FB2020_06, released Dec 22, 2020

Gene: Dmel\Caf1-180

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General Information
Symbol
Dmel\Caf1-180
Species
D. melanogaster
Name
Chromatin assembly factor 1, p180 subunit
Annotation Symbol
CG12109
Feature Type
protein_coding_gene
FlyBase ID
FBgn0030054
Gene Model Status
Current
Stock Availability
4 publicly available
Gene Snapshot
Chromatin assembly factor 1, p180 subunit (Caf1-180) encodes a component of the chromatin assembly factor-1, which couples DNA replication to histone deposition. The product of Caf1-180 is involved in nucleosome organization, DNA endoduplication and double-strand DNA break repair. [Date last reviewed: 2019-08-01]
Other Summaries
Also Known As

p180, NURF, CAF1-p180

Key Links
Genomic Location
Cytogenetic map
7F8-7F8
Sequence location
X:8,602,137..8,606,304 [-]
Recombination map

1-23

RefSeq locus
NC_004354 REGION:8602137..8606304
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (10 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
contributes_to histone binding
inferred by curator from GO:0033186
(Tyler et al., 2001)
Biological Process (7 terms)
Terms Based on Experimental Evidence (7 terms)
CV Term
Evidence
References
involved_in DNA endoreduplication
inferred from mutant phenotype
(Klapholz et al., 2009)
involved_in double-strand break repair via homologous recombination
inferred from mutant phenotype
(Song et al., 2007)
involved_in imaginal disc development
inferred from mutant phenotype
(Klapholz et al., 2009)
involved_in multicellular organism growth
inferred from mutant phenotype
(Klapholz et al., 2009)
involved_in nucleosome assembly
inferred from direct assay
(Tyler et al., 2001)
involved_in nucleosome organization
inferred from mutant phenotype
(Klapholz et al., 2009)
involved_in response to gamma radiation
inferred from mutant phenotype
(Song et al., 2007)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
involved_in nucleosome assembly
inferred from biological aspect of ancestor with PANTHER:PTN000392234
(assigned by GO_Central )
(Gaudet et al., 2011)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
part_of CAF-1 complex
inferred from direct assay
(Tyler et al., 2001)
located_in nucleus
inferred from direct assay
(Song et al., 2007)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
part_of CAF-1 complex
inferred from biological aspect of ancestor with PANTHER:PTN000392234
(assigned by GO_Central )
(Gaudet et al., 2011)
located_in nucleus
inferred from biological aspect of ancestor with PANTHER:PTN000392234
(assigned by GO_Central )
(Gaudet et al., 2011)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Group (FlyBase)
CHROMATIN ASSEMBLY FACTOR 1 -
Chromatin assembly factor 1 (CAF-1) is a highly conserved three-subunit histone chaperone in eukaryotes, which facilitates chromatin assembly by depositing histone H3 and H4 onto newly synthesized DNA. CAF-1 is also implicated in epigenetic regulation. (Adapted from FBrf0222414).
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Caf1-180 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

Low-frequency RNA-Seq exon junction(s) not annotated.

Gene model reviewed during 5.47

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Caf1-180-RB
FBtr0071228
NM_132267
4043
1183
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
Caf1-180-PB
FBpp0071172
133.5
1183
7.02
NP_572495
AAF46399
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)
Comments
External Data
Crossreferences
InterPro - A database of protein families, domains and functional sites
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\Caf1-180 using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Expression Data
Expression Summary Ribbons
Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.
Transcript Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
western blot
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage 1 -- 9
organism

Comment: maternal

(Klapholz et al., 2009)
embryonic stage 13 -- 16
organism

Comment: maternal

(Klapholz et al., 2009)
first instar larval stage
organism

Comment: zygotic

(Klapholz et al., 2009)
second instar larval stage
organism

Comment: zygotic

(Klapholz et al., 2009)
Additional Descriptive Data

Caf1-180 protein is detected in 0-4 hr embryos and 10-14 hr embryos but not in 20-24 hr embryos by western blot. The maternal pool of Caf1-180 protein is depleted at the end of embryogenesis and zygotic protein is detected in larval extracts from 20-24hr and 44-48 hr.

(Klapholz et al., 2009)
Marker for
 
Subcellular Localization
CV Term
Evidence
References
part_of CAF-1 complex
inferred from direct assay
(Tyler et al., 2001)
located_in nucleus
inferred from direct assay
(Song et al., 2007)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Caf1-180 in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Bulk Downloads
RNA-Seq RPKM values for all genes
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
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 6 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 10 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Caf1-180
Transgenic constructs containing regulatory region of Caf1-180
Deletions and Duplications ( 0 )
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
lethal, with Scer\GAL4Act5C.PI
lethal, with Scer\GAL4en.PU
lethal, with Scer\GAL4ey.PH
lethal, with Scer\GAL4Mef2.PR
lethal | recessive
lethal - all die before end of larval stage | recessive
lethal - all die before end of second instar larval stage
partially lethal - majority die, with Scer\GAL4pnr-MD237
viable, with Dcr-2UAS.cDa, Scer\GAL4elav.PLu
viable, with Scer\GAL4tin.CΔ4
Sterility
Allele
female sterile germline-dependent | germline clone | oogenesis stage S10
Other Phenotypes
Allele
decreased occurrence of cell division | larval stage
endomitotic cell cycle defective | larval stage
increased cell death, with Scer\GAL4ey.PH
radiation sensitive | dominant
size defective | adult stage, with Scer\GAL4ey.PH
some die during larval stage | recessive
some die during pupal stage, with Scer\GAL4pnr-MD237
some die during second instar larval stage
suppressor of variegation | dominant, with In(2)Heidi-P{Winkelried}D
suppressor of variegation | dominant, with T(2;3)SbV
visible, with Scer\GAL4en-e16E
visible, with Scer\GAL4ey.PH
visible, with Scer\GAL4pnr-MD237
visible | adult stage, with Scer\GAL4en.PU
visible | adult stage, with Scer\GAL4ey.PH
visible | adult stage, with Scer\GAL4nub.PK
visible | somatic clone
wild-type
Phenotype manifest in
Allele
embryonic/larval salivary gland
eye, with Scer\GAL4ey.PH
eye | somatic clone
fat body
imaginal disc
mesothoracic tergum, with Scer\GAL4pnr-MD237
ommatidium | somatic clone
posterior crossvein, with Scer\GAL4nub.PK
trichogen cell, with Scer\GAL4pnr-MD237
wing, with Scer\GAL4en.PU
wing, with Scer\GAL4en-e16E
wing blade, with Scer\GAL4nub.PK
wing vein, with Scer\GAL4nub.PK
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Hsap\CHAF1A
8 of 15
Yes
Yes
1  
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (2)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Mmus\Chaf1a
7 of 15
Yes
Yes
Mmus\Acin1
1 of 15
No
No
Rattus norvegicus (Norway rat) (1)
Rnor\Chaf1a
4 of 13
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
Xtro\chaf1a
4 of 12
Yes
Yes
Danio rerio (Zebrafish) (1)
Drer\chaf1a
8 of 15
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\chaf-1
7 of 15
Yes
Yes
Arabidopsis thaliana (thale-cress) (2)
Atha\FAS1
4 of 9
Yes
Yes
Atha\AT4G20160
1 of 9
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\RLF2
2 of 15
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (2)
Spom\pcf1
2 of 12
Yes
Yes
Spom\SPCC63.14
1 of 12
No
Yes
Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG0919040Z )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00004727
Drosophila simulans
Dsim\GD24564
Drosophila sechellia
Dsec\GM21191
Drosophila erecta
Dere\GG19033
Drosophila yakuba
Dyak\GE17439
Drosophila ananassae
Dana\GF22650
Drosophila pseudoobscura pseudoobscura
Dpse\GA11402
Drosophila willistoni
Dwil\GK18390
Drosophila virilis
Dvir\GJ19324
Drosophila mojavensis
Dmoj\GI15227
Drosophila grimshawi
Dgri\GH24209
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG0915015K )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17017946
Glossina morsitans
Tsetse fly
Gmor\GMOY000172
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_08954
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL012725
Anopheles darlingi
American malaria mosquito
Adar\ADAC000448
Anopheles gambiae
Malaria mosquito
Agam\AGAP001104
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ015799
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ015800
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W0IBI )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bmor\BGIBMGA001457
Danaus plexippus
Monarch butterfly
Dple\DPOGS206255-PA
Apis florea
Little honeybee
Aflo\2147520627
Apis mellifera
Western honey bee
Amel\GB43403
Bombus impatiens
Common eastern bumble bee
Bimp\BIMP17127
Bombus terrestris
Buff-tailed bumblebee
Bter\15205030
Linepithema humile
Argentine ant
Lhum\LH22906
Megachile rotundata
Alfalfa leafcutting bee
Mrot\MROTU:0012fe
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG013225
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_11915
Tribolium castaneum
Red flour beetle
Tcas\TC031939
Pediculus humanus
Human body louse
Phum\PHUM243340
Rhodnius prolixus
Kissing bug
Rpro\RPRC014304
Cimex lectularius
Bed bug
Clec\CLEC008166
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI002847
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_04858
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0IF6 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Smar\SMAR013244
Stegodyphus mimosarum
African social velvet spider
Smim\KFM69809.1
Tetranychus urticae
Two-spotted spider mite
Turt\tetur01g14310
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_264049
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_322245
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_269697
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_322373
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_307549
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_322375
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_336411
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0VQK )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Chaf1a
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000008952
Gallus gallus
Domestic chicken
Ggal\CHAF1A
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (0)
No records found.
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Model Summary Ribbon
    Disease Ontology (DO) Annotations
    Models Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Evidence
    References
    Potential Models Based on Orthology ( 0 )
    Human Ortholog
    Disease
    Evidence
    References
    Modifiers Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Interaction
    References
    Disease Associations of Human Orthologs (via DIOPT v8.0 and OMIM)
    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
    DO term
    Complementation?
    Transgene?
    CHAF1A; chromatin assembly factor 1 subunit A
    8 of 15
    601246
         
        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
        Summary of Genetic Interactions
        esyN Network Diagram
        esyN Network Key:
        Suppression
        Enhancement
        View in Interactions Browser
        Please look at the allele data for full details of the genetic interactions
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        Caf1-180
        suppressible
        asf1
        (Song et al., 2007)
        Caf1-180
        suppressible
        Blm
        (Song et al., 2007)
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        Pc
        enhanceable
        Caf1-180
        (Song et al., 2007)
        External Data
        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.
        MIST (protein-protein) - An integrated Molecular Interaction Database
        Pathways
        Signaling Pathways (FlyBase)
        Metabolic Pathways
        External Data
        Linkouts
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        X
        Recombination map

        1-23

        Cytogenetic map
        7F8-7F8
        Sequence location
        X:8,602,137..8,606,304 [-]
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        7F8-7F8
        Limits computationally determined from genome sequence between P{EP}CG1632EP1583 and P{EP}MoeEP1652
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        Experimentally Determined Recombination Data
        Location

        1-23

        (FlyBase, 2016)

        1-24.0

        (Comeron et al., 2012)
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (4)
        Genomic Clones (10)
         

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

        cDNA Clones (19)
         

        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 sequenced
        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)
          BDGP DGC clones
          Other clones
          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
           

          polyclonal

          (Doyen et al., 2013, Huang et al., 2010)
          Commercially Available Antibodies
           
          Other Information
          Relationship to Other Genes
          Source for database identify of

          Source for identity of: Caf1-180 CG12109

          (FlyBase, 1996-)
          Source for database merge of
          Additional comments

          Source for identity of Caf1-180 CG12109 was sequence comparison ( date:010418 ).

          (FlyBase, 1996-)
          Other Comments
          Origin and Etymology
          Discoverer
          Etymology
          Identification
          External Crossreferences and Linkouts ( 36 )
          Sequence 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/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
          Other crossreferences
          Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
          Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
          Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
          Flygut - An atlas of the Drosophila adult midgut
          GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
          iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
          InterPro - A database of protein families, domains and functional sites
          KEGG Genes - Molecular building blocks of life in the genomic space.
          modMine - A data warehouse for the modENCODE project
          Linkouts
          BioGRID - A database of protein and genetic interactions.
          DroID - A comprehensive database of gene and protein interactions.
          DRSC - Results frm RNAi screens
          FLIGHT - Cell culture data for RNAi and other high-throughput technologies
          FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
          FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
          FlyMine - An integrated database for Drosophila genomics
          InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
          MIST (protein-protein) - An integrated Molecular Interaction Database
          Synonyms and Secondary IDs (18)
          Datasets (0)
          Study focus (0)
          Experimental Role
          Project
          Project Type
          Title
          References (68)