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General Information
Symbol
Dmel\cid
Species
D. melanogaster
Name
centromere identifier
Annotation Symbol
CG13329
Feature Type
FlyBase ID
FBgn0040477
Gene Model Status
Stock Availability
Gene Snapshot
centromere identifier (cid) encodes a centromere-specific histone H3 variant. The nucleosomes containing the product of cid function as an epigenetic mark for centromere identity, and initiate an assembly process that recruits additional centromere proteins (like the product of Cenp-C) as well as kinetochore proteins at the start of mitotic and meiotic divisions. [Date last reviewed: 2019-03-07]
Also Known As
CENP-A, CenH3, CID/CENP-A, cenpA, centromere protein A
Key Links
Genomic Location
Cytogenetic map
Sequence location
2R:13,485,617..13,486,631 [+]
Recombination map
2-68
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Protein Family (UniProt)
Belongs to the histone H3 family. (Q9V6Q2)
Molecular Function (GO)
[Detailed GO annotations]
Summaries
Protein Function (UniProtKB)
Histone H3-like variant which exclusively replaces conventional H3 in the nucleosome core of centromeric chromatin at the inner plate of the kinetochore. Required for recruitment and assembly of kinetochore proteins, mitotic progression and chromosome segregation. May serve as an epigenetic mark that propagates centromere identity through replication and cell division.
(UniProt, Q9V6Q2)
Summary (Interactive Fly)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the GBrowse view of Dmel\cid or the JBrowse view of Dmel\cid 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 5.49
Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0087667
1015
225
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
FBpp0086787
26.0
225
10.72
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
cid protein was used as a marker for kinetochores during early embryogenesis.
External Data
Subunit Structure (UniProtKB)
Forms a nucleosome-like histone octamer containing two molecules each of H2A, H2B, cid and H4 assembled in one cid-H4 heterotetramer and two H2A-H2B heterodimers. The cid-H4 heterotetramer is more compact and structurally more rigid than corresponding H3-H4 heterotetramers (By similarity). Interacts with the condensin subunit Cap-G.
(UniProt, Q9V6Q2)
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\cid 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 (4 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
inferred from direct assay
(assigned by UniProt )
inferred from physical interaction with FLYBASE:cal1; FB:FBgn0038478
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
inferred from electronic annotation with InterPro:IPR000164, InterPro:IPR007125
(assigned by InterPro )
inferred from electronic annotation with InterPro:IPR009072
(assigned by InterPro )
Biological Process (7 terms)
Terms Based on Experimental Evidence (7 terms)
CV Term
Evidence
References
inferred from mutant phenotype
inferred from mutant phenotype
inferred from direct assay
(assigned by UniProt )
inferred from mutant phenotype
inferred from mutant phenotype
Terms Based on Predictions or Assertions (0 terms)
Cellular Component (6 terms)
Terms Based on Experimental Evidence (6 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (0 terms)
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
No Assay Recorded
Stage
Tissue/Position (including subcellular localization)
Reference
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
cell

Comment: Localization observed at interphase and during mitosis; assayed in S2R+ cells

Additional Descriptive Data
No more than eight cid foci are present in wild-type meiosis I at any stage.
Protein can be detected as 4 distinct foci of staining at the centromere region of chromatids of developing spermatozoa. While staining cannot be detected in very late spermatids and mature spermatozoa, the highly compact nature of the sperm nuclei have been shown to exclude antibodies and therefore prevent visualization of proteins associated with these structures. Shortly after fertilization protein can be detected again as discrete spots on the apposed pronuclei.
Marker for
Subcellular Localization
CV Term
Evidence
References
Expression Deduced from Reporters
Reporter: P{gcid-mRFP-cid}
Stage
Tissue/Position (including subcellular localization)
Reference
cell

Comment: Localization observed at interphase and during mitosis of embryonic cycle 14

High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\cid 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
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
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 11 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 21 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of cid
Transgenic constructs containing regulatory region of cid
Deletions and Duplications ( 0 )
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
Other Phenotypes
Allele
Phenotype manifest in
Allele
Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (18)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
2 of 15
Yes
Yes
 
2 of 15
No
Yes
 
1 of 15
No
No
 
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
 
1 of 15
No
No
 
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
 
1 of 15
No
No
1 of 15
No
No
 
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (15)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
2 of 15
Yes
Yes
2 of 15
No
Yes
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Rattus norvegicus (Norway rat) (8)
3 of 13
Yes
Yes
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (3)
2 of 12
Yes
Yes
1 of 12
No
No
1 of 12
No
No
Danio rerio (Zebrafish) (11)
1 of 15
Yes
No
1 of 15
Yes
No
1 of 15
Yes
No
1 of 15
Yes
No
1 of 15
Yes
No
1 of 15
Yes
No
1 of 15
Yes
No
1 of 15
Yes
No
1 of 15
Yes
No
1 of 15
Yes
No
1 of 15
Yes
No
Caenorhabditis elegans (Nematode, roundworm) (21)
3 of 15
Yes
Yes
3 of 15
Yes
Yes
2 of 15
No
Yes
2 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Arabidopsis thaliana (thale-cress) (1)
1 of 9
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (3)
4 of 15
Yes
Yes
 
1 of 15
No
No
1 of 15
No
No
Schizosaccharomyces pombe (Fission yeast) (0)
No records found.
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG09190FMO )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Drosophila suzukii
Spotted wing Drosophila
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) ( EOG09150B2E )
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
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( None identified )
No non-Dipteran orthologies identified
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( None identified )
No non-Insect Arthropod orthologies identified
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( None identified )
No non-Arthropod Metazoa orthologies identified
Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (25)
2 of 10
2 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
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
    Comments on Models/Modifiers Based on Experimental Evidence ( 0 )
     
    Disease Associations of Human Orthologs (via DIOPT v7.1 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?
    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 see the Physical Interaction reports below for full details
    protein-protein
    Physical Interaction
    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)
    Forms a nucleosome-like histone octamer containing two molecules each of H2A, H2B, cid and H4 assembled in one cid-H4 heterotetramer and two H2A-H2B heterodimers. The cid-H4 heterotetramer is more compact and structurally more rigid than corresponding H3-H4 heterotetramers (By similarity). Interacts with the condensin subunit Cap-G.
    (UniProt, Q9V6Q2 )
    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 (genetic) - An integrated Molecular Interaction Database
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Pathways
    Gene Group - Pathway Membership (FlyBase)
    External Data
    Linkouts
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    2R
    Recombination map
    2-68
    Cytogenetic map
    Sequence location
    2R:13,485,617..13,486,631 [+]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    50A11-50A11
    Limits computationally determined from genome sequence between P{EP}DpEP358 and P{lacW}drkk13809&P{EP}mip120EP606
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    Experimentally Determined Recombination Data
    Location
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (9)
    Genomic Clones (24)
    cDNA Clones (6)
     

    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)
    BDGP DGC 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
    Commercially Available Antibodies
     
    Other Information
    Relationship to Other Genes
    Source for database identify of
    Source for database merge of
    Source for merge of: cid CG13329
    Source for merge of: cid BcDNA:RE21270
    Additional comments
    Source for merge of cid CG13329 was sequence comparison ( date:000601 ).
    Source for merge of cid BcDNA:RE21270 was a shared cDNA ( date:030728 ).
    Other Comments
    RNAi screen using dsRNA made from templates generated with primers directed against this gene results in chromosome misalignment on the metaphase spindle and the formation of aberrantly long spindles when assayed in S2 cells. This phenotype can be observed when the screen is performed with or without Cdc27 dsRNA.
    New incorporation of cid protein into centromeres takes place during anaphase of the syncytial divisions of embryos. This incorporation is independent of DNA replication and of normal pulling forces generated by the mitotic spindle, but is strictly coupled to mitotic progression.
    SL2 cells treated with dsRNA against cid show mitotic arrest and chromosomes are displaced from the metaphase plate.
    dsRNA made from templates generated with primers directed against this gene tested in RNAi screen for effects on Kc167 and S2R+ cell morphology.
    Origin and Etymology
    Discoverer
    Etymology
    Identification
    External Crossreferences and Linkouts ( 40 )
    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/Swiss-Prot - Manually annotated and reviewed 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
    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
    FlyMine - An integrated database for Drosophila genomics
    Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    MIST (genetic) - An integrated Molecular Interaction Database
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Synonyms and Secondary IDs (27)
    Reported As
    Symbol Synonym
    BcDNA:RE21270
    CENP-A/Cid
    CID
    (Hanlon et al., 2018, Horard and Loppin, 2015, Lake et al., 2015, Lipinszki et al., 2015, Oliveira et al., 2014, Eichinger et al., 2013, Feijão et al., 2013, Unhavaithaya and Orr-Weaver, 2013, Unhavaithaya and Orr-Weaver, 2013, Yan and McKee, 2013, Carmena et al., 2012, Pek et al., 2012, Venkei et al., 2012, Hughes et al., 2011, Mellone et al., 2011, Olszak et al., 2011, Orr and Sunkel, 2011, Pane et al., 2011, Pek and Kai, 2011, Przewloka et al., 2011, Tsai et al., 2011, Venkei et al., 2011, Meyer et al., 2010, Moutinho-Pereira et al., 2010, Nishiyama et al., 2010, Podhraski et al., 2010, Savoian and Glover, 2010, Yan et al., 2010, Brust-Mascher et al., 2009, Chlamydas et al., 2009, Furuyama and Henikoff, 2009, Klattenhoff et al., 2009, Liu et al., 2009, Maresca and Salmon, 2009, Matos et al., 2009, Salvany et al., 2009, Yokoyama et al., 2009, Erhardt et al., 2008, Fanti et al., 2008, Gao et al., 2008, Gause et al., 2008, Mische et al., 2008, Yang and Fan, 2008, Zhang and Karpen, 2008, Brittle et al., 2007, Grewal and Elgin, 2007, Khetani and Bickel, 2007, Mellone et al., 2007, Mentelova et al., 2007, Oliveira et al., 2007, Orr et al., 2007, Przewloka et al., 2007, Williams et al., 2007, Anonymous, 2006, Cesario et al., 2006, Furuyama and Henikoff, 2006, Heun et al., 2006, Laycock et al., 2006, Maiato et al., 2006, Muller et al., 2006, Thakar et al., 2006, Cullen et al., 2005, Deshpande et al., 2005, Dunleavy et al., 2005, Erhardt et al., 2005, Furuyama et al., 2005, Oliveira et al., 2005, Perez-Mongiovi et al., 2005, Savvidou et al., 2005, Thomas et al., 2005, Sullivan and Karpen, 2004, Webber et al., 2004, Parry et al., 2003, Huang and Raff, 2002, Sullivan and Karpen, 2001)
    Secondary FlyBase IDs
    • FBgn0033843
    • FBgn0063052
    Datasets (0)
    Study focus (0)
    Experimental Role
    Project
    Project Type
    Title
    References (280)