FlyBase Gene Report: Dmel\yata

General Information

Symbol

Dmel\yata

Species

D. melanogaster

Name

yata

Annotation Symbol

CG1973

Feature Type

protein_coding_gene

FlyBase ID

FBgn0260990

Gene Model Status

Current

Stock Availability

12 publicly available

Gene Summary

kinase domain (inactive) - controls intracellular trafficking of the APPL protein - mislocalized Yata causes the mislocalization of COPI, indicating that YATA plays a role in directing COPI to the proper subcellular site - abnormal cellular structures are located in the vicinity of rhabdomeres in aged white; yata mutants - expression of APP resulted in the loss of proper control of synapse formation, which is reversed in yata mutants - secretory vesicles (Interactive Fly, yata )

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Gene Group
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

99B10-99B10

Sequence location

3R:29,749,219..29,754,528 [+]

Recombination map

3-99

RefSeq locus

NT_033777 REGION:29749219..29754528

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 (2 terms)

Molecular Function (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

enables ATP binding

inferred from electronic annotation with InterPro:IPR000719

(InterPro Project Members, 2004-)

NOT enables protein kinase activity

inferred from key residues

(Anamika et al., 2009)

Biological Process (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Cellular Component (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Gene Group (FlyBase)

SCYL PSEUDOKINASES

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Group (FlyBase)

SCYL PSEUDOKINASES -: The SCYL family of pseudokinases is found in almost all eukaryotes. Members of this family have been shown to be involved in intracellular trafficking, nuclear tRNA export and chromosome biology. (Adapted from PMID:26981075.)

Summary (Interactive Fly)

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\yata 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 Q9VAH7)

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 5.46

Tissue-specific extension of 3' UTRs observed during later stages (FBrf0218523, FBrf0219848); all variants may not be annotated

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

yata-RA

FBtr0085477

NM_143465

3565

873

yata-RB

FBtr0333822

NM_001276153

4765

873

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

yata-PA

FBpp0084843

97.2

873

6.68

FBpp0305956

97.2

873

6.68

Q9VAH7

NP_001263082

AGB96462

Polypeptides with Identical Sequences

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

873 aa isoforms: yata-PA, yata-PB

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\yata using the Feature Mapper tool.

External Data

Crossreferences

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

yata_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).

0.08

Transcript Expression

northern blot

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage

Comment: most abundant in early embryos

(Sone et al., 2009)

third instar larval stage

(Sone et al., 2009)

pupal stage

(Sone et al., 2009)

adult stage

(Sone et al., 2009)

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)

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\yata in JBrowse

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

View exonic expression by developmental stage for Dmel\yata

View exonic expression by tissue for Dmel\yata

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

43508/tissue=All

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

FBgn0260990

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0039692

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

FBgn0260990

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

CG1973

Flygut - An atlas of the Drosophila adult midgut

FBgn0260990

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 4 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 12 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of yata

Transgenic constructs containing regulatory region of yata

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(3R)Exel9025

(Ryder, 2004.4.26)

Inferred from location ( 7 )

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

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

yata^GD8890

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

yata^GD8890

viable, with Scer\GAL4^Mef2.PR

yata^GD8890

viable, with Scer\GAL4^tin.CΔ4

yata^GD8890

Sterility

Allele

female semi-sterile, with Scer\GAL4^{VP16.nanos.UTR}, Scer\GAL4^VP16.otu, Scer\GAL4^nanos.PG

Other Phenotypes

Allele

abnormal neuroanatomy | adult stage

yata^KE2.1

abnormal planar polarity | adult stage

yata^KE2.1

short lived

yata^KE2.1

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

yata^GD8890

visible, with Scer\GAL4^pnr-MD237

yata^GD8890

Phenotype manifest in

Allele

interommatidial bristle

yata^KE2.1

lens

yata^KE2.1

ommatidium

yata^KE2.1

rhabdomere

yata^KE2.1

supraesophageal ganglion

yata^KE2.1

trichogen cell, with Scer\GAL4^pnr-MD237

yata^GD8890

wing

yata^KE2.1

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\SCYL1

14 of 14

Yes

3 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

Hsap\SIK1B

1 of 14

Hsap\SIK1

1 of 14

Hsap\ULK3

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) (21)

Rnor\Scyl1

14 of 14

Yes

3 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

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Mus musculus (laboratory mouse) (21)

Mmus\Scyl1

14 of 14

Yes

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

Xenopus tropicalis (Western clawed frog) (15)

Xtro\scyl1

11 of 13

Yes

2 of 13

2 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

Xtro\ulk3

1 of 13

Danio rerio (Zebrafish) (20)

Drer\scyl1

10 of 14

Yes

3 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

Caenorhabditis elegans (Nematode, roundworm) (13)

Cele\scyl-1

14 of 14

Yes

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) (10)

Agam\AgaP_AGAP001091

11 of 12

Yes

3 of 12

2 of 12

2 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (36)

Atha\CTEXP

13 of 13

Yes

2 of 13

2 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

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

Yes

Atha\CIPK22

1 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

Saccharomyces cerevisiae (Brewer's yeast) (5)

Scer\CEX1

10 of 13

Yes

2 of 13

1 of 13

1 of 13

1 of 13

Schizosaccharomyces pombe (Fission yeast) (5)

Spom\ppk3

9 of 12

Yes

2 of 12

1 of 12

1 of 12

1 of 12

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:yata. 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) (9)

CG1344

5 of 13

CG1951

3 of 13

bma

2 of 13

Eip63E

1 of 13

mbt

1 of 13

Nuak

1 of 13

Sik2

1 of 13

Wnk

1 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

spinocerebellar ataxia, autosomal recessive 21

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 1 )

Allele

Disease

Evidence

References

yata^KE2.1

model of autosomal recessive spinocerebellar ataxia 21

CEA

(Sone et al., 2009)

Potential Models Based on Orthology ( 1 )

Human Ortholog

Disease

Evidence

References

SCYL1; SCY1 like pseudokinase 1

model of autosomal recessive spinocerebellar ataxia 21

IEA

(FlyBase, 2019-)

Modifiers Based on Experimental Evidence ( 2 )

Allele

Disease

Interaction

References

yata^KE2.1

model of autosomal recessive spinocerebellar ataxia 21

is ameliorated by hig^UAS.Tag:HA

(Sone et al., 2009)

is ameliorated by Appl^UAS.Tag:HA

(Sone et al., 2009)

ameliorates Alzheimer's disease 1

modeled by Hsap\APP^{695-Swedish.UAS.Tag:MYC}

(Furotani et al., 2018)

yata^NIG.1973R

ameliorates Alzheimer's disease 1

modeled by Hsap\APP^{695-Swedish.UAS.Tag:MYC}

(Furotani et al., 2018)

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?

SCYL1; SCY1 like pseudokinase 1

14 of 14

607982

SPINOCEREBELLAR ATAXIA, AUTOSOMAL RECESSIVE 21; SCAR21

autosomal recessive spinocerebellar ataxia 21

SCYL3; SCY1 like pseudokinase 3

3 of 14

608192

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

yata - Raf

anti tag coimmunoprecipitation, peptide massfingerprinting

(Friedman et al., 2011)

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

yata

enhanceable

Appl

(Sone et al., 2009)

yata

suppressible

Appl

(Sone et al., 2009)

yata

suppressible

hig

(Sone et al., 2009)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

enhanceable

yata

(Arimoto et al., 2020)

External Data

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0260990

MIST (genetic) - An integrated Molecular Interaction Database

43508

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

43508

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

SignaLink - A signaling pathway resource with multi-layered regulatory networks.

Q9VAH7

Class of Gene

gene

(Sone et al., 2007)

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-99

Cytogenetic map

99B10-99B10

Sequence location

3R:29,749,219..29,754,528 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

99B10-99B10

Limits computationally determined from genome sequence between P{PZ}l(3)06743⁰⁶⁷⁴³ and P{PZ}ncd⁰⁵⁸⁸⁴

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-99

(FlyBase, 2016)

3-96.7

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (12)

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

Bloomington

602793

y¹ v¹; P{CFD4FLPOUT-CG1344-yata}attP40/CyO

32986

y¹ sc^* v¹ sev²¹; P{TRiP.HMS00786}attP2

34100

y¹ sc^* v¹ sev²¹; P{TRiP.HMS01005}attP2/TM3, Sb¹

FlyORF

F001645

M{UAS-yata.ORF}ZH-86Fb

F001011

M{UAS-yata.ORF.3xHA}ZH-86Fb

NIG-Fly

1973R-2

P{NIG.1973R}2

1973R-3

P{NIG.1973R}3

HMS00786

y¹ sc^* v¹ sev²¹; P{TRiP.HMS00786}attP2

HMS01005

y¹ sc^* v¹ sev²¹; P{TRiP.HMS01005}attP2/TM3, Sb¹

VDRC

v110214

P{KK102668}VIE-260B

v19275

w¹¹¹⁸; P{GD8890}v19275

v341051

P{hsFLP}1, y¹ w¹¹¹⁸; P{HD_CFD00057}attP40/CyO-GFP

Genomic Clones (15)

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

cDNA Clones (46)

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

RE62393

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.

FBgn0260990

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0260990

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

yata regulates the subcellular localisation of Appl protein.

(Sone et al., 2009)

yata mutant flies exhibit morphological defects in compound eyes and die early after eclosion. Exogenous expression of yata in neurons results in rescue of the early apopotosis phenotype.

(Sone et al., 2007)

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: yata CG1973

(Sone et al., 2009)

Additional comments

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

The gene is named "yata" after the legendary crow that guided an ancient Japanese emperor, since its gene product is suggested to control protein localization.

(Sone et al., 2009)

Synonyms and Secondary IDs (3)

Reported As

Symbol Synonym

Name Synonyms

CG1973

yata

Secondary FlyBase IDs

FBgn0039692
FBgn0086225

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.

43508

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

BI637851

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.

Q9VAH7

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

Q9VAH7

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.

Q9VAH7

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

43508/tissue=All

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

FBgn0260990

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

FBgn0260990

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

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

dme:Dmel_CG1973

MARRVEL_MODEL - MARRVEL (model organism gene)

43508

Linkouts

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

FBgn0260990

DroID - A comprehensive database of gene and protein interactions.

FBgn0260990

DRSC - Results frm RNAi screens

FBgn0260990

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

yata_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0039692

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0260990

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

CG1973

Flygut - An atlas of the Drosophila adult midgut

FBgn0260990

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

TC008834

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

Interactive Fly

MIST (genetic) - An integrated Molecular Interaction Database

43508

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

43508

SignaLink - A signaling pathway resource with multi-layered regulatory networks.

Q9VAH7

References (62)

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

0.08

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