FlyBase Gene Report: Dmel\cid

General Information

Symbol

Dmel\cid

Species

D. melanogaster

Name

centromere identifier

Annotation Symbol

CG13329

Feature Type

protein_coding_gene

FlyBase ID

FBgn0040477

Gene Model Status

Current

Stock Availability

11 publicly available

Gene Summary

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] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
UniProtKB
Interactive Fly

Also Known As

CENP-A, CenH3, CID/CENP-A, dCENP-A, cenpA

Key Links

Genomic Location

Cytogenetic map

50A11-50A11

Sequence location

2R:13,485,617..13,486,631 [+]

Recombination map

2-68

RefSeq locus

NT_033778 REGION:13485617..13486631

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

Gene Ontology (GO) Annotations (18 terms)

Molecular Function (4 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (4 terms)

CV Term

Evidence

References

enables DNA binding

inferred from electronic annotation with InterPro:IPR000164, InterPro:IPR007125

(InterPro Project Members, 2004-)

enables nucleosomal DNA binding

inferred from biological aspect of ancestor with PANTHER:PTN008967730

(GO Reference Genome Project, 2011-)

enables protein heterodimerization activity

inferred from electronic annotation with InterPro:IPR009072

(InterPro Project Members, 2004-)

enables structural constituent of chromatin

inferred from biological aspect of ancestor with PANTHER:PTN008967730

(GO Reference Genome Project, 2011-)

inferred from electronic annotation with InterPro:IPR000164

(InterPro Project Members, 2004-)

Biological Process (7 terms)

Terms Based on Experimental Evidence (7 terms)

CV Term

Evidence

References

involved_in chromosome segregation

inferred from mutant phenotype

(Przewloka et al., 2007)

involved_in heterochromatin formation

inferred from genetic interaction with FLYBASE:BubR1; FB:FBgn0263855

(Torras-Llort et al., 2010)

involved_in kinetochore assembly

inferred from mutant phenotype

(Blower et al., 2006)

involved_in kinetochore organization

inferred from direct assay

(Blower and Karpen, 2001)

involved_in mitotic cell cycle

inferred from mutant phenotype

(Blower et al., 2006)

involved_in mitotic metaphase chromosome alignment

inferred from mutant phenotype

(Przewloka et al., 2007)

involved_in spindle assembly

inferred from mutant phenotype

(Blower et al., 2006)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

involved_in heterochromatin formation

inferred from biological aspect of ancestor with PANTHER:PTN008967730

(GO Reference Genome Project, 2011-)

involved_in kinetochore assembly

inferred from biological aspect of ancestor with PANTHER:PTN008517672

(GO Reference Genome Project, 2011-)

involved_in mitotic metaphase chromosome alignment

inferred from biological aspect of ancestor with PANTHER:PTN008517672

(GO Reference Genome Project, 2011-)

Cellular Component (7 terms)

Terms Based on Experimental Evidence (6 terms)

CV Term

Evidence

References

part_of CENP-A containing nucleosome

inferred from direct assay

(Lipinszki et al., 2015)

located_in chromosome, centromeric region

inferred from direct assay

(Bobkov et al., 2020, Boltengagen et al., 2016, Torras-Llort et al., 2010)

located_in condensed chromosome, centromeric region

inferred from direct assay

(Schuh et al., 2007)

part_of inner kinetochore

inferred from direct assay

(Blower and Karpen, 2001)

inferred from direct assay

(Henikoff et al., 2000)

located_in kinetochore

inferred from direct assay

(Orr and Sunkel, 2011, Schittenhelm et al., 2007)

part_of nucleosome

inferred from physical interaction with FLYBASE:His2A; FB:FBgn0001196,FLYBASE:His2B; FB:FBgn0001198,FLYBASE:His4; FB:FBgn0001200

(Dalal et al., 2007)

Terms Based on Predictions or Assertions (4 terms)

CV Term

Evidence

References

part_of CENP-A containing nucleosome

inferred from biological aspect of ancestor with PANTHER:PTN008320273

(GO Reference Genome Project, 2011-)

is_active_in kinetochore

inferred from biological aspect of ancestor with PANTHER:PTN008517672

(GO Reference Genome Project, 2011-)

part_of nucleosome

inferred from electronic annotation with InterPro:IPR000164

(InterPro Project Members, 2004-)

is_active_in nucleus

inferred from biological aspect of ancestor with PANTHER:PTN008967730

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

Protein Family (UniProt)

Belongs to the histone H3 family. (Q9V6Q2)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

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 (PubMed:11483958, PubMed:16839185). Required for recruitment and assembly of kinetochore proteins, mitotic progression and chromosome segregation (PubMed:11483958, PubMed:16839185, PubMed:24703848). May serve as an epigenetic mark that propagates centromere identity through replication and cell division (PubMed:11483958, PubMed:16839185).

(UniProt, Q9V6Q2)

Summary (Interactive Fly)

a variant of histone H3 - localizes exclusively to centromeres - chromatin component that plays a key role in assembling the kinetochore at meiosis and mitosis

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see 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

Structure

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry Q9V6Q2)

If you don't see a structure in the viewer, refresh your browser.

Model Confidence:

Very high (pLDDT > 90)
Confident (90 > pLDDT > 70)
Low (70 > pLDDT > 50)
Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures

Crossreferences

PDB - An information portal to biological macromolecular structures

6XWS
6XWT

Comments on Gene Model

Gene model reviewed during 5.49

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

cid-RA

FBtr0087667

NM_079006

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

UniProt

RefSeq ID

GenBank

cid-PA

FBpp0086787

26.0

225

10.72

Q9V6Q2

NP_523730

AAF58371

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)

225 (aa)

(Henikoff et al., 2000)

Comments

cid protein was used as a marker for kinetochores during early embryogenesis.

(Maiato et al., 2002)

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 (By similarity). 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 (PubMed:15592865). Interacts with Chrac-14 (PubMed:24703848).

(UniProt, Q9V6Q2)

Crossreferences

InterPro - A database of protein families, domains and functional sites

PDB - An information portal to biological macromolecular structures

6XWS
6XWT

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Q9V6Q2

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.

cid_1

Linkouts

Expression Data

Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

0.09

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

No Assay Recorded

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage

(Maiato et al., 2002)

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

fertilized egg stage

female pronucleus

• chromatin

(Loppin et al., 2001)

male pronucleus

• chromatin

(Loppin et al., 2001)

embryonic stage

cell

• kinetochore

(Jager et al., 2005)

adult stage

spermatid

• kinetochore

(Loppin et al., 2001)

adult stage | male

spermatocyte

• chromosome, centromeric region

(Yan et al., 2010)

adult stage | female

germarium

• chromosome, centromeric region

(Yan and McKee, 2013)

cell

• chromosome, centromeric region

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

(Schittenhelm et al., 2007)

Additional Descriptive Data

No more than eight cid foci are present in wild-type meiosis I at any stage.

(Yan et al., 2010)

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.

(Loppin et al., 2001)

Marker for

kinetochore

(Jager et al., 2005, Maiato et al., 2002)

Subcellular Localization

CV Term

Evidence

References

part_of CENP-A containing nucleosome

inferred from direct assay

(Lipinszki et al., 2015)

located_in chromosome, centromeric region

inferred from direct assay

(Bobkov et al., 2020, Boltengagen et al., 2016, Torras-Llort et al., 2010)

located_in condensed chromosome, centromeric region

inferred from direct assay

(Schuh et al., 2007)

part_of inner kinetochore

inferred from direct assay

(Blower and Karpen, 2001)

inferred from direct assay

(Henikoff et al., 2000)

located_in kinetochore

inferred from direct assay

(Orr and Sunkel, 2011, Schittenhelm et al., 2007)

part_of nucleosome

inferred from physical interaction with FLYBASE:His2A; FB:FBgn0001196,FLYBASE:His2B; FB:FBgn0001198,FLYBASE:His4; FB:FBgn0001200

(Dalal et al., 2007)

Expression Deduced from Reporters

Reporter: P{gcid-mRFP-cid}

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 4 -- 5

cell

• chromosome, centromeric region

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

(Schittenhelm et al., 2007)

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\cid in JBrowse

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\cid

View exonic expression by tissue for Dmel\cid

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

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

36495/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0040477

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0040477

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0040477

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG13329

Flygut - An atlas of the Drosophila adult midgut

FBgn0040477

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 12 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 32 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of cid

Transgenic constructs containing regulatory region of cid

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 6 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Lethality

Allele

lethal

lethal, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

cid^GD4436

lethal, with Scer\GAL4^insc-Mz1407

cid^GD4436

lethal - all die during embryonic stage

lethal - all die during embryonic stage, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

cid^GD4436

lethal - all die during embryonic stage (with cid^T11-2)

lethal - all die during embryonic stage (with cid^T12-1)

lethal - all die during embryonic stage (with cid^T21-3)

lethal - all die during embryonic stage (with cid^T22-4)

partially lethal - majority die, with Scer\GAL4^pnr-MD237

cid^GD4436

Other Phenotypes

Allele

abnormal cell cycle (with cid^T11-2)

cid^T22-4

abnormal cell cycle (with cid^T22-4)

cid^T11-2

abnormal mitotic cell cycle | embryonic stage (with cid^T11-2)

cid^T22-4

abnormal mitotic cell cycle | embryonic stage (with cid^T22-4)

cid^T11-2

abnormal neuroanatomy (with cid^T11-2)

cid^T22-4

abnormal neuroanatomy (with cid^T22-4)

cid^T11-2

abnormal neuroanatomy | larval stage, with Scer\GAL4^insc-Mz1407

cid^GD4436

some die during embryonic stage

some die during embryonic stage (with cid^T11-2)

some die during embryonic stage (with cid^T12-1)

some die during embryonic stage (with cid^T21-3)

some die during embryonic stage (with cid^T22-4)

some die during pupal stage, with Scer\GAL4^pnr-MD237

cid^GD4436

visible, with Scer\GAL4^ey.PH

visible, with Scer\GAL4^GMR.PF

cid^UAS.cJa

visible, with Scer\GAL4^pnr-MD237

cid^GD4436

Phenotype manifest in

Allele

anaphase (with cid^T11-2)

cid^T22-4

anaphase (with cid^T22-4)

cid^T11-2

centrosome | spermatogenesis | increased number

centrosome | spermatogenesis | increased number, with Scer\GAL4^VP16.bam

cid^KK110670

chromosome (with cid^T11-2)

cid^T22-4

chromosome (with cid^T22-4)

cid^T11-2

eye, with Scer\GAL4^ey.PH

eye, with Scer\GAL4^GMR.PF

cid^UAS.cJa

ganglion mother cell | larval stage, with Scer\GAL4^insc-Mz1407

cid^GD4436

larval neuroblast | larval stage, with Scer\GAL4^insc-Mz1407

cid^GD4436

mesonotum, with Scer\GAL4^pnr-MD237

cid^GD4436

metaphase plate (with cid^T11-2)

cid^T22-4

metaphase plate (with cid^T22-4)

cid^T11-2

nucleus (with cid^T11-2)

cid^T22-4

nucleus (with cid^T22-4)

cid^T11-2

ommatidium, with Scer\GAL4^GMR.PF

cid^UAS.cJa

spermatocyte

spermatocyte, with Scer\GAL4^VP16.bam

cid^KK110670

telophase (with cid^T11-2)

cid^T22-4

telophase (with cid^T22-4)

cid^T11-2

trichogen cell, with Scer\GAL4^pnr-MD237

cid^GD4436

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (22)

Hsap\CENPA

3 of 14

Yes

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (12)

Rnor\Cenpa

3 of 14

Yes

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

Mus musculus (laboratory mouse) (18)

Mmus\Cenpa

3 of 14

Yes

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

Yes

Xenopus tropicalis (Western clawed frog) (21)

Xtro\cenpa

2 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Danio rerio (Zebrafish) (19)

Drer\cenpa

2 of 14

Yes

Drer\h3f3a

2 of 14

Yes

Drer\h3f3c

2 of 14

Yes

Drer\h3f3d

2 of 14

Yes

Drer\hist2h3c

2 of 14

Yes

Drer\si:ch211-113a14.27

2 of 14

Yes

Drer\si:ch1073-429i10.3

2 of 14

Yes

Drer\zgc:113983

2 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Drer\si:ch1073-153i20.2

1 of 14

Drer\si:dkey-108k21.25

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (25)

Cele\cpar-1

4 of 14

Yes

Cele\hcp-3

4 of 14

Yes

Cele\F20D6.9

2 of 14

Yes

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

Yes

Cele\his-74

2 of 14

Cele\his-72

1 of 14

Cele\ZC155.2

1 of 14

Yes

Anopheles gambiae (African malaria mosquito) (11)

Agam\AgaP_AGAP007508

6 of 12

Yes

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (14)

Atha\HTR12

4 of 13

Yes

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

Saccharomyces cerevisiae (Brewer's yeast) (3)

Scer\CSE4

3 of 13

Yes

Scer\HHT1

2 of 13

Scer\HHT2

2 of 13

Schizosaccharomyces pombe (Fission yeast) (4)

Spom\hht1

2 of 12

Yes

Spom\hht2

2 of 12

Yes

Spom\hht3

2 of 12

Yes

Spom\cnp1

1 of 12

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:cid. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (25)

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

2 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

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 v9.1 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?

CENPA; centromere protein A

3 of 14

117139

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

Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

cid

anti tag coimmunoprecipitation, western blot, cross-linking study

(Zhang et al., 2012, Erhardt et al., 2008)

cid - ATPsynβ

pull down, anti tag western blot, Identification by mass spectrometry

(Collins et al., 2018)

cid - ATPsynβL

pull down, anti tag western blot

(Collins et al., 2018)

cid - BubR1

phenotype-based detection assay, fluorescence microscopy, inferred by author

(Torras-Llort et al., 2010)

cid - CTCF

anti tag coimmunoprecipitation, western blot

(Padeken et al., 2013)

cid - Caf1-55

pull down, autoradiography, molecular weight estimation by coomasie staining, Identification by mass spectrometry, anti tag coimmunoprecipitation, cross-linking study, western blot, peptide massfingerprinting, anti tag western blot, tandem affinity purification

(Demirdizen et al., 2019, Boltengagen et al., 2016, Furuyama and Henikoff, 2006, Furuyama et al., 2006)

cid - Cap-G

two hybrid

(Jager et al., 2005)

cid - Cenp-C

protein three hybrid, anti tag coimmunoprecipitation, peptide massfingerprinting, phenotype-based detection assay, inferred by author, fluorescence microscopy, western blot

(Roure et al., 2019, Lipinszki et al., 2015, Schittenhelm et al., 2010, Erhardt et al., 2008)

cid - Chrac-14

anti tag coimmunoprecipitation, western blot, pull down

(Mathew et al., 2014)

cid - D19A

anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based

(Rhee et al., 2014)

cid - Hat1

anti tag coimmunoprecipitation, peptide massfingerprinting, anti tag western blot, anti bait coimmunoprecipitation, molecular sieving, western blot

(Boltengagen et al., 2016)

cid - His2A

anti tag coimmunoprecipitation, western blot, anti bait coimmunoprecipitation, Identification by mass spectrometry

(Zhang et al., 2012, Dalal et al., 2007)

cid - His2B

anti bait coimmunoprecipitation, Identification by mass spectrometry

(Dalal et al., 2007)

cid - His3

cosedimentation, western blot, anti bait coimmunoprecipitation, anti tag western blot

(Demirdizen et al., 2019, Zhang et al., 2012)

cid - Kap-α3

anti tag coimmunoprecipitation, peptide massfingerprinting

(Boltengagen et al., 2016)

cid - MTA1-like

anti tag coimmunoprecipitation, cross-linking study, Identification by mass spectrometry, two hybrid, western blot

(Demirdizen et al., 2019)

cid - Mi-2

anti tag coimmunoprecipitation, western blot, anti bait coimmunoprecipitation, anti tag western blot, cross-linking study, Identification by mass spectrometry

(Demirdizen et al., 2019)

cid - Nlp

anti bait coimmunoprecipitation, western blot, anti tag coimmunoprecipitation

(Padeken et al., 2013)

cid - Ppa

pull down, western blot, two hybrid, autoradiography

(Moreno-Moreno et al., 2011)

cid - Spt6

anti bait coimmunoprecipitation, anti tag western blot, pull down, molecular weight estimation by staining

(Bobkov et al., 2020)

cid - Ssrp

anti tag coimmunoprecipitation, peptide massfingerprinting, western blot

(Boltengagen et al., 2016)

cid - Zw10

two hybrid

(Pauleau et al., 2019)

cid - blw

pull down, Identification by mass spectrometry, anti tag western blot, peptide array

(Collins et al., 2018)

cid - dre4

anti tag coimmunoprecipitation, peptide massfingerprinting, western blot

(Boltengagen et al., 2016)

cid - mod

anti tag coimmunoprecipitation, western blot, peptide massfingerprinting

(Boltengagen et al., 2016, Padeken et al., 2013)

Summary of Genetic Interactions

Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

Please look at the allele data for full details of the genetic interactions

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

cid

suppressible

BubR1

(Blower et al., 2006)

cid

enhanceable

Cap-G

(Jager et al., 2005)

cid

enhanceable

Cenp-C

(Heeger et al., 2005)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Myt1

suppressible

cid

(Willms et al., 2020)

External Data

Subunit Structure (UniProtKB)

(UniProt, Q9V6Q2 )

Linkouts

BioGRID - A database of protein and genetic interactions.

62254

DroID - A comprehensive database of gene and protein interactions.

FBgn0040477

MIST (genetic) - An integrated Molecular Interaction Database

36495

MIST (protein-protein) - An integrated Molecular Interaction Database

36495

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-68

Cytogenetic map

50A11-50A11

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}Dp^EP358 and P{lacW}drk^k13809&P{EP}mip120^EP606

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

50A-50A

(Ahmad, 2000.3.13)

Experimentally Determined Recombination Data

Location

2-68

(FlyBase, 2016)

2-72.3

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (11)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Bloomington

25047

w¹¹¹⁸; P{GFP-cid.H}8-10

27628

w¹¹¹⁸; cid^T11-2/SM5

606337

w^*; PBac{CR7T.U6:3-cid.gRNA(FE)}VK00027

29695

y¹ w^*; P{EP}cid^G5950/CyO

91709

w^*; P{UAS-cid.EGFP}III.1/TM3, Ser¹

27629

w¹¹¹⁸; cid^T21-3/CyO, P{GAL4-Kr.C}DC3, P{UAS-GFP.S65T}DC7

40912

y¹ sc^* v¹ sev²¹; P{TRiP.HMS02160}attP2

91708

w^*; P{gcid-EGFP-cid}CalpB^III.2 P{His2Av-mRFP1}III.1/TM6B, Tb¹

27627

w¹¹¹⁸; al¹ Adc^b-1 cid^T22-4 c¹ speck¹/SM5

VDRC

v102090

P{KK110670}VIE-260B

v43857

w¹¹¹⁸; P{GD4436}v43857

Genomic Clones (24)

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

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 JBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA clones, fully sequenced

BDGP DGC clones

RE21270

Other clones

FI17120

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.

FBgn0040477

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

RE02255

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0040477

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Huang et al., 2019, Bobkov et al., 2018, Hanlon et al., 2018, Talbert et al., 2018, Buster et al., 2013, Jager et al., 2005, Henikoff et al., 2000)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

New stable cell line derived from S2R+ : Stable cell lines containing separase cleavage reporter constructs consisting of the MtnA promoter driving expression of cid for centromere localization fused to RFP(Unk) and EGFP separated by uno or vtd wild-type and mutant separase cleavage sites.
(Weber et al., 2020)
New stable cell line derived from S2-unspecified : A stable S2 cell line that contains inducible EGFP-tagged cid was created.
(Podhraski et al., 2010)
New stable cell line derived from S2-unspecified : CRISPR/Cas9 used to tag endogenous Spt6 with GFP; stably transfected versions of the resulting Spt6-GFP cell line were generated with a small molecule inducible version of the geGradeFP system, a tamoxifen inducible HA-cid and/or a version of cid capable of recombination induced tag exchange (RITE).
(Bobkov et al., 2020)
New stable cell line derived from S2-ThermoFischer : A stable S2- mCherry:Tubulin-GFP:cid cell line was created. This was accomplished by transfecting cells stably expressing GFP:CID (from Gary Karpen) with inducible mCherry-alpha-tubulin.
(Dewey et al., 2020)
New stable cell line derived from S2-ATCC : Stable cell lines expressing RNAi resistant, GFP tagged Cenp-C as well as variously tagged versions of cid, baf, Nup107 and Cenp-C.
(Torras-Llort et al., 2020)

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.

(Goshima et al., 2007)

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.

(Schuh et al., 2007)

SL2 cells treated with dsRNA against cid show mitotic arrest and chromosomes are displaced from the metaphase plate.

(Muller et al., 2006)

dsRNA made from templates generated with primers directed against this gene tested in RNAi screen for effects on Kc167 and S2R⁺ cell morphology.

(Kiger et al., 2003)

Relationship to Other Genes

Source for database merge of

Source for merge of: cid CG13329

(FlyBase, 1996-)

Source for merge of: cid BcDNA:RE21270

(FlyBase, 1996-)

Additional comments

Source for merge of cid CG13329 was sequence comparison ( date:000601 ).

(FlyBase, 1996-)

Source for merge of cid BcDNA:RE21270 was a shared cDNA ( date:030728 ).

(FlyBase, 1996-)

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (30)

Reported As

Symbol Synonym

BcDNA:RE21270

CENH3

(Mendiburo et al., 2011)

CENP-A

(Chabot et al., 2024, Pang et al., 2023, Kotov et al., 2022, Marsano and Dimitri, 2022, Urban et al., 2022, Carty and Dunleavy, 2020, Fellmeth and McKim, 2020, Palladino et al., 2020, Torras-Llort et al., 2020, Wooten et al., 2020, Chang et al., 2019, Demirdizen et al., 2019, Huang et al., 2019, Moreno-Moreno et al., 2019, Saha and Mishra, 2019, Collins et al., 2018, Mehrotra and Deshpande, 2018, Mills et al., 2018, Talbert et al., 2018, Rosin and Mellone, 2017, Boltengagen et al., 2016, Rosin and Mellone, 2016, Lipinszki et al., 2015, Chen et al., 2014, Liang et al., 2014, Mathew et al., 2014, Carmena et al., 2012, Phansalkar et al., 2012, Przewloka et al., 2011, Erhardt et al., 2008, Goshima et al., 2008, Kwon et al., 2008, Grewal and Elgin, 2007, Przewloka et al., 2007, Schuh et al., 2007, Schuh et al., 2007, Blower et al., 2006, Gunjan et al., 2006, Laycock et al., 2006, Polo and Almouzni, 2006, Lam et al., 2005, Savvidou et al., 2005, Blower et al., 2003, Cleveland et al., 2003, Cavalli, 2002, Sullivan and Karpen, 2001)

CENP-A/CID

(Sullivan and Karpen, 2001)

CENP-A/Cid

(Adams et al., 2001)

CENP-A/Cnp1

(Liu et al., 2020)

CENPA

(Brust-Mascher et al., 2009)

CG13329

(Hosono et al., 2015, Ni et al., 2010.12.1, Keleman et al., 2009.8.5, Veenstra et al., 2008, Goshima et al., 2007, Henikoff, 2000.4.2)

CID

(Choudhury et al., 2024, Fellmeth et al., 2023, Kochendoerfer et al., 2023, Ranjan and Chen, 2022, Kochendoerfer et al., 2021, Lukacs et al., 2021, Vidaurre and Chen, 2021, Shatskikh et al., 2020, Walther et al., 2020, Billmyre et al., 2019, Carvalhal et al., 2018, 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)

CID/CENP-A

(Przewloka et al., 2007, Zaratiegui, 2007, Heidmann et al., 2005, Sullivan et al., 2002, Sullivan and Karpen, 2001)

CenH3

(Moreno-Moreno et al., 2011, Podhraski et al., 2010, Torras-Llort et al., 2010, Furuyama and Henikoff, 2009, Wang et al., 2008, Dalal et al., 2007, Dalal et al., 2007, Furuyama and Henikoff, 2006, Furuyama et al., 2006)

CenH3^CID

(Torras-Llort et al., 2010)

CenH3^Cid

(Morris and Moazed, 2007)

Cenp-A

(Althoff et al., 2012, Schittenhelm et al., 2010, Schittenhelm et al., 2009, Lehner et al., 2007, Pandey et al., 2007, Schittenhelm et al., 2007)

CenpA

(Meireles et al., 2011, Somma et al., 2008)

CenpA/CID

(Erhardt et al., 2007)

Cid

(Gleason and Chen, 2023, Tirgar et al., 2023, García-Puga et al., 2022, Popova et al., 2022, Sunchu et al., 2022, Chen et al., 2021, Lauria Sneideman and Meller, 2021, Vernizzi and Lehner, 2021, Weber et al., 2020, Pavlova et al., 2019, Horard et al., 2018, Mills et al., 2018, Tubman et al., 2018, Kursel and Malik, 2017, Buster et al., 2013, Herzog et al., 2013, Ross et al., 2013, Thomae et al., 2013, Althoff et al., 2012, Maheshwari and Barbash, 2012, Meireles et al., 2011, Rangone et al., 2011, Van Damme et al., 2011, Oliveira et al., 2010, Orsi et al., 2010, Royou et al., 2010, Schittenhelm et al., 2010, Ding et al., 2009, Martins et al., 2009, McCleland et al., 2009, Rath et al., 2009, Reis et al., 2009, Sakai et al., 2009, Kwon et al., 2008, Pauli et al., 2008, Pimenta-Marques et al., 2008, Royou et al., 2008, Buster et al., 2007, Gilliland et al., 2007, Goshima et al., 2007, Griffis et al., 2007, Schittenhelm et al., 2007, Cullen et al., 2005, Goshima and Vale, 2005, Siller et al., 2005, Logarinho et al., 2004, Rogers et al., 2004, Chang et al., 2003, Coelho et al., 2003, Perrod and Gasser, 2003, Weissmann et al., 2003, Ahmad and Henikoff, 2002, Malik et al., 2002, Aquadro et al., 2001, van Steensel and Henikoff, 2000)

Cid^Mel

(Vermaak et al., 2002)

cenH3

(Padeken et al., 2013, Furuyama et al., 2005)

cenp-a

(Bade et al., 2014)

cenpA

(Brust-Mascher and Scholey, 2002, Brust-Mascher and Scholey, 2001)

cid

(Trujillo et al., 2024, Li et al., 2023, Kabakci et al., 2022, Koreman et al., 2021, Dattoli et al., 2020, Willms et al., 2020, Park et al., 2019, Tanabe et al., 2019, Collins et al., 2018, Horard et al., 2018, Rosin et al., 2018, Blattner et al., 2016, Boltengagen et al., 2016, Reid and O'Brochta, 2016, Beck and Llopart, 2015, Bonnay et al., 2014, Chen et al., 2014, Liang et al., 2014, Toshima et al., 2014, Vartiainen et al., 2014, Xue et al., 2014, Orsi et al., 2013, Wang et al., 2013, Kalajdzic et al., 2012, Raychaudhuri et al., 2012, Sawamura, 2012, Neumüller et al., 2011, Dubruille et al., 2010, Oliveira et al., 2010, Torras-Llort et al., 2010, Wang et al., 2010, Cook, 2009.6.17, Cook, 2009.6.17, Kaufman, 2009.6.18, May and Schiek, 2009, Schittenhelm et al., 2009, Pauli et al., 2008, Sedat, 2008.5.22, Somma et al., 2008, Jones and Holloway, 2007, Morris and Moazed, 2007, Pandey et al., 2007, Schuh et al., 2007, Schuh et al., 2007, Blower et al., 2006, Colombie et al., 2006, Moreno-Moreno et al., 2006, Heeger et al., 2005, Jager et al., 2005, Sainz et al., 2003)

dCENP-A

(Kyriacou and Heun, 2023, Bobkov et al., 2020, Roure et al., 2019, Bobkov et al., 2018)

dCenpA

(Kochanova et al., 2020)

Name Synonyms

Centromere Identifier

(Moutinho-Pereira et al., 2010)

Centromere identifier

(Ding et al., 2009, Pimenta-Marques et al., 2008)

Centromere identifier protein

(Van Damme et al., 2011)

Centromeric Histone H3

(Torras-Llort et al., 2010)

centromere identifier

(Lipinszki et al., 2015, Toshima et al., 2014, Sawamura, 2012, Erhardt et al., 2008, Thakar et al., 2006, Sainz et al., 2003, Ahmad et al., 2000)

centromere protein A

(Erhardt et al., 2008, Cullen et al., 2005)

Secondary FlyBase IDs

FBgn0033843
FBgn0063052

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 45 )

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.

36495

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/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.

Q9V6Q2

UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information

Q9V6Q2

Other crossreferences

AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.

Q9V6Q2

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

36495/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0040477

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0040477

FlyMine - An integrated database for Drosophila genomics

FBgn0040477

InterPro - A database of protein families, domains and functional sites

KEGG Genes - Molecular building blocks of life in the genomic space.

dme:Dmel_CG13329

MARRVEL_MODEL - MARRVEL (model organism gene)

36495

PDB - An information portal to biological macromolecular structures

6XWS
6XWT

Linkouts

BioGRID - A database of protein and genetic interactions.

62254

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0040477

DroID - A comprehensive database of gene and protein interactions.

FBgn0040477

DRSC - Results frm RNAi screens

FBgn0040477

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

cid_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0040477

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0040477

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG13329

Flygut - An atlas of the Drosophila adult midgut

FBgn0040477

Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution

Interactive Fly

MIST (genetic) - An integrated Molecular Interaction Database

36495

MIST (protein-protein) - An integrated Molecular Interaction Database

36495

References (343)

The following external sites may use different assemblies or annotations than FlyBase.

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