General Information
Symbol
Dmel\RfC4
Species
D. melanogaster
Name
Replication factor C subunit 4
Annotation Symbol
CG14999
Feature Type
FlyBase ID
FBgn0260985
Gene Model Status
Stock Availability
Gene Snapshot
In progress.Contributions welcome.
Also Known As
RfC40, l(3)e20, l(3)64Ai
Genomic Location
Cytogenetic map
Sequence location
3L:4,134,860..4,136,038 [-]
Recombination map
3-10
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
GO Summary Ribbons
Families, Domains and Molecular Function
Gene Group Membership (FlyBase)
Protein Family (UniProt, Sequence Similarities)
Belongs to the activator 1 small subunits family. (P53034)
Molecular Function (see GO section for details)
Experimental Evidence
Predictions / Assertions
ATP binding; contributes_tocontributes_to DNA clamp loader activity
Summaries
Gene Group Membership
ELG1 COMPLEX -
The Elg1 complex (Elg1-C) is a pentameric replication factor C (RFC)-like complex. Elg1-C unloads the DNA polymerase processivity factor proliferating cell nuclear antigen (PCNA) from chromatin. (Adapted from FBrf0232456).
UniProt Contributed Function Data
The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins proliferating cell nuclear antigen (PCNA) and activator 1. Subunit 2 binds ATP.
(UniProt, P53034)
Phenotypic Description from the Red Book (Lindsley and Zimm 1992)
l(3)SG13
Homozygous larvae contain rudimentary imaginal discs, but disc primordia do not grow during larval development; testes and ovaries smaller than normal, and cell number in central nervous system reduced. Mutant gonads do not survive metamorphosis when implanted into wild-type larvae. Homozygous cuticular clones appear to develop normally. Mutant larvae support growth of implanted wild-type discs. Normal gene product postulated to be required for cell proliferation; survival of somatic epidermal clones attributed to perdurance. Larval ganglia exhibit extremely low mitotic index; chromosomes irregularly condensed; extensive chromosome fragmentation observed frequently (Gatti and Baker, 1989, Genes Dev. 3: 438-53); salivary chromosomes appear normal.
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the GBrowse view of Dmel\RfC4 or the JBrowse view of Dmel\RfC4 for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)
Isoform displayed:
Pfam protein domains
InterPro name
classification
start
end
Protein Domains (via SMART)
Isoform displayed:
SMART protein domains
InterPro name
classification
start
end
Comments on Gene Model
Gene model reviewed during 5.43
Gene model reviewed during 5.45
Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0073264
1127
331
Additional Transcript Data and Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0073120
37.2
331
7.82
Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments
Reported size (kDa)
331 (aa); 40 (kD observed)
Comments
External Data
Subunit Structure (UniProtKB)
Heteropentamer of subunits of 140/145, 40, 38, 37, and 36.5 kDa that forms a complex with PCNA in the presence of ATP.
(UniProt, P53034)
Linkouts
Sequences Consistent with the Gene Model
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\RfC4 using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Gene Ontology (17 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
inferred from mutant phenotype
(assigned by UniProt )
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
inferred from electronic annotation with InterPro:IPR003959
(assigned by InterPro )
contributes_tocontributes_to DNA clamp loader activity
inferred from sequence or structural similarity with SGD:S000005454
inferred from biological aspect of ancestor with PANTHER:PTN000186209
(assigned by GO_Central )
Biological Process (11 terms)
Terms Based on Experimental Evidence (6 terms)
CV Term
Evidence
References
inferred from mutant phenotype
inferred from mutant phenotype
(assigned by UniProt )
inferred from mutant phenotype
inferred from high throughput mutant phenotype
inferred from high throughput mutant phenotype
inferred from high throughput mutant phenotype
Terms Based on Predictions or Assertions (6 terms)
CV Term
Evidence
References
traceable author statement
traceable author statement
inferred from biological aspect of ancestor with PANTHER:PTN000186208
(assigned by GO_Central )
inferred from sequence or structural similarity with SGD:S000005454
inferred from sequence or structural similarity with SGD:S000005454
Cellular Component (3 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
inferred from direct assay
inferred from direct assay
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000186209
(assigned by GO_Central )
inferred from sequence or structural similarity with SGD:S000005454
inferred from biological aspect of ancestor with PANTHER:PTN000186209
(assigned by GO_Central )
Expression Data
Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
organism

Comment: maternally deposited

antennal primordium

Comment: reported as procephalic ectoderm primordium

central brain primordium

Comment: reported as procephalic ectoderm primordium

visual primordium

Comment: reported as procephalic ectoderm primordium

dorsal head epidermis primordium

Comment: reported as procephalic ectoderm primordium

lateral head epidermis primordium

Comment: reported as procephalic ectoderm primordium

ventral head epidermis primordium

Comment: reported as procephalic ectoderm primordium

Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
western blot
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
RfC4 protein is distributed in zones of proliferation in the larval central nervous system.
RfC4 protein is detected throughout embryogenesis on Western blots. It is detected in the nuclei of blastoderm stage embryos.
Marker for
 
Subcellular Localization
CV Term
Evidence
References
inferred from direct assay
inferred from direct assay
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\RfC4 in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Reference
See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
Developmental Proteome: Life Cycle
Developmental Proteome: Embryogenesis
External Data and Images
Linkouts
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
Alleles, Insertions, Transgenic Constructs and Phenotypes
Classical and Insertion Alleles ( 8 )
For All Classical and Insertion Alleles Show
 
Allele of RfC4
Class
Mutagen
Associated Insertion
Stocks
Known lesion
    0
    --
    Other relevant insertions
    Transgenic Constructs ( 5 )
    Deletions and Duplications ( 7 )
    Summary of Phenotypes
    For more details about a specific phenotype click on the relevant allele symbol.
    Lethality
    Allele
    Other Phenotypes
    Allele
    Phenotype manifest in
    Allele
    anaphase & condensed nuclear chromosome
    metaphase & condensed nuclear chromosome
    mitosis & nuclear chromosome
    Orthologs
    Human Orthologs (via DIOPT v7.1)
    Homo sapiens (Human) (3)
    Species\Gene Symbol
    Score
    Best Score
    Best Reverse Score
    Alignment
    Complementation?
    Transgene?
    14 of 15
    Yes
    Yes
    1 of 15
    No
    No
    1 of 15
    No
    No
    Model Organism Orthologs (via DIOPT v7.1)
    Mus musculus (laboratory mouse) (2)
    Species\Gene Symbol
    Score
    Best Score
    Best Reverse Score
    Alignment
    Complementation?
    Transgene?
    15 of 15
    Yes
    Yes
    1 of 15
    No
    No
    Rattus norvegicus (Norway rat) (3)
    12 of 13
    Yes
    Yes
    1 of 13
    No
    No
    1 of 13
    No
    No
    Xenopus tropicalis (Western clawed frog) (1)
    8 of 12
    Yes
    Yes
    Danio rerio (Zebrafish) (4)
    10 of 15
    Yes
    Yes
    1 of 15
    No
    No
    1 of 15
    No
    No
    1 of 15
    No
    No
    Caenorhabditis elegans (Nematode, roundworm) (3)
    15 of 15
    Yes
    Yes
    1 of 15
    No
    No
    1 of 15
    No
    No
    Arabidopsis thaliana (thale-cress) (3)
    9 of 9
    Yes
    Yes
    1 of 9
    No
    No
    1 of 9
    No
    No
    Saccharomyces cerevisiae (Brewer's yeast) (3)
    15 of 15
    Yes
    Yes
    1 of 15
    No
    No
    1 of 15
    No
    No
    Schizosaccharomyces pombe (Fission yeast) (3)
    12 of 12
    Yes
    Yes
    1 of 12
    No
    No
    1 of 12
    No
    No
    Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG09190BHG )
    Organism
    Common Name
    Gene
    AAA Syntenic Ortholog
    Multiple Dmel Genes in this Orthologous Group
    Drosophila melanogaster
    fruit fly
    Drosophila simulans
    Drosophila sechellia
    Drosophila erecta
    Drosophila yakuba
    Drosophila ananassae
    Drosophila pseudoobscura pseudoobscura
    Drosophila persimilis
    Drosophila willistoni
    Drosophila virilis
    Drosophila mojavensis
    Drosophila grimshawi
    Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091506UR )
    Organism
    Common Name
    Gene
    Multiple Dmel Genes in this Orthologous Group
    Musca domestica
    House fly
    Glossina morsitans
    Tsetse fly
    Lucilia cuprina
    Australian sheep blowfly
    Aedes aegypti
    Yellow fever mosquito
    Anopheles darlingi
    American malaria mosquito
    Anopheles gambiae
    Malaria mosquito
    Culex quinquefasciatus
    Southern house mosquito
    Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W07V8 )
    Organism
    Common Name
    Gene
    Multiple Dmel Genes in this Orthologous Group
    Bombyx mori
    Silkmoth
    Danaus plexippus
    Monarch butterfly
    Heliconius melpomene
    Postman butterfly
    Apis florea
    Little honeybee
    Apis mellifera
    Western honey bee
    Bombus impatiens
    Common eastern bumble bee
    Bombus terrestris
    Buff-tailed bumblebee
    Bombus terrestris
    Buff-tailed bumblebee
    Linepithema humile
    Argentine ant
    Megachile rotundata
    Alfalfa leafcutting bee
    Nasonia vitripennis
    Parasitic wasp
    Dendroctonus ponderosae
    Mountain pine beetle
    Tribolium castaneum
    Red flour beetle
    Pediculus humanus
    Human body louse
    Rhodnius prolixus
    Kissing bug
    Cimex lectularius
    Bed bug
    Acyrthosiphon pisum
    Pea aphid
    Zootermopsis nevadensis
    Nevada dampwood termite
    Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X08LU )
    Organism
    Common Name
    Gene
    Multiple Dmel Genes in this Orthologous Group
    Ixodes scapularis
    Black-legged tick
    Stegodyphus mimosarum
    African social velvet spider
    Tetranychus urticae
    Two-spotted spider mite
    Tetranychus urticae
    Two-spotted spider mite
    Daphnia pulex
    Water flea
    Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0CKT )
    Organism
    Common Name
    Gene
    Multiple Dmel Genes in this Orthologous Group
    Strongylocentrotus purpuratus
    Purple sea urchin
    Strongylocentrotus purpuratus
    Purple sea urchin
    Strongylocentrotus purpuratus
    Purple sea urchin
    Strongylocentrotus purpuratus
    Purple sea urchin
    Ciona intestinalis
    Vase tunicate
    Ciona intestinalis
    Vase tunicate
    Ciona intestinalis
    Vase tunicate
    Gallus gallus
    Domestic chicken
    Gallus gallus
    Domestic chicken
    Gallus gallus
    Domestic chicken
    Gallus gallus
    Domestic chicken
    Human Disease Model Data
    FlyBase Human Disease Model Reports
      Alleles Reported to Model Human Disease (Disease Ontology)
      Download
      Models ( 0 )
      Allele
      Disease
      Evidence
      References
      Interactions ( 0 )
      Allele
      Disease
      Interaction
      References
      Comments ( 0 )
       
      Human Orthologs (via DIOPT v7.1)
      Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
      Homo sapiens (Human)
      Gene name
      Score
      OMIM
      OMIM Phenotype
      Complementation?
      Transgene?
      Functional Complementation Data
      Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
      Interactions
      Summary of Physical Interactions
      esyN Network Diagram
      Show neighbor-neighbor interactions:
      Select Layout:
      Legend:
      Protein
      RNA
      Selected Interactor(s)
      Interactions Browser

      Please look at the Interaction Group reports for full details of the physical interactions
      protein-protein
      Interacting group
      Assay
      References
      Summary of Genetic Interactions
      esyN Network Diagram
      esyN Network Key:
      Suppression
      Enhancement

      Please look at the allele data for full details of the genetic interactions
      Starting gene(s)
      Interaction type
      Interacting gene(s)
      Reference
      Starting gene(s)
      Interaction type
      Interacting gene(s)
      Reference
      External Data
      Subunit Structure (UniProtKB)
      Heteropentamer of subunits of 140/145, 40, 38, 37, and 36.5 kDa that forms a complex with PCNA in the presence of ATP.
      (UniProt, P53034 )
      Linkouts
      BioGRID - A database of protein and genetic interactions.
      DroID - A comprehensive database of gene and protein interactions.
      InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
      Pathways
      Genomic Location and Detailed Mapping Data
      Chromosome (arm)
      3L
      Recombination map
      3-10
      Cytogenetic map
      Sequence location
      3L:4,134,860..4,136,038 [-]
      FlyBase Computed Cytological Location
      Cytogenetic map
      Evidence for location
      64A7-64A7
      Limits computationally determined from genome sequence between P{PZ}l(3)rG166rG166 and P{PZ}sinu06524
      Experimentally Determined Cytological Location
      Cytogenetic map
      Notes
      References
      64A10-64A11
      (determined by in situ hybridisation)
      Experimentally Determined Recombination Data
      Left of (cM)
      Right of (cM)
      Notes
      Stocks and Reagents
      Stocks (9)
      Genomic Clones (13)
       

      Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

      cDNA Clones (35)
       

      Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see GBrowse for alignment of the cDNAs and ESTs to the gene model.

      cDNA clones, fully sequences
      BDGP DGC clones
      Other clones
        Drosophila Genomics Resource Center cDNA clones

        For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

        cDNA Clones, End Sequenced (ESTs)
        RNAi and Array Information
        Linkouts
        DRSC - Results frm RNAi screens
        GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
        Antibody Information
        Laboratory Generated Antibodies
         
        Commercially Available Antibodies
         
        Other Information
        Relationship to Other Genes
        Source for database identify of
        Source for database merge of
        Source for merge of: l(3)dsl1 l(3)SG13
        Source for merge of: RfC4 RfC40 l(3)SG13
        Additional comments
        Other Comments
        Identified with: GH24992 <up>FlyBase curator comment: EST subsequently found to be chimeric</up>.
        Candidate gene for tibia length quantitative trait locus.
        EST GH24992 is chimeric; the 5' portion (AI405079) corresponds to part of SP2637, the 3' portion (BG633345) corresponds to part of RfC40.
        Clonal analysis demonstrates disc proliferation is reduced in mutant individuals. Discussed during genetic analysis of the Ras64B-Rop region.
        Origin and Etymology
        Discoverer
        Etymology
        Identification
        External Crossreferences and Linkouts ( 48 )
        Crossreferences
        NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
        GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.
        GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
        RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
        UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
        Linkouts
        BioGRID - A database of protein and genetic interactions.
        Drosophila Genomics Resource Center - Drosophila Genomics Resource Center cDNA clones
        DroID - A comprehensive database of gene and protein interactions.
        DRSC - Results frm RNAi screens
        Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
        FLIGHT - Cell culture data for RNAi and other high-throughput technologies
        Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
        Flygut - An atlas of the Drosophila adult midgut
        FlyMine - An integrated database for Drosophila genomics
        GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
        InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
        KEGG Genes - Molecular building blocks of life in the genomic space.
        modMine - A data warehouse for the modENCODE project
        Synonyms and Secondary IDs (25)
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        References (79)