FlyBase Gene Report: Dmel\cyr

General Information

Symbol

Dmel\cyr

Species

D. melanogaster

Name

cypher

Annotation Symbol

CG15335

Feature Type

protein_coding_gene

FlyBase ID

FBgn0030001

Gene Model Status

Current

Stock Availability

9 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

7D6-7D14

Sequence location

X:8,121,280..8,135,713 [-]

Recombination map

1-22

RefSeq locus

NC_004354 REGION:8121280..8135713

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 (4 terms)

Molecular Function (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

involved_in cell morphogenesis

inferred from biological aspect of ancestor with PANTHER:PTN008709643

(GO Reference Genome Project, 2011-)

involved_in epithelial cell morphogenesis

inferred from sequence or structural similarity with FLYBASE:dyl; FB:FBgn0066365

(Fernandes et al., 2010)

Cellular Component (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

is_active_in apical plasma membrane

inferred from biological aspect of ancestor with PANTHER:PTN008709643

(GO Reference Genome Project, 2011-)

located_in membrane

inferred from sequence model

(Fernandes et al., 2010)

Gene Group (FlyBase)

Protein Family (UniProt)

Protein Signatures (InterPro)

Zona pellucida domain

Summaries

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\cyr 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 Q9W3K2)

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

Comments on Gene Model

Gene model reviewed during 5.50

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

cyr-RB

FBtr0071193

NM_132214

2452

513

cyr-RC

FBtr0340160

NM_001298075

2555

513

cyr-RD

FBtr0340161

NM_001298076

2378

454

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

cyr-PB

FBpp0071141

56.1

513

8.99

FBpp0309146

56.1

513

8.99

FBpp0309147

49.4

454

9.35

X2JCY5

NP_001285005

AHN59476

Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

513 aa isoforms: cyr-PB, cyr-PC

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Crossreferences

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

Zona pellucida domain

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\cyr using the Feature Mapper tool.

External Data

Crossreferences

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

cyr_1
cyr_2

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).

1.77

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 11 -- 12

labial sensory complex primordium

(Fisher et al., 2012)

embryonic stage 13 -- 16

embryonic dorsal epidermis

(Fisher et al., 2012)

embryonic esophagus

(Fisher et al., 2012)

embryonic head sensory system

(Fisher et al., 2012)

embryonic hindgut

(Fisher et al., 2012)

embryonic labial sensory complex

(Fisher et al., 2012)

embryonic stage 15

trichome

(Fernandes et al., 2010)

Additional Descriptive Data

cyr transcripts are expressed in the trichomes at embryonic stage 15. Expression is restricted to dorsal cells at stage 15, then switches to ventral stripes at stage 16/17.

(Fernandes et al., 2010)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\cyr in JBrowse

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

View exonic expression by developmental stage for Dmel\cyr

View exonic expression by tissue for Dmel\cyr

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

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0030001

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

31733/tissue=All

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

FBgn0030001

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0030001

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

FBgn0030001

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

CG15335

Flygut - An atlas of the Drosophila adult midgut

FBgn0030001

Images

FlyExpress - Embryonic expression images (BDGP data)

Show all FlyExpress processed images for Dmel\cyr

Stages(s) 1-3
Stages(s) 7-8
Stages(s) 11-12
Stages(s) 13-16

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 7 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 5 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of cyr

Transgenic constructs containing regulatory region of cyr

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 18 )

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

cyr^GD13114

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

cyr^GD13114

viable

cyr^EY11622

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

cyr^GD1167

viable, with Scer\GAL4^Mef2.PR

viable, with Scer\GAL4^pnr-MD237

Sterility

Allele

fertile

cyr^EY11622

Phenotype manifest in

Allele

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) (9)

Hsap\COL6A2

1 of 14

Yes

Hsap\COL6A3

1 of 14

Yes

Hsap\COL6A5

1 of 14

Yes

Hsap\COL6A6

1 of 14

Yes

Hsap\COL12A1

1 of 14

Yes

Hsap\COL21A1

1 of 14

Yes

Hsap\COL28A1

1 of 14

Yes

Hsap\MATN1

1 of 14

Yes

Hsap\MATN2

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) (0)

Mus musculus (laboratory mouse) (0)

Xenopus tropicalis (Western clawed frog) (3)

Xtro\col6a5

1 of 13

Yes

Xtro\col21a1

1 of 13

Yes

Xtro\LOC100491712

1 of 13

Yes

Danio rerio (Zebrafish) (0)

Caenorhabditis elegans (Nematode, roundworm) (36)

Cele\cutl-24

4 of 14

Yes

2 of 14

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Anopheles gambiae (African malaria mosquito) (12)

Agam\AgaP_AGAP007051

3 of 12

Yes

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

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:cyr. 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) (17)

pio

4 of 13

CG15020

3 of 13

dyl

3 of 13

zye

3 of 13

CG10005

2 of 13

CG12814

2 of 13

CG17111

1 of 13

dpy

1 of 13

mey

1 of 13

neo

1 of 13

nompA

1 of 13

nyo

1 of 13

pot

1 of 13

qsm

1 of 13

tyn

1 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?

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

Summary of Genetic Interactions

Interaction Browsers

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0030001

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

1-22

Cytogenetic map

7D6-7D14

Sequence location

X:8,121,280..8,135,713 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

7D6-7D14

Limits computationally determined from genome sequence between P{EP}Ubc-E2H^EP1303 and P{EP}CG1583^EP1516&P{EP}CG1583^EP325

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

1-22

(FlyBase, 2016)

1-22.3

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (9)

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

Bloomington

85357

w¹¹¹⁸ PBac{PB}cyr^c02379

59259

y¹ w^* Mi{MIC}cyr^MI14109

20687

y¹ w^67c23 P{EPgy2}cyr^EY11622

13036

y¹ P{SUPor-P}CG2116^KG00028 cyr^KG00028

Kyoto

104074

y^* w^* P{GawB}cyr^NP2059 / FM7c

111885

y¹ w^* P{lacW}cyr^G0199 P{lacW}dome^G0199b, l(1)G0199^G0199 P{neoFRT}19A/FM7c; P{ey-FLP.N}5

NIG-Fly

15335R-2

P{NIG.15335R}2

VDRC

v3294

w¹¹¹⁸; P{GD1167}v3294

v28555

w¹¹¹⁸; P{GD13114}v28555

Genomic Clones (22)

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

RE22259

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.

FBgn0030001

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

RE05815

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0030001

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Shows particularly robust cycling of transcription in adult heads, as assessed by expression analysis using high density oligonucleotide arrays with probe generated during three 12-point time course experiments over the course of 6 days.

(Claridge-Chang et al., 2001)

Relationship to Other Genes

Source for database merge of

Source for merge of: CG15335 CG15338

(FlyBase Genome Annotators, 2002-2003)

Additional comments

Annotations CG15335 and CG15338 merged as CG15335 in release 3 of the genome annotation.

(FlyBase Genome Annotators, 2002-2003)

Nomenclature History

Source for database identify of

Source for identity of: cyr CG15335

(Fernandes et al., 2010)

Nomenclature comments

Etymology

Identified as a putative component of the matrix, and named after one of the characters in the eponymous movie.

(Fernandes et al., 2010)

Synonyms and Secondary IDs (4)

Reported As

Symbol Synonym

CG15335

(Japanese National Institute of Genetics, 2012.5.21, Buffin and Gho, 2010, Fernandes et al., 2010, FlyBase Curators, 2008-)

CG15338

(Luschnig, 2003.12.17)

cyr

(Menoret et al., 2013, Fernandes et al., 2010, Fernandes et al., 2010)

Name Synonyms

cypher

(Fernandes et al., 2010)

Secondary FlyBase IDs

FBgn0030002

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

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.

31733

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.

Q9W3K2

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.

Q9W3K2

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0030001

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

31733/tissue=All

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

FBgn0030001

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

FBgn0030001

FlyMine - An integrated database for Drosophila genomics

FBgn0030001

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

Zona pellucida domain

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

dme:Dmel_CG15335

MARRVEL_MODEL - MARRVEL (model organism gene)

31733

Linkouts

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

FBgn0030001

DroID - A comprehensive database of gene and protein interactions.

FBgn0030001

DRSC - Results frm RNAi screens

FBgn0030001

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

cyr_1
cyr_2

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0030001

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0030001

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

CG15335

Flygut - An atlas of the Drosophila adult midgut

FBgn0030001

iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)

TC010196

References (32)

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

1.77

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