rfc1 (SPBC23E6.07c)


Gene Standard Namerfc1 Characterisation Statuspublished
Systematic IDSPBC23E6.07c Feature Typeprotein coding
Synonyms Name Description
ProductDNA replication factor C complex subunit Rfc1 Product Size934aa, 103.49 kDa
Genomic Location Chromosome II, 3856111-3852657 (3455nt); CDS:3855942-3852962 (2981nt)

Ensembl Gene Location
GO Molecular Function
Term NameCount
ATP binding559
Annotation ExtensionEvidenceWith/FromReference
chromatin binding29
Annotation ExtensionEvidenceWith/FromReference
DNA clamp loader activity11
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
Term NameCount
DNA strand elongation involved in DNA replication26
Annotation ExtensionEvidenceWith/FromReference
mitotic DNA replication leading strand elongation9
Annotation ExtensionEvidenceWith/FromReference
UV-damage excision repair17
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
nuclear chromatin359
Annotation ExtensionEvidenceWith/FromReference
nuclear DNA replication factor C complex6
Annotation ExtensionEvidenceWith/FromReference
nuclear replication fork61
Annotation ExtensionEvidenceWith/FromReference
nucleolus365
Annotation ExtensionEvidenceWith/FromReference
nucleus2692
Annotation ExtensionEvidenceWith/FromReference
FYPO Single-Allele Phenotypes
Gene Deletion Viability: Inviable

Population Phenotype

Term NameGenotypesCount
abolished cell population growth at high temperaturerfc1-44 (pentapeptide insertion in C-terminal domain)34
decreased cell population growth at high temperaturerfc1-54 (insertion L780-PVGVP-P781)172
decreased cell population growth on glucose carbon sourcerfc1+319
inviable vegetative cell populationrfc1::ura4+1451
ΔC-terminal domain (720-935)
rfc1-43 (insertion I753-QGVPL-Q754)
rfc1Δ
loss of viability at high temperaturerfc1-44 (pentapeptide insertion in C-terminal domain)56
sensitive to hydroxyurearfc1-33 (D739A)580
rfc1-46 (insertion Q852-SRGTP-S853)
rfc1-53 (insertion Y650-LMGVP-L651)
rfc1-49 (insertion K638-LGVPQ-L639)
rfc1-52 (insertion M880-LGVPL-L881)
sensitive to methyl methanesulfonaterfc1-46 (insertion Q852-SRGTP-S853)318
rfc1-49 (insertion K638-LGVPQ-L639)
rfc1-33 (D739A)
rfc1-53 (insertion Y650-LMGVP-L651)
rfc1-52 (insertion M880-LGVPL-L881)
viable vegetative cell populationrfc1-45 (insertion A601-VRGTP-V602)3840
rfc1-44 (pentapeptide insertion in C-terminal domain)
rfc1-33 (D739A)
rfc1-40 (R839K)
rfc1-48 (insertion L622-HGGVP-H623)
rfc1-39 (K834A)
rfc1-51 (insertion P858-MKGYP-M859)
rfc1-35 (R748A)
rfc1-41 (D842A)
rfc1-37 (D808A)
rfc1-49 (insertion K638-LGVPQ-L639)
rfc1-34 (K745A)
rfc1-38 (E814A)
rfc1-46 (insertion Q852-SRGTP-S853)
rfc1-36 (E807A)
rfc1-54 (insertion L780-PVGVP-P781)
rfc1-53 (insertion Y650-LMGVP-L651)
rfc1-50 (insertion E870-VGVPH-V871)
rfc1-52 (insertion M880-LGVPL-L881)
rfc1-47 (insertion K677-HLGAP-L678)

Cell Phenotype

Term NameGenotypesCount
abnormal cell cycle arrest in mitotic S phaserfc1-44 (pentapeptide insertion in C-terminal domain)16
abnormal mitotic cell cyclerfc1Δ877
abolished protein polyubiquitination during cellular response to UV4
affecting cdt1rfc1-44 (pentapeptide insertion in C-terminal domain)
decreased protein degradation during cellular response to UV5
affecting cdt1rfc1-44 (pentapeptide insertion in C-terminal domain)
decreased protein degradation during mitotic S phase3
affecting cdt1rfc1-44 (pentapeptide insertion in C-terminal domain)
elongated vegetative cellrfc1Δ793
increased nuclear protein level during vegetative growth12
affecting cdt1rfc1-44 (pentapeptide insertion in C-terminal domain)
inviable after spore germination, multiple cell divisions, abnormal morphologyΔC-terminal domain (720-935)205
inviable after spore germination, multiple cell divisions, cell cycle arrest in mitotic interphase, elongated cellsrfc1Δ88
inviable after spore germination, multiple cell divisions, elongated cellrfc1::ura4+121

FYPO Multi-allele Phenotypes

Population Phenotype

Term NameGenotypes
decreased cell population growth on glucose carbon sourcerfc1-44 (pentapeptide insertion in C-terminal domain), ctf18+
rfc1-44 (pentapeptide insertion in C-terminal domain), hta1-S129A (S129A), hta2-S128A (S128A)
inviable vegetative cell populationdcc1Δ, rfc1-44 (pentapeptide insertion in C-terminal domain)
rfc1-44 (pentapeptide insertion in C-terminal domain), dna2-C2 (T3236C)
ctf18Δ, rfc1-44 (pentapeptide insertion in C-terminal domain)
cdc27-P11 (G57E), rfc1-44 (pentapeptide insertion in C-terminal domain)
cdc27-D1 (160-372), rfc1-44 (pentapeptide insertion in C-terminal domain)
elg1+, rfc1-44 (pentapeptide insertion in C-terminal domain)
pol3-ts3, rfc1-44 (pentapeptide insertion in C-terminal domain)
cdc1-P13 (D389G), rfc1-44 (pentapeptide insertion in C-terminal domain)
ctf8Δ, rfc1-44 (pentapeptide insertion in C-terminal domain)
normal cell population growth at high temperaturerfc5-S6 (insertion P76-SRGTP-S77), rfc1-44 (pentapeptide insertion in C-terminal domain)
rfc5-S1 (insertion T75-PSRGT-P76), rfc1-44 (pentapeptide insertion in C-terminal domain)
sensitive to hydroxyurearfc5-S1 (insertion T75-PSRGT-P76), rfc1-44 (pentapeptide insertion in C-terminal domain)
rfc5-S6 (insertion P76-SRGTP-S77), rfc1-44 (pentapeptide insertion in C-terminal domain)
sensitive to methyl methanesulfonaterfc5-S6 (insertion P76-SRGTP-S77), rfc1-44 (pentapeptide insertion in C-terminal domain)
rfc5-S1 (insertion T75-PSRGT-P76), rfc1-44 (pentapeptide insertion in C-terminal domain)

Cell Phenotype

Term NameGenotypes
inviable elongated vegetative cellelg1+, rfc1-44 (pentapeptide insertion in C-terminal domain)
Target Of
OntologyRelationshipGeneProduct
FYPO affected by mutation in cdc24 DNA replication protein Cdc24
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons3856111..3855871, 3855802..3855684, 3855635..3855576, 3855515..3852657
Intron3855870..3855803, 3855683..3855636, 3855575..3855516
mRNA3856111..3852657
5' UTR3856111..3855943PMID:21511999
CDS3855942..3855871, 3855802..3855684, 3855635..3855576, 3855515..3852962
3' UTR3852961..3852657PMID: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
PF00004 Pfam IPR003959 ATPase, AAA-type, core 412 520 32
PF08519 Pfam IPR013725 DNA replication factor RFC1, C-terminal 689 843 1
PF00533 Pfam IPR001357 BRCT domain 237 313 6
SM00292 SMART IPR001357 BRCT domain 238 316 10
SM00382 SMART IPR003593 AAA+ ATPase domain 408 542 70
PS50172 Prosite Profiles IPR001357 BRCT domain 236 310 13
PTHR23389:SF10 HMMPANTHER 177 933 1
PTHR23389 HMMPANTHER 177 933 3
3.40.50.10190 Gene3D IPR001357 BRCT domain 236 314 13
1.10.8.60 Gene3D Peptidase M41 541 611 35
1.20.272.10 Gene3D DNA polymerase III, subunit gamma/ tau 613 732 6
3.40.50.300 Gene3D IPR027417 P-loop containing nucleoside triphosphate hydrolase 359 532 288
SSF48019 SuperFamily IPR008921 DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal 612 760 6
SSF52113 SuperFamily IPR001357 BRCT domain 235 314 12
SSF52540 SuperFamily IPR027417 P-loop containing nucleoside triphosphate hydrolase 359 603 294
PIRSF036578 PIRSF IPR012178 Replication factor C subunit 1 1 934 1
Coil ncoils Predicted coiled-coil protein (DUF2205) 326 346 1057

View domain organization at Pfam

Term IDTerm NameReferenceCount
PBO:0000443BRCT domainTemporary processing gif - replaced by AJAX with count of genes annotated with the term PBO:0000443
PBO:0000539AAA family ATPaseTemporary processing gif - replaced by AJAX with count of genes annotated with the term PBO:0000539

Protein Properties

Ave. residue weight 110.80 Da
Charge 30.00
Codon Adaptation Index 0.39
Isoelectric point 9.62
Molecular weight 103.49 kDa
Number of residues 934
Modifications

Protein Modifications

Term NameResidueCount
O-phospho-L-serine 1676
present during mitotic M phaseS887
present during mitotic M phaseS22
present during mitotic M phaseS885
present during mitotic M phaseS27
present during mitotic M phaseS42
S42
Annotation ExtensionEvidenceResidueReference
present during mitotic M phase experimental evidence S887 PMID:21712547
present during mitotic M phase experimental evidence S22 PMID:21712547
present during mitotic M phase experimental evidence S885 PMID:21712547
present during mitotic M phase experimental evidence S27 PMID:21712547
present during mitotic M phase experimental evidence S42 PMID:21712547
experimental evidence S42 PMID:24763107
O-phospho-L-threonine 701
present during mitotic M phaseT26
present during mitotic M phaseT24
Annotation ExtensionEvidenceResidueReference
present during mitotic M phase experimental evidence T26 PMID:21712547
present during mitotic M phase experimental evidence T24 PMID:21712547
phosphorylated residue 1931
Annotation ExtensionEvidenceResidueReference
IDA PMID:19547744
Sequence
Gene Expression

Quantitative Gene Expression

View graphical display of gene expression data for rfc1 (SPBC23E6.07c)

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
4814during GO:0000080PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
4491during GO:0000084PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
4530during GO:0000085PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
4145during GO:0000087PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
4893during GO:0072690PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
3262.17during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
2403.74during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
3during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
0.91during 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)3092
conserved in fungi4606
conserved in eukaryotes4516
conserved in metazoa3424
conserved in vertebrates3399
conserved in eukaryotes only2506
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

Load genes that interact physically with SPBC23E6.07c into the Query Builder
View all interactions in esyN
View the HCPIN interactions in esyN

Gene Product Evidence Reference
affinity captured bycdc24DNA replication protein Cdc24 Affinity Capture-WesternPMID:9891039
affinity captured byepe1Jmjc domain chromatin associated protein Epe1 Affinity Capture-MSPMID:24013502
Genetic Interactions

Source: BioGRID

Load genes that interact genetically with SPBC23E6.07c into the Query Builder
View these interactions in esyN

Gene Product Evidence Reference
synthetic growth defect withrad3ATR checkpoint kinase Rad3 Synthetic Growth DefectPMID:26368543
synthetic growth defect withbrc1BRCT domain protein Brc1 Synthetic Growth DefectPMID:26368543
inviable in presence of overexpressedelg1DNA replication factor C complex subunit Elg1 Dosage LethalityPMID:16040599
synthetic lethal withctf18RFC-like complex subunit Ctf18 Synthetic LethalityPMID:16040599
synthetic lethal withdcc1Ctf18 RFC-like complex subunit Dcc1 Synthetic LethalityPMID:16040599
overexpression rescuescdc24DNA replication protein Cdc24 Dosage RescuePMID:9891039
synthetically rescued byrfc5DNA replication factor C complex subunit Rfc5 (predicted) Synthetic RescuePMID:16040599
External References
Database Identifier Description
NBRP SPBC23E6.07c Fission yeast strain database, National BioResource Project (Japan)
YOGY SPBC23E6.07c Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPBC23E6.07c BioGRID Interaction Datasets
Expression Viewer SPBC23E6.07c Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPBC23E6.07c Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPBC23E6.07c Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPBC23E6.07c Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPBC23E6.07c Polyadenylation Viewer (Gullerova lab)
pombeTV SPBC23E6.07c Transcriptome Viewer (Bähler Lab)
GEO SPBC23E6.07c GEO profiles
PInt SPBC23E6.07c Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPBC23E6.07c Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPBC23E6.07c Fission yeast phenotypic data & analysis
Cyclebase SPBC23E6.07c.1 Cell Cycle Data
SPD / RIKEN29/29G10Orfeome Localization Data
UniProtKB/SwissProtO60182Replication factor C subunit 1
ModBaseO60182Database of comparative protein structure models
STRINGO60182Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_596607DNA replication factor C complex subunit Rfc1
RefSeq mRNANM_001022528972h- DNA replication factor C complex subunit Rfc1 (rfc1), mRNA

Literature for rfc1

Search: Europe PMC or PubMed

Release Version: PomBase:30_59 - 12 Apr 2016