FlyBase Gene Report: Dmel\cal1

General Information

Symbol

Dmel\cal1

Species

D. melanogaster

Name

chromosome alignment defect 1

Annotation Symbol

CG5148

Feature Type

protein_coding_gene

FlyBase ID

FBgn0038478

Gene Model Status

Current

Stock Availability

13 publicly available

Gene Summary

chromosome alignment defect 1 (cal1) encodes a protein that is required for maintenance of the epigenetic marks specifying centromeres. It binds to newly synthesized centromere-specific histone H3 variant encoded by cid and recruits it to the centromere by binding to the centromere protein encoded by Cenp-C. [Date last reviewed: 2019-03-07] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

89E12-89E12

Sequence location

3R:17,088,280..17,091,938 [+]

Recombination map

3-59

RefSeq locus

NT_033777 REGION:17088280..17091938

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 (8 terms)

Molecular Function (2 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

enables chromatin-protein adaptor activity

inferred from physical interaction with FLYBASE:cid; FB:FBgn0040477,FLYBASE:Cenp-C; FB:FBgn0266916

(Schittenhelm et al., 2010)

enables histone chaperone activity

inferred from direct assay

(Chen et al., 2014)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (3 terms)

Terms Based on Experimental Evidence (3 terms)

CV Term

Evidence

References

involved_in CENP-A containing chromatin assembly

inferred from direct assay

(Chen et al., 2014)

involved_in female meiosis chromosome segregation

inferred from mutant phenotype

(Unhavaithaya and Orr-Weaver, 2013)

involved_in kinetochore assembly

inferred from direct assay

(Chen et al., 2014)

inferred from mutant phenotype

(Schittenhelm et al., 2010)

Terms Based on Predictions or Assertions (0 terms)

Cellular Component (3 terms)

Terms Based on Experimental Evidence (3 terms)

CV Term

Evidence

References

located_in chromosome, centromeric region

inferred from direct assay

(Schittenhelm et al., 2010)

located_in kinetochore

inferred from direct assay

(Goshima et al., 2007)

located_in nucleolus

inferred from direct assay

(Schittenhelm et al., 2010)

Terms Based on Predictions or Assertions (0 terms)

Gene Group (FlyBase)

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

Summary (Interactive Fly)

substochiometric centromeric linker protein involved in centromere propagation - regulator of centromeric deposition of Cenp-A/Cid and Cenp-C during exit from mitosis

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\cal1 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 Q9VEN2)

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

Comments on Gene Model

Gene model reviewed during 5.48

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

cal1-RA

FBtr0083400

NM_142340

3602

979

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

cal1-PA

FBpp0082841

109.5

979

8.17

Q9VEN2

NP_650597

AAF55389

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

PDB - An information portal to biological macromolecular structures

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\cal1 using the Feature Mapper tool.

External Data

Crossreferences

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

cal1_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).

-0.15

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

day 5 of adulthood | male -- day 7 of adulthood | male

spermatozoon

(Wasbrough et al., 2010)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in chromosome, centromeric region

inferred from direct assay

(Schittenhelm et al., 2010)

located_in kinetochore

inferred from direct assay

(Goshima et al., 2007)

located_in nucleolus

inferred from direct assay

(Schittenhelm et al., 2010)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\cal1 in JBrowse

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

View exonic expression by developmental stage for Dmel\cal1

View exonic expression by tissue for Dmel\cal1

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

42065/tissue=All

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

FBgn0038478

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0038478

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

FBgn0038478

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

CG5148

Flygut - An atlas of the Drosophila adult midgut

FBgn0038478

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 6 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 14 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of cal1

Transgenic constructs containing regulatory region of cal1

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(3R)Exel6176

(Unhavaithaya et al., 2013, Schittenhelm et al., 2010, Ryder, 2004.4.26)

Inferred from location ( 4 )

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 | recessive

cal1^MB04866

lethal - all die during embryonic stage | recessive

cal1^c03646

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

cal1^GD11553

viable, with Scer\GAL4^pnr-MD237

cal1^GD11553

Other Phenotypes

Allele

abnormal meiotic cell cycle | semidominant

cal1^2k32

abnormal mitotic cell cycle | embryonic cycle 16, with Scer\GAL4^prd.RG1

cal1^UAS.EGFP

abnormal neuroanatomy | embryonic stage | recessive

some die during embryonic stage | recessive

cal1^c03646

visible, with Scer\GAL4^pnr-MD237

cal1^GD11553

Phenotype manifest in

Allele

larval central nervous system | embryonic stage

cal1^2k32

mesonotum, with Scer\GAL4^pnr-MD237

cal1^GD11553

nucleus

cal1^2k32

nucleus | embryonic stage

cal1^c03646

presumptive embryonic/larval central nervous system

cal1^c03646

trichogen cell, with Scer\GAL4^pnr-MD237

cal1^GD11553

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) (0)

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (0)

Mus musculus (laboratory mouse) (0)

Xenopus tropicalis (Western clawed frog) (0)

Danio rerio (Zebrafish) (0)

Caenorhabditis elegans (Nematode, roundworm) (0)

Anopheles gambiae (African malaria mosquito) (0)

Arabidopsis thaliana (thale-cress) (0)

Saccharomyces cerevisiae (Brewer's yeast) (0)

Schizosaccharomyces pombe (Fission yeast) (0)

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:cal1. 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) (0)

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?

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

cal1

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

(Roure et al., 2019)

cal1 - Cenp-C

x-ray crystallography, anti tag coimmunoprecipitation, western blot, two hybrid, phenotype-based detection assay, fluorescence microscopy, inferred by author, molecular sieving, molecular weight estimation by staining, cosedimentation, molecular weight, anti bait coimmunoprecipitation

(Medina-Pritchard et al., 2020, Roure et al., 2019, Chen et al., 2015, Schittenhelm et al., 2010, Erhardt et al., 2008)

cal1 - His4

cross-linking study, Identification by mass spectrometry, molecular sieving, predetermined participant, x-ray crystallography, pull down, molecular weight estimation by staining, static light scattering

(Medina-Pritchard et al., 2020, Chen et al., 2014)

cal1 - Polr2A

anti bait coimmunoprecipitation, western blot

(Chen et al., 2015)

cal1 - Ssrp

anti bait coimmunoprecipitation, western blot, anti tag coimmunoprecipitation, Identification by mass spectrometry, pull down, autoradiography

(Chen et al., 2015)

cal1 - Zw10

anti tag coimmunoprecipitation, western blot, two hybrid, pull down

(Pauleau et al., 2019)

cal1 - dre4

anti tag coimmunoprecipitation, Identification by mass spectrometry, anti bait coimmunoprecipitation, western blot, pull down, autoradiography

(Chen et al., 2015)

cal1 - mod

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

(Chen et al., 2015, Chen et al., 2012)

cal1 - rdx

two hybrid, anti tag coimmunoprecipitation, western blot

(Bade et al., 2014)

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

cal1

enhanceable

Cenp-C

(Unhavaithaya and Orr-Weaver, 2013)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Cenp-C

enhanceable

cal1

(Unhavaithaya and Orr-Weaver, 2013)

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

67105

DroID - A comprehensive database of gene and protein interactions.

FBgn0038478

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

42065

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

3-59

Cytogenetic map

89E12-89E12

Sequence location

3R:17,088,280..17,091,938 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

89E12-89E12

Limits computationally determined from genome sequence between P{EP}CG5208^EP562&P{EP}Dad^EP3196 and P{PZ}l(3)07882⁰⁷⁸⁸²

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-59

(FlyBase, 2016)

3-59.2

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (13)

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

Bloomington

91719

w^*; P{gcal1-EGFP}II.1

91720

w^*; P{gcal1-EGFP}III.2

91721

w^*; P{UAS-cal1.EGFP}II.1

91722

w^*; P{UAS-cal1.EGFP}III.1

11309

w¹¹¹⁸; PBac{PB}cal1^c03646/TM6B, Tb¹

24832

w¹¹¹⁸; Mi{ET1}cal1^MB04866/TM6C, Sb¹

55730

y¹ sc^* v¹ sev²¹; P{TRiP.GL01832}attP40

77856

cal1^2k32 e^s/TM3, P{Ubx-lacZ.w⁺}TM3, Sb¹

NIG-Fly

5148R-1

P{NIG.5148R}1

HMJ22024

y¹ v¹; P{TRiP.HMJ22024}attP40/CyO

VDRC

v45248

w¹¹¹⁸; P{GD11553}v45248

v45249

w¹¹¹⁸; P{GD11553}v45249/TM3

More stocks available...

Genomic Clones (9)

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

cDNA Clones (105)

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

SD02553

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.

FBgn0038478

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0038478

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Bade et al., 2014)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

New stable cell line derived from S2-unspecified : A stable S2 cell line was created expressing cal1 tagged with GFP and lacI under the control of a Cu2+ inducible promoter.
(Chen et al., 2015)

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 a spindle that is aberrantly long when assayed in S2 cells. This phenotype can be observed when the screen is performed with or without Cdc27 dsRNA.

(Goshima et al., 2007)

Relationship to Other Genes

Source for database merge of

Additional comments

Nomenclature History

Source for database identify of

Source for identity of: cal1 CG5148

(Goshima et al., 2007)

Nomenclature comments

Etymology

Named "chromosome alignment defect 1" after the observed cellular phenotype following treatment of S2 cells with cal1 dsRNA.

(Goshima et al., 2007)

Synonyms and Secondary IDs (7)

Reported As

Symbol Synonym

CG5148

(Boltengagen et al., 2016, Hosono et al., 2015, Japanese National Institute of Genetics, 2012.5.21, Ni et al., 2010.12.1, Wright et al., 2010, Erhardt et al., 2008, Goshima et al., 2007, Goshima et al., 2007)

CLD2

(Erhardt et al., 2008)

Cal1

(Choudhury et al., 2024, Tang et al., 2024, Moreno-Moreno et al., 2019, Wright et al., 2010, Goshima et al., 2007)

cal1

(Lehner, 2020.12.4, Noble et al., 2016, Luck et al., 2014, Unhavaithaya and Orr-Weaver, 2013, Unhavaithaya and Orr-Weaver, 2013, Unhavaithaya et al., 2013, Joyce et al., 2012, Raychaudhuri et al., 2012, Venkei et al., 2011, Schittenhelm et al., 2010, Wasbrough et al., 2010)

Name Synonyms

CG5148

Chromosome alignment defect 1

(Phansalkar et al., 2012)

chromosome alignment defect 1

(Goshima et al., 2007)

Secondary FlyBase IDs

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 34 )

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.

42065

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.

Q9VEN2

UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information

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.

Q9VEN2

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

42065/tissue=All

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

FBgn0038478

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

FBgn0038478

FlyMine - An integrated database for Drosophila genomics

FBgn0038478

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

dme:Dmel_CG5148

MARRVEL_MODEL - MARRVEL (model organism gene)

42065

PDB - An information portal to biological macromolecular structures

Linkouts

BioGRID - A database of protein and genetic interactions.

67105

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

FBgn0038478

DroID - A comprehensive database of gene and protein interactions.

FBgn0038478

DRSC - Results frm RNAi screens

FBgn0038478

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

cal1_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0038478

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0038478

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

CG5148

Flygut - An atlas of the Drosophila adult midgut

FBgn0038478

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

Interactive Fly

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

42065

References (80)

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

-0.15

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