FlyBase Gene Report: Dmel\ORY

General Information

Symbol

Dmel\ORY

Species

D. melanogaster

Name

Occludin-Related Y

Annotation Symbol

CG40446

Feature Type

protein_coding_gene

FlyBase ID

FBgn0046323

Gene Model Status

Current

Stock Availability

2 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

Sequence location

Y:3,561,745..3,618,339 [+]

Recombination map

Y-

RefSeq locus

NC_024512 REGION:3561745..3618339

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

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

NCBI

UCSC

Ensembl

Function

Gene Ontology (GO) Annotations (1 term)

Molecular Function (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Cellular Component (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

is_active_in cytoskeleton

inferred from biological aspect of ancestor with PANTHER:PTN000788381

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

Protein Family (UniProt)

Protein Signatures (InterPro)

Cilia- and flagella-associated protein 58, central coiled coil

Summaries

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\ORY 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 Q5LJN3)

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 5.57

Gene model reviewed during 6.02

Sequence Ontology: Class of Gene

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

ORY-RD

FBtr0346720

NM_001015498

2745

914

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

ORY-PD

FBpp0312331

106.6

914

9.20

Q5LJN3

NP_001015498

EAL24524

Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Crossreferences

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

Cilia- and flagella-associated protein 58, central coiled coil

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\ORY using the Feature Mapper tool.

External Data

Crossreferences

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).

4.22

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

adult head

• membrane

(Aradska et al., 2015)

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

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\ORY in JBrowse

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

View exonic expression by developmental stage for Dmel\ORY

View exonic expression by tissue for Dmel\ORY

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

3355174/tissue=All

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

FBgn0046323

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0046323

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

FBgn0046323

Flygut - An atlas of the Drosophila adult midgut

FBgn0046323

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 0 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 2 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of ORY

Transgenic constructs containing regulatory region of ORY

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 0 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

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

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) (5)

Hsap\CFAP58

7 of 14

Yes

Hsap\CCDC146

2 of 14

Yes

Hsap\LAMA1

1 of 14

Hsap\LAMA2

1 of 14

Hsap\LAMA3

1 of 14

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (3)

Rnor\Cfap58

7 of 14

Yes

Rnor\Ccdc146

1 of 14

Yes

Rnor\Lama2

1 of 14

Mus musculus (laboratory mouse) (5)

Mmus\Cfap58

6 of 14

Yes

Mmus\Ccdc146

2 of 14

Yes

Mmus\Lama1

1 of 14

Mmus\Lama2

1 of 14

Mmus\Lama3

1 of 14

Xenopus tropicalis (Western clawed frog) (3)

Xtro\cfap58

3 of 13

Yes

Xtro\ccdc146

1 of 13

Yes

Xtro\mbd2

1 of 13

Danio rerio (Zebrafish) (4)

Drer\cfap58

8 of 14

Yes

Drer\ccdc146

2 of 14

Yes

Drer\lama1

1 of 14

Drer\lama5

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (1)

Cele\epi-1

1 of 14

Yes

Anopheles gambiae (African malaria mosquito) (1)

Agam\AgaP_AGAP003679

6 of 12

Yes

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:ORY. 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) (3)

CG6059

9 of 13

CG5882

8 of 13

LanA

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 ( 1 )

Human Ortholog

Disease

Evidence

References

CFAP58; cilia and flagella associated protein 58

model of spermatogenic failure 49

IEA

(FlyBase, 2019-)

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?

CFAP58; cilia and flagella associated protein 58

7 of 14

619129

SPERMATOGENIC FAILURE 49; SPGF49

spermatogenic failure 49

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

Interactions Browser

Summary of Genetic Interactions

esyN Network Diagram

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.

FBgn0046323

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

Y-

Cytogenetic map

Sequence location

Y:3,561,745..3,618,339 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

h1-h25B

(Drosophila Heterochromatin Genome Project, 2004)

Experimentally Determined Recombination Data

Location

Y-

(de Carvalho, 2001.10.4)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (2)

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

NIG-Fly

HMJ22558

y¹ v¹; P{TRiP.HMJ22558}attP40/CyO

VDRC

v110132

P{KK115840}VIE-260B

Genomic Clones (1)

CH322-175E21

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

cDNA Clones (0)

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

Other clones

Drosophila Genomics Resource Center cDNA clones

For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0046323

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Sequence of transcript(s) changed in r6 genomic release relative to r5 release.

(FlyBase Genome Annotators, 2014)

New annotation (CG40446) in release 3 of the genome annotation.

(FlyBase Genome Annotators, 2002-2003)

Relationship to Other Genes

Source for database merge of

Source for merge of: Ory CG40446

(FlyBase, 1996-)

Additional comments

FlyBase curator comment: The symbol "CG17653" has been used erroneously in FlyBase to name 2 separate annotations on the Y chromosome in different releases of the genome annotation. The two annotations map to the same region of the genome on the same strand, but share no exons. The annotation labelled "CG17653" in release 2 of the genome annotation is not annotated in releases 3.1 or 3.2 of the genome annotation. Release 3.2 annotation CG40446 (which corresponds to Ory) was mistakenly labelled "CG17653" in release 3.1 of the genome annotation, but does not overlap any exons of release 2 "CG17653".

(FlyBase Genome Annotators, 2004)

Source for merge of Ory CG40446 was sequence comparison ( date:031111 ).

(FlyBase, 1996-)

Nomenclature History

Source for database identify of

Source for identity of: ORY Ory

(FlyBase, 2009-)

Nomenclature comments

Gene symbol changed from 'Ory' to 'ORY' to reflect the capitalization used in the original publication (FBrf0141717) and general usage since.

(FlyBase, 2009-)

Etymology

Synonyms and Secondary IDs (6)

Reported As

Name Synonyms

Occludin-Related Y

(Garlovsky et al., 2022, Hoskins et al., 2015, de Carvalho et al., 2001)

Occludin-related Y

(Lemos et al., 2008)

Secondary FlyBase IDs

FBgn0058446
FBan0040446

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 29 )

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.

3355174

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.

Q5LJN3

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.