FlyBase Gene Report: Dmel\FDY

General Information

Symbol

Dmel\FDY

Species

D. melanogaster

Name

flagrante delicto Y

Annotation Symbol

CG41503

Feature Type

protein_coding_gene

FlyBase ID

FBgn0265047

Gene Model Status

Incomplete

Stock Availability

8 publicly available

Gene Summary

flagrante delicto Y (FDY) is a gene inserted in the Y chromosome originated from a duplication of vig2. [Date last reviewed: 2019-03-07] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

Sequence location

Y:3,022,289..3,024,024 [+]

Recombination map

Y-

RefSeq locus

NC_024512 REGION:3022289..3024024

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 (3 terms)

Molecular Function (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

enables RNA binding

inferred from biological aspect of ancestor with PANTHER:PTN000266096

(GO Reference Genome Project, 2011-)

inferred from electronic annotation with InterPro:IPR039764

(InterPro Project Members, 2004-)

Biological Process (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

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 cytoplasm

inferred from biological aspect of ancestor with PANTHER:PTN000266096

(GO Reference Genome Project, 2011-)

is_active_in nucleus

inferred from biological aspect of ancestor with PANTHER:PTN000266096

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

flagrante delicto Y (FDY) is a gene inserted in the Y chromosome originated from a duplication of vig2. [Date last reviewed: 2019-03-07]

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\FDY 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 D2A6L8)

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 incomplete due to gap in genomic sequence (terminal domain is truncated); polypeptide sequences represent the complete gene, based on GenBank accession KR781487.

Within a region on the Y chromosome that appears to have been originally derived from a contiguous region on 3R; the 3R region includes CG11844, CG10238, Clbn (CG11847), and CG11848.

Gene model reviewed during 6.04

Gene model reviewed during 6.19

Sequence Ontology: Class of Gene

gene

nuclear_gene

(FlyBase Genome Annotators, 2009)

protein_coding_gene

(FlyBase Genome Annotators, 2009)

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

FDY-RD

FBtr0473381

NM_001370012

1113

402

FDY-RE

FBtr0473382

NM_001316650

1117

402

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

FDY-PD

FBpp0422977

44.3

402

9.93

EFA98714

FDY-PE

FBpp0422978

44.3

402

9.93

ALI51677

Polypeptides with Identical Sequences

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

402 aa isoforms: FDY-PD, FDY-PE

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Crossreferences

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

Linkouts

Sequences Consistent with the Gene Model

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\FDY 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).

3.91

Transcript Expression

RT-PCR

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage | male

testis

(Carvalho et al., 2015)

Additional Descriptive Data

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\FDY in JBrowse

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

View exonic expression by developmental stage for Dmel\FDY

View exonic expression by tissue for Dmel\FDY

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

8674077/tissue=All

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

FBgn0265047

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

FBgn0265047

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 5 )

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 FDY

Transgenic constructs containing regulatory region of FDY

Aberrations (Deficiencies and Duplications) ( 8 )

Inferred from experimentation ( 8 )

Gene not disrupted in

Ts(1Lt;YLt)V8

(Carvalho et al., 2015)

Ts(1Lt;YSt)V24

(Carvalho et al., 2015)

Gene disrupted in

Df(YL)F63

(Hafezi et al., 2020)

Ts(1Rt;YLt)V24

(Carvalho et al., 2015)

Ts(1Rt;YSt)V8

(Carvalho et al., 2015)

Gene partially disrupted in

Df(YL)F11

(Hafezi et al., 2020)

Df(YL)F16

(Hafezi et al., 2020)

Df(YL)F52

(Hafezi et al., 2020)

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.

Sterility

Allele

male fertile

male fertile, with Scer\GAL4^VP16.bam

FDY^HMJ24080

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) (19)

Hsap\SERBP1

9 of 14

Yes

8 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

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (2)

Rnor\Serbp1

9 of 14

Yes

Rnor\Habp4

8 of 14

Mus musculus (laboratory mouse) (2)

Mmus\Serbp1

9 of 14

Yes

Mmus\Habp4

8 of 14

Xenopus tropicalis (Western clawed frog) (2)

Xtro\habp4

8 of 13

Yes

Xtro\serbp1

6 of 13

Yes

Danio rerio (Zebrafish) (3)

Drer\serbp1a

9 of 14

Yes

Drer\zgc:103482

9 of 14

Yes

Drer\serbp1b

8 of 14

Caenorhabditis elegans (Nematode, roundworm) (1)

Cele\vig-1

8 of 14

Yes

Anopheles gambiae (African malaria mosquito) (1)

Agam\AgaP_AGAP013112

10 of 12

Yes

Arabidopsis thaliana (thale-cress) (3)

Atha\AT4G16830

4 of 13

Yes

Atha\AT4G17520

4 of 13

Yes

Atha\AT5G47210

4 of 13

Yes

Saccharomyces cerevisiae (Brewer's yeast) (0)

Schizosaccharomyces pombe (Fission yeast) (1)

Spom\SPBC16A3.08c

1 of 12

Yes

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:FDY. 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)

vig2

8 of 13

vig

8 of 13

PPYR1

3 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?

SERBP1; SERPINE1 mRNA binding protein 1

9 of 14

607378

HABP4; hyaluronan binding protein 4

8 of 14

617369

Functional Complementation Data

Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.

Interactions

Summary of Physical Interactions

esyN Network Diagram

Show neighbor-neighbor interactions:

Off

Show/hide secondary interactors
(data from AllianceMine provided by esyN)

Select Layout:

Force Directed

Circle

Concentric

Legend:

Protein

RNA

Selected Interactor(s)

Other 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

FDY - Pdk1

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

Summary of Genetic Interactions

esyN Network Diagram

Other Interaction Browsers

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Linkouts

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

8674077

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:3,022,289..3,024,024 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

FDY maps to the long arm of the Y chromosome.

(Hafezi et al., 2020)

YLt-h17

(Hafezi et al., 2020)

Experimentally Determined Recombination Data

Location

Y-

(de Carvalho and Clark, 2003)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (8)

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

Bloomington

602710

FDY^L3.2

602709

FDY^L71.4

93011

w^*; P{U6:3-FDY.gRNA}attP2

62536

y¹ v¹; P{TRiP.HMJ24080}attP40/CyO

83549

y¹ sc^* v¹ sev²¹; P{TKO.GS04330}attP40

NIG-Fly

HMJ24080

y¹ v¹; P{TRiP.HMJ24080}attP40/CyO

VDRC

v330644

P{VSH330644}attP40

v330645

P{VSH330645}attP40

Genomic Clones (1)

CH322-91L7

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

cDNA Clones (17)

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.

FBgn0265047

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Annotation CR41503 renamed CG41503 in release 5.21 of the genome annotation.

(FlyBase Genome Annotators, 2009)

New annotation (CR41503) in release 5.2 of the genome annotation.

(Drosophila Heterochromatin Genome Project, 2007)

Relationship to Other Genes

Source for database merge of

Source for merge of: fdy CG41503

(FlyBase, 1992-)

Additional comments

The Y-linked FDY gene arose from a duplication of the autosomal vig2 gene onto the Y chromosome.

(Carvalho et al., 2015)

Nomenclature History

Source for database identify of

Source for identity of: FDY fdy

(FlyBase, 2009-)

Nomenclature comments

Gene symbol changed from 'fdy' to 'FDY' to reflect the capitalization used in the original publication (FBrf0154622) and general usage since.

(FlyBase, 2009-)

Etymology

The gene is named "flagrante delicto Y" because it provides direct evidence of the origin of Y-linked genes.

(Carvalho et al., 2015)

Synonyms and Secondary IDs (6)

Reported As

Symbol Synonym

CG41503

(Meadows, 2018.10.31, Hosono et al., 2015, FlyBase Genome Annotators, 2009)

CR41503

(Perkins et al., 2009, Drosophila Heterochromatin Genome Project, 2007)

FDY

(Kotov et al., 2022, Bartolo et al., 2021, Hafezi et al., 2020, Zhang et al., 2020, Gärtner et al., 2019, Transgenic RNAi Project members, 2017-, Carvalho et al., 2015, Hoskins et al., 2015, Koerich et al., 2008, Koerich et al., 2007, Carvalho et al., 2006, Gvozdev et al., 2005, de Carvalho and Clark, 2003)

Fdy

(Chang et al., 2022)

fdy

Name Synonyms

flagrante delicto Y

(Carvalho et al., 2015, Hoskins et al., 2015, Gvozdev et al., 2005, de Carvalho and Clark, 2003)

Secondary FlyBase IDs

FBgn0064184
FBan0041503
FBgn0085787

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 19 )

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.

8674077

GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.

KR781487

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.

D2A6L8

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

D2A6L8

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.

D2A6L8

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

8674077/tissue=All

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

FBgn0265047

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

FBgn0265047

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

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

dme:Dmel_CG41503

MARRVEL_MODEL - MARRVEL (model organism gene)

8674077

Linkouts

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

FBgn0265047

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0265047

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

8674077

References (28)

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

3.91

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