pmc1 (SPAPB2B4.04c)


Gene Standard Namepmc1 Characterisation Statuspublished
Systematic IDSPAPB2B4.04c Feature Typeprotein coding
Synonyms Name Description
Productvacuolar calcium transporting P-type ATPase P2 type, Pmc1 Product Size1292aa, 142.24 kDa
Genomic Location Chromosome I, 2718444-2712704 (5741nt); CDS:2716931-2713053 (3879nt)

Ensembl Gene Location
GO Molecular Function
Term NameCount
ATP binding560
Annotation ExtensionEvidenceWith/FromReference
calcium ion binding39
Annotation ExtensionEvidenceWith/FromReference
calcium-transporting ATPase activity5
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
Term NameCount
calcium ion transmembrane transport15
Annotation ExtensionEvidenceWith/FromReference
cellular calcium ion homeostasis15
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
integral component of fungal-type vacuolar membrane6
Annotation ExtensionEvidenceWith/FromReference
FYPO Single-Allele Phenotypes
Gene Deletion Viability: Viable

Population Phenotype

Term NameGenotypesCount
normal growth on calcium ionpmc1Δ8
normal vegetative cell population growth ratepmc1Δ79
sensitive to calciumpmc1Δ22
viable vegetative cell populationpmc1Δ3844

Cell Phenotype

Term NameGenotypesCount
increased cytosolic calcium levelpmc1Δ6
increased transcription from CDRE promoter in response to calcium ionpmc1Δ6
viable vegetative cell with normal cell morphologypmc1Δ3100

FYPO Multi-allele Phenotypes

Population Phenotype

Term NameGenotypes
normal growth on calcium ioncta5Δ, pmc1Δ
pmr1+, pmc1Δ, cta5Δ
sensitive to amiodaronecta5Δ, pmc1Δ
sensitive to calciumSPCC1672.11cΔ, pmc1Δ
cta5Δ, pmc1Δ
sensitive to manganese depletionpmc1Δ, cta5Δ
pmc1Δ, SPCC1672.11cΔ
slow vegetative cell population growthpmc1Δ, cta5Δ
pmc1Δ, SPCC1672.11cΔ
Target Of
OntologyRelationshipGeneProduct
GO substrate of sst2 human AMSH/STAMBP protein homolog, ubiquitin specific-protease
GO substrate of ubp15 ubiquitin C-terminal hydrolase Ubp15
GO substrate of ubp4 ubiquitin C-terminal hydrolase Ubp4
GO substrate of ubp5 ubiquitin C-terminal hydrolase Ubp5
GO substrate of ubp9 ubiquitin C-terminal hydrolase Ubp9
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons2718444..2712704
mRNA2718444..2712704
5' UTR2718444..2716932PMID:21511999
CDS2716931..2713053
3' UTR2713052..2712704PMID: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
PF00122 Pfam IPR008250 P-type ATPase, A domain 282 534 12
PF00690 Pfam IPR004014 Cation-transporting P-type ATPase, N-terminal 207 248 6
PF00702 Pfam 542 893 6
PF00689 Pfam IPR006068 Cation-transporting P-type ATPase, C-terminal 966 1137 3
SM00831 SMART IPR004014 Cation-transporting P-type ATPase, N-terminal 140 253 5
TMhelix TMHMM 1086 1108 953
TMhelix TMHMM 939 961 953
TMhelix TMHMM 274 296 953
TMhelix TMHMM 1018 1040 953
TMhelix TMHMM 490 512 953
TMhelix TMHMM 448 470 953
TMhelix TMHMM 1118 1136 953
TMhelix TMHMM 237 259 953
PS00154 Prosite Patterns IPR018303 P-type ATPase, phosphorylation site 545 551 14
PTHR24093:SF254 HMMPANTHER 111 1017 1
PTHR24093 HMMPANTHER 1033 1162 9
PTHR24093 HMMPANTHER 111 1017 9
PTHR24093:SF254 HMMPANTHER 1033 1162 1
1.20.1110.10 Gene3D IPR023298 P-type ATPase, transmembrane domain 858 1143 5
1.20.1110.10 Gene3D IPR023298 P-type ATPase, transmembrane domain 354 431 5
3.40.1110.10 Gene3D IPR023299 P-type ATPase, cytoplasmic domain N 533 784 13
SSF56784 SuperFamily IPR023214 HAD-like domain 720 986 41
0049473 SuperFamily 144 170 14
SSF56784 SuperFamily IPR023214 HAD-like domain 542 561 41
SSF81660 SuperFamily IPR023299 P-type ATPase, cytoplasmic domain N 552 784 11
0049471 SuperFamily 315 424 14
0049473 SuperFamily 929 1144 14
0049473 SuperFamily 212 313 14
0049473 SuperFamily 429 537 14
PR00119 PRINTS 777 788 14
PR00119 PRINTS 361 375 14
PR00119 PRINTS 903 915 14
PR00119 PRINTS 799 809 14
PR00119 PRINTS 879 898 14
PR00119 PRINTS 543 557 14
TIGR01494 TIGRFAM IPR001757 P-type ATPase 846 961 14
TIGR01494 TIGRFAM IPR001757 P-type ATPase 479 559 14
TIGR01517 TIGRFAM IPR006408 P-type ATPase, subfamily IIB 605 1141 1

View domain organization at Pfam

Term IDTerm NameReferenceCount
SO:0001812transmembrane_helix465

Protein Properties

Ave. residue weight 110.09 Da
Charge -1.00
Codon Adaptation Index 0.45
Isoelectric point 6.46
Molecular weight 142.24 kDa
Number of residues 1292
Modifications

Protein Modifications

Term NameResidueCount
O-phospho-L-serine 1677
present during mitotic M phaseS15
present during mitotic M phaseS193
present during mitotic M phaseS18
S193
Annotation ExtensionEvidenceResidueReference
present during mitotic M phase experimental evidence S15 PMID:21712547
present during mitotic M phase experimental evidence S193 PMID:21712547
present during mitotic M phase experimental evidence S18 PMID:21712547
experimental evidence S193 PMID:24763107
phosphorylated residue 1932
Annotation ExtensionEvidenceResidueReference
IDA PMID:19547744
ubiquitinylated lysineK451, K473 512
Annotation ExtensionEvidenceResidueReference
mass spectrometry evidence K451 PMID:26412298
mass spectrometry evidence K473 PMID:26412298
IDA PMID:26412298
Sequence
Gene Expression

Qualitative Gene Expression

DescriptionLevelEvidenceReference
RNA levelincreased in presence of purvalanol A expression microarray evidencePMID:22840777

Quantitative Gene Expression

View graphical display of gene expression data for pmc1 (SPAPB2B4.04c)

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
3128during GO:0000080PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
3504during GO:0000084PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
3227during GO:0000085PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
3582during GO:0000087PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
1686.07during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
3595during GO:0072690PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
1597.92during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
2.2during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
1.5during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
Disease Association
DescriptionQualifierReferenceCount
deafness3
Warning
DescriptionQualifierReferenceCount
gene name conflict19
Taxonomic Conservation
DescriptionQualifierReferenceCount
conserved in fungi4606
conserved in eukaryotes4516
conserved in metazoa3424
conserved in vertebrates3399
conserved in eukaryotes only2505
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

Load genes that interact physically with SPAPB2B4.04c into the Query Builder
View all interactions in esyN
View the HCPIN interactions in esyN

Gene Product Evidence Reference
affinity captured bycrp79poly(A) binding protein Crp79 Affinity Capture-RNAPMID:20531409
Genetic Interactions

Source: BioGRID

Load genes that interact genetically with SPAPB2B4.04c into the Query Builder
View these interactions in esyN

Gene Product Evidence Reference
rescued by overexpression ofpmr1P-type ATPase, calcium transporting Pmr1 Dosage RescuePMID:15470240
synthetic lethal withpmr1P-type ATPase, calcium transporting Pmr1 Synthetic LethalityPMID:15470240
positive genetic interaction withjmj2histone demethylase Jmj2 Positive GeneticPMID:22681890
positive genetic interaction withres1MBF transcription factor complex subunit Res1 Positive GeneticPMID:22681890
positive genetic interaction withpar1protein phosphatase PP2A regulatory subunit B-56 Par1 Positive GeneticPMID:22681890
positive genetic interaction withccr4CCR4-Not complex subunit Ccr4 (predicted) Positive GeneticPMID:22681890
positive genetic interaction withelp3elongator complex subunit Elp3 (predicted) Positive GeneticPMID:22681890
positive genetic interaction withset1histone lysine methyltransferase Set1 Positive GeneticPMID:22681890
positive genetic interaction withngg1SAGA complex subunit Ngg1 Positive GeneticPMID:22681890
positive genetic interaction withhus1checkpoint clamp complex protein Hus1 Positive GeneticPMID:22681890
positive genetic interaction withypa2protein phosphatase type 2A regulator, PTPA family Ypa2 Positive GeneticPMID:22681890
positive genetic interaction withprw1Clr6 histone deacetylase complex subunit Prw1 Positive GeneticPMID:22681890
positive genetic interaction withvps35retromer complex subunit Vps35 Positive GeneticPMID:22681890
negative genetic interaction withspc34DASH complex subunit Spc34 Negative GeneticPMID:22681890
negative genetic interaction withask1DASH complex subunit Ask1 Negative GeneticPMID:22681890
negative genetic interaction withplb1phospholipase B homolog Plb1 Negative GeneticPMID:22681890
negative genetic interaction withprz1calcineurin responsive transcription factor Prz1 Negative GeneticPMID:22681890
negative genetic interaction withvph2endoplasmic reticulum membrane protein involved in assembly of the V-ATPase (predicted) Negative GeneticPMID:22681890
External References
Database Identifier Description
NBRP SPAPB2B4.04c Fission yeast strain database, National BioResource Project (Japan)
YOGY SPAPB2B4.04c Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPAPB2B4.04c BioGRID Interaction Datasets
Expression Viewer SPAPB2B4.04c Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPAPB2B4.04c Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPAPB2B4.04c Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPAPB2B4.04c Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPAPB2B4.04c Polyadenylation Viewer (Gullerova lab)
pombeTV SPAPB2B4.04c Transcriptome Viewer (Bähler Lab)
GEO SPAPB2B4.04c GEO profiles
PInt SPAPB2B4.04c Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPAPB2B4.04c Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPAPB2B4.04c Fission yeast phenotypic data & analysis
Cyclebase SPAPB2B4.04c.1 Cell Cycle Data
IntEnz3.6.3.8Integrated relational Enzyme database
Rhea3.6.3.8Annotated reactions database
UniProtKB/SwissProtQ9HDW7Calcium-transporting ATPase 2
ModBaseQ9HDW7Database of comparative protein structure models
STRINGQ9HDW7Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_593890vacuolar calcium transporting P-type ATPase P2 type, Pmc1
RefSeq mRNANM_001019320972h- vacuolar calcium transporting P-type ATPase P2 type, Pmc1 (SPAPB2B4.04c), mRNA
European Nucleotide ArchiveBAA87254.1ENA Protein Mapping
European Nucleotide ArchiveCAC21470.1ENA Protein Mapping
UniParcUPI000006AEE7UniProt Archive

Literature for pmc1

Search: Europe PMC or PubMed

Release Version: PomBase:30_60 - 12 May 2016