phosphatidyl-N-dimethylethanolamine N-methyltransferase Negative GeneticPMID:22681890
negative genetic interaction withptc1protein phosphatase 2C Ptc1 Negative GeneticPMID:22681890
negative genetic interaction withvph2endoplasmic reticulum membrane protein involved in assembly of the V-ATPase (predicted) Negative GeneticPMID:22681890
positive genetic interaction withres1MBF transcription factor complex subunit Res1 Positive GeneticPMID:22681890
positive genetic interaction withccr4CCR4-Not complex subunit Ccr4 (predicted) Positive GeneticPMID:22681890
positive genetic interaction withSPBC31F10.10czf-MYND type zinc finger protein Positive GeneticPMID:22681890
positive genetic interaction withiwr1RNA polymerase II nuclear import protein Iwr1 (predicted) Positive GeneticPMID:22681890
positive genetic interaction withmkh1MEK kinase (MEKK) Mkh1 Positive GeneticPMID:22681890
positive genetic interaction withssm4dynactin microtubule-binding subunit, p150-Glued Ssm4 Positive GeneticPMID:22681890
External References
Database Identifier Description
NBRP SPAC644.12 Fission yeast strain database, National BioResource Project (Japan)
YOGY SPAC644.12 Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPAC644.12 BioGRID Interaction Datasets
Expression Viewer SPAC644.12 Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPAC644.12 Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPAC644.12 Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPAC644.12 Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPAC644.12 Polyadenylation Viewer (Gullerova lab)
pombeTV SPAC644.12 Transcriptome Viewer (Bähler Lab)
GEO SPAC644.12 GEO profiles
PInt SPAC644.12 Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPAC644.12 Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPAC644.12 Fission yeast phenotypic data & analysis
Cyclebase SPAC644.12.1 Cell Cycle Data
SPD / RIKEN38/38E01Orfeome Localization Data
UniProtKB/SwissProtP39964Pre-mRNA-splicing factor cdc5
ModBaseP39964Database of comparative protein structure models
STRINGP39964Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_593880cell division control protein, splicing factor Cdc5
RefSeq mRNANM_001019310972h- cell division control protein, splicing factor Cdc5 (cdc5), mRNA
European Nucleotide ArchiveCU329670ENA EMBL mapping
European Nucleotide ArchiveL19525ENA EMBL mapping
ePDB3JB9The European PDB
PDB3JB9PDB
PDBsum3JB9PDBsum
European Nucleotide ArchiveAAA17515ENA Protein Mapping
European Nucleotide ArchiveCAB90139ENA Protein Mapping
UniParcUPI0000127257UniProt Archive

Literature for cdc5

Search: Europe PMC or PubMed

Release Version: PomBase:30_57 - 27 Jan 2016