SPAC24C9.12c


Gene Standard NameUnassigned Characterisation Statusbiological_role_inferred
Systematic IDSPAC24C9.12c Feature Typeprotein coding
Synonyms Name Description
Productglycine hydroxymethyltransferase (predicted) Product Size467aa, 51.86 kDa
Genomic Location Chromosome I, 3071192-3069322 (1871nt); CDS:3071017-3069614 (1404nt)

Ensembl Gene Location
GO Molecular Function
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0004372glycine hydroxymethyltransferase activityISSUniProtKB:P37291GO_REF:00000012
GO:0030170pyridoxal phosphate bindingIEAIPR015421GO_REF:000000226
GO Biological Process
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0006563L-serine metabolic processISSUniProtKB:P37291GO_REF:000000112
GO:0006544glycine metabolic processISSUniProtKB:P37291GO_REF:00000019
GO:0006730one-carbon metabolic processISSUniProtKB:P37291GO_REF:000000110
GO:0035999tetrahydrofolate interconversionIEA UniPathway:UPA00193GO_REF:00000417
GO Cellular Component
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0005737cytoplasmISSUniProtKB:P37291GO_REF:00000014201
Fission Yeast Phenotype Ontology

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002060viable vegetative cell populationMicroscopySPAC24C9.12cΔNullPMID:204732893730
MicroscopySPAC24C9.12cΔNullPECO:0000005, PECO:0000137PMID:23697806

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002177viable vegetative cell with normal cell morphology3088
penetrance FYPO_EXT:0000001MicroscopySPAC24C9.12cΔNullPECO:0000005, PECO:0000137PMID:23697806
Transcript
Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
130711923069322

UTRs

Region Coordinates Reference
five_prime_UTR3071192..3071018PMID: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
PF00464 Pfam IPR001085 Serine hydroxymethyltransferase 12 410 2
PS00096 Prosite Patterns IPR019798 Serine hydroxymethyltransferase, pyridoxal phosphate binding site 235 251 2
PTHR11680 HMMPANTHER IPR001085 Serine hydroxymethyltransferase 1 463 2
PTHR11680:SF5 HMMPANTHER 1 463 1
3.40.640.10 Gene3D IPR015421 Pyridoxal phosphate-dependent transferase, major region, subdomain 1 41 309 31
3.90.1150.10 Gene3D IPR015422 Pyridoxal phosphate-dependent transferase, major region, subdomain 2 310 464 25
SSF53383 SuperFamily IPR015424 Pyridoxal phosphate-dependent transferase 8 464 31
PIRSF000412 PIRSF IPR001085 Serine hydroxymethyltransferase 1 466 2

View domain organization at Pfam

Protein Properties

Ave. residue weight 111.05 Da
Charge 7.00
Isoelectric point 7.94
Molecular weight 51.86 kDa
Number of residues 467
Modifications

Protein Modifications

Term IDTerm NameEvidenceResidueReferenceCount
MOD:00046O-phospho-L-serineS6PMID:247631071669
MOD:00047O-phospho-L-threonineT10PMID:24763107689
MOD:00696phosphorylated residueNASPMID:195477441921
Sequence
Gene Expression

Quantitative Gene Expression

Protein Level

Molecules/Cell (average)DuringConditionScaleEvidenceReference
444690during GO:0000080PECO:0000005,
PECO:0000126
mass spectrometry evidencePMID:24763107
455806during GO:0000084PECO:0000005,
PECO:0000126
mass spectrometry evidencePMID:24763107
459910during GO:0000085PECO:0000005,
PECO:0000126
mass spectrometry evidencePMID:24763107
453003during GO:0000087PECO:0000005,
PECO:0000126
mass spectrometry evidencePMID:24763107
457986during GO:0072690PECO:0000005,
PECO:0000126
mass spectrometry evidencePMID:24763107
184036.17during GO:0072690PECO:0000014,
PECO:0000005
experimental evidencePMID:23101633
56511.76during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000014,
PECO:0000127,
PECO:0000005
experimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)DuringConditionScaleEvidenceReference
82during GO:0072690PECO:0000014,
PECO:0000005
experimental evidencePMID:23101633
7.9during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000014,
PECO:0000127,
PECO:0000005
experimental evidencePMID:23101633
Species Distribution
DescriptionQualifierReferenceCount
conserved in fungi4569
conserved in eukaryotes4482
conserved in bacteria1001
conserved in metazoa3419
conserved in vertebrates3393
conserved in archaea237
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Genetic Interactions

Source: BioGRID

Gene Product Evidence Reference
vps35retromer complex subunit Vps35 Negative GeneticPMID:22681890
prp4serine/threonine protein kinase Prp4 Negative GeneticPMID:22681890
php5CCAAT-binding factor complex subunit Php5 Negative GeneticPMID:22681890
rxt2histone deacetylase complex subunit Rxt2 Negative GeneticPMID:22681890
pef1Pho85/PhoA-like cyclin-dependent kinase Pef1 Positive GeneticPMID:22681890
elp3elongator complex subunit Elp3 (predicted) Positive GeneticPMID:22681890
sty1MAP kinase Sty1 Negative GeneticPMID:22681890
ers1RNA-silencing factor Ers1 Negative GeneticPMID:22681890
pst2Clr6 histone deacetylase complex subunit Pst2 Negative GeneticPMID:22681890
cph1Clr6 histone deacetylase associated PHD protein-1 Cph1 Negative GeneticPMID:22681890
dsc3Golgi Dsc E3 ligase complex subunit Dsc3 Negative GeneticPMID:21504829
SPBC31F10.10czf-MYND type zinc finger protein Positive GeneticPMID:22681890
ptc1protein phosphatase 2C Ptc1 Negative GeneticPMID:22681890
ypa1protein phosphatase type 2A regulator, PTPA family Ypa1 Negative GeneticPMID:22681890
hrr1Helicase Required for RNAi-mediated heterochromatin assembly Hrr1 Negative GeneticPMID:22681890
atb2tubulin alpha 2 Positive GeneticPMID:22681890
trt1telomerase reverse transcriptase 1 protein Trt1 Negative GeneticPMID:22681890
sfp1transcription factor Sfp1 (predicted) Negative GeneticPMID:22681890
spf1Set1C PHD Finger protein Spf1 Negative GeneticPMID:22681890
php3CCAAT-binding factor complex subunit Php3 Negative GeneticPMID:22681890
elp2elongator complex subunit Elp2 (predicted) Positive GeneticPMID:22681890
sep1forkhead transcription factor Sep1 Positive GeneticPMID:22681890
SPAC19B12.11czinc finger protein, human ZNF593 ortholog Positive GeneticPMID:22681890
Physical Interactions

Source: BioGRID

Gene Product Evidence Reference
ddb1damaged DNA binding protein Ddb1 Affinity Capture-MSPMID:18794354
cbf11CBF1/Su(H)/LAG-1 family transcription factor Cbf11 Affinity Capture-MSPMID:22540037
bdf2BET family double bromodomain protein Bdf2 Affinity Capture-MSPMID:24013502
nak1PAK-related kinase Nak1 Affinity Capture-MSPMID:23462181
hhp1serine/threonine protein kinase Hhp1 Affinity Capture-MSPMID:24055157
tea1cell end marker Tea1 Affinity Capture-MSPMID:21652630
hhp2serine/threonine protein kinase Hhp2 Affinity Capture-MSPMID:24055157
External References
Database Identifier Description
NBRP SPAC24C9.12c Fission yeast strain database, National BioResource Project (Japan)
YOGY SPAC24C9.12c Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPAC24C9.12c BioGRID Interaction Datasets
Expression Viewer SPAC24C9.12c Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPAC24C9.12c Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPAC24C9.12c Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPAC24C9.12c Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPAC24C9.12c Polyadenylation Viewer (Gullerova lab)
pombeTV SPAC24C9.12c Transcriptome Viewer (Bähler Lab)
Cyclebase SPAC24C9.12c Cell Cycle Data
GEO SPAC24C9.12c GEO profiles
PInt SPAC24C9.12c Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPAC24C9.12c Peptides identified in tandem mass spectrometry proteomics experiments
SPD / RIKEN21/21G01Orfeome Localization Data
KEGGMAP00310KEGG Pathway Database
KEGGMAP00680KEGG Pathway Database
IntEnz2.1.2.1Integrated relational Enzyme database
Rhea2.1.2.1Annotated reactions database
KEGGMAP00460KEGG Pathway Database
KEGGMAP00260KEGG Pathway Database
KEGGMAP00670KEGG Pathway Database
WikiGene2542651glycine hydroxymethyltransferase (predicted)
EntrezGene2542651glycine hydroxymethyltransferase (predicted)
UniProtKB/SwissProtO13972Probable serine hydroxymethyltransferase, cytosolic
ModBaseO13972Database of comparative protein structure models
STRINGO13972Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_594037glycine hydroxymethyltransferase (predicted)
RefSeq mRNANM_001019462972h- glycine hydroxymethyltransferase (predicted) (SPAC24C9.12c), mRNA
European Nucleotide ArchiveCAB11269ENA Protein Mapping
European Nucleotide ArchiveCAB11269.1ENA Protein Mapping
UniParcUPI000012B893UniProt Archive

Literature for SPAC24C9.12c

Search: Europe PMC or PubMed

Release Version: PomBase:22_45 - 08 Aug 2014