FlyBase Gene Report: Dmel\RluA-1

General Information

Symbol

Dmel\RluA-1

Species

D. melanogaster

Name

RluA pseudouridine synthase 1

Annotation Symbol

CG31719

Feature Type

protein_coding_gene

FlyBase ID

FBgn0051719

Gene Model Status

Current

Stock Availability

6 publicly available

Gene Snapshot

RluA pseudouridine synthase 1 (RluA-1) encodes a pseudouridine synthase, an enzyme catalyzing the formation of the most abundant nucleoside modification of RNA, pseudouridine. [Date last reviewed: 2019-03-14]

Other Summaries

Alliance
Auto summary
Gene Group
Interactive Fly

Also Known As

multiple, RluA1

Key Links

Genomic Location

Cytogenetic map

31E6-31F1

Sequence location

2L:10,463,340..10,474,349 [-]

Recombination map

2-42

RefSeq locus

NT_033779 REGION:10463340..10474349

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse GBrowse

Help me choose

Other Genome Views

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

Function

GO Summary Ribbons

Gene Ontology (GO) Annotations (3 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 pseudouridine synthase activity

inferred from biological aspect of ancestor with PANTHER:PTN001311753

(assigned by GO_Central )

(Gaudet et al., 2011)

enables RNA binding

inferred from electronic annotation with InterPro:IPR006145, InterPro:IPR006224, InterPro:IPR006225, InterPro:IPR020103

(assigned by InterPro )

(FlyBase Curators et al., 2004-)

Biological Process (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

involved_in enzyme-directed rRNA pseudouridine synthesis

inferred from biological aspect of ancestor with PANTHER:PTN001311753

(assigned by GO_Central )

(Gaudet et al., 2011)

Cellular Component (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Gene Group (FlyBase)

PSEUDOURIDINE SYNTHASES

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Group (FlyBase)

PSEUDOURIDINE SYNTHASES -: Pseudouridine synthases catalyze the site-specific isomerization of uridine residues that are already part of an RNA chain, which is the most abundant post-transcriptional modification of cellular RNAs. Their activity is specific for a particular RNA (e.g. tRNA or rRNA class). They can be classified into five families named after the E. coli enzymes RluA, RsuA, TruA, TruB, and TruD. (Adapted from PMID:17113994.)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\RluA-1 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

Comments on Gene Model

Annotated transcripts do not represent all supported alternative splices within 5' UTR.

Low-frequency RNA-Seq exon junction(s) not annotated.

Alternative translation stop created by use of multiphasic reading frames within coding region.

Gene model reviewed during 5.48

Sequence Ontology: Class of Gene

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

RluA-1-RA

FBtr0080039

NM_164930

3073

739

RluA-1-RB

FBtr0080040

NM_164931

3207

739

RluA-1-RC

FBtr0080041

NM_164932

2914

739

RluA-1-RD

FBtr0337008

NM_001273422

2715

378

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

RefSeq ID

GenBank

RluA-1-PA

FBpp0079629

82.3

739

7.70

NP_723592

AAF52959

RluA-1-PB

FBpp0079630

82.3

739

7.70

NP_723593

AAF52960

RluA-1-PC

FBpp0079631

82.3

739

7.70

NP_723594

AAN10755

RluA-1-PD

FBpp0307937

41.4

378

9.50

NP_001260351

AGB92886

Polypeptides with Identical Sequences

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

739 aa isoforms: RluA-1-PA, RluA-1-PB, RluA-1-PC

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

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\RluA-1 using the Feature Mapper tool.

External Data

Crossreferences

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

RluA-1_1

Linkouts

Expression Data

Expression Summary Ribbons

Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.

For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 14

dorsal pharyngeal muscle

(Wang et al., 2011)

embryonic stage 16 -- 17

neuron of embryonic/larval peripheral nervous system

(Wang et al., 2011)

embryonic/larval dorsal vessel

(Wang et al., 2011)

Additional Descriptive Data

At embryonic stage 14, RluA-1 is expressed in cells that appear iteratively in peripheral tissues and in dorsal pharyngeal muscle. At stage 17, it is observed in PNS neurons and in the dorsal vessel but not in the CNS.

(Wang et al., 2011)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 16

multidendritic neuron

(Wang et al., 2011)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

Expression Deduced from Reporters

Reporter: P{RluA1-GAL4.JN}

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

abdominal dorsal multidendritic neuron ddaC

(Shimono et al., 2009)

abdominal dorsal multidendritic neuron ddaE

(Shimono et al., 2009)

abdominal lateral multidendritic neuron ldaA

(Shimono et al., 2009)

abdominal anterior ventral multidendritic neuron vdaa

(Shimono et al., 2009)

adult abdominal lateral multidendritic neuron ldaA-like

(Shimono et al., 2009)

High-Throughput Expression Data

Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\RluA-1 in GBrowse 2

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

View exonic expression by developmental stage for Dmel\RluA-1

View exonic expression by tissue for Dmel\RluA-1

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

FBgn0051719

FLIGHT - Cell culture data for RNAi and other high-throughput technologies

FBgn0051719

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG31719-RA

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

CG31719

Flygut - An atlas of the Drosophila adult midgut

FBgn0051719

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, and Transgenic Constructs

Classical and Insertion Alleles ( 5 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 4 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of RluA-1

Transgenic constructs containing regulatory region of RluA-1

Deletions and Duplications ( 1 )

Disrupted in

Df(2L)Exel7048

(Ryder, 2004.4.26)

Phenotypes

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

Lethality

Allele

viable

RluA-1^EY13178

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

RluA-1^GD10341

viable, with Scer\GAL4^Mef2.PR

RluA-1^GD10341

viable, with Scer\GAL4^pnr-MD237

RluA-1^GD10341

viable, with Scer\GAL4^tin.CΔ4

RluA-1^GD10341

Sterility

Allele

fertile

RluA-1^EY13178

Phenotype manifest in

Allele

Orthologs

Downloads

Download All DIOPT Orthologs

Download All OrthoDB Orthologs

Human Orthologs (via DIOPT v8.0)

Homo sapiens (Human) (4)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Hsap\RPUSD2

12 of 15

Yes

Hsap\RPUSD1

1 of 15

Yes

Hsap\RPUSD3

1 of 15

Yes

Hsap\RPUSD4

1 of 15

Yes

Model Organism Orthologs (via DIOPT v8.0)

Mus musculus (laboratory mouse) (4)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Rpusd2

11 of 15

Yes

Mmus\Rpusd1

2 of 15

Yes

Mmus\Rpusd3

1 of 15

Yes

Mmus\Rpusd4

1 of 15

Yes

Rattus norvegicus (Norway rat) (5)

Rnor\LOC100911166

11 of 13

Yes

Rnor\Rpusd2

5 of 13

Yes

Rnor\Rpusd1

2 of 13

Yes

Rnor\Rpusd3

1 of 13

Yes

Rnor\Rpusd4

1 of 13

Yes

Xenopus tropicalis (Western clawed frog) (3)

Xtro\rpusd2

8 of 12

Yes

Xtro\rpusd1

1 of 12

Yes

Xtro\rpusd3

1 of 12

Yes

Danio rerio (Zebrafish) (3)

Drer\rpusd2

8 of 15

Yes

Drer\rpusd1

2 of 15

Yes

Drer\rpusd4

1 of 15

Yes

Caenorhabditis elegans (Nematode, roundworm) (1)

Cele\K07E8.7

13 of 15

Yes

Arabidopsis thaliana (thale-cress) (2)

Atha\AT5G51140

8 of 9

Yes

Atha\AT1G76050

1 of 9

Yes

Saccharomyces cerevisiae (Brewer's yeast) (4)

Scer\PUS9

11 of 15

Yes

Scer\RIB2

11 of 15

Yes

Scer\PUS6

5 of 15

Yes

Scer\PUS5

1 of 15

Yes

Schizosaccharomyces pombe (Fission yeast) (1)

Spom\SPAC18B11.02c

9 of 12

Yes

Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG091904HW )

Organism

Common Name

Gene

AAA Syntenic Ortholog

Multiple Dmel Genes in this Orthologous Group

Drosophila suzukii

Spotted wing Drosophila

Drosophila simulans

Drosophila sechellia

Drosophila erecta

Drosophila yakuba

Drosophila ananassae

Drosophila pseudoobscura pseudoobscura

Dpse\GA24957

Drosophila persimilis

Dper\GL19017

Drosophila willistoni

Dwil\GK15253

Drosophila virilis

Dvir\GJ13872

Drosophila mojavensis

Dmoj\GI20532

Drosophila grimshawi

Dgri\GH13618

Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG0915032W )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Musca domestica

House fly

Mdoa\17013788

Glossina morsitans

Tsetse fly

Gmor\GMOY010588

Lucilia cuprina

Australian sheep blowfly

Lcup\FF38_03157

Mayetiola destructor

Hessian fly

Mdes\Mdes015072

Mayetiola destructor

Hessian fly

Mdes\Mdes017364

Aedes aegypti

Yellow fever mosquito

Aaeg\AAEL001242

Anopheles darlingi

American malaria mosquito

Adar\ADAC005477

Anopheles gambiae

Malaria mosquito

Agam\AGAP009693

Culex quinquefasciatus

Southern house mosquito

Cqui\CPIJ002499

Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W03UI )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Bombyx mori

Silkmoth

Bmor\BGIBMGA006020

Danaus plexippus

Monarch butterfly

Dple\DPOGS211835-PA

Heliconius melpomene

Postman butterfly

Hmel\HMEL003310

Apis florea

Little honeybee

Aflo\2147512387

Apis mellifera

Western honey bee

Amel\LOC410341

Bombus impatiens

Common eastern bumble bee

Bimp\BIMP20607

Bombus terrestris

Buff-tailed bumblebee

Bter\15210576

Linepithema humile

Argentine ant

Lhum\LH24429

Megachile rotundata

Alfalfa leafcutting bee

Mrot\MROTU:00288d

Nasonia vitripennis

Parasitic wasp

Nvit\Nasvi2EG000265

Dendroctonus ponderosae

Mountain pine beetle

Dpod\YQE_06308

Tribolium castaneum

Red flour beetle

Tcas\TC014142

Pediculus humanus

Human body louse

Phum\PHUM068990

Rhodnius prolixus

Kissing bug

Rpro\RPRC008042

Cimex lectularius

Bed bug

Clec\CLEC012890

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI007239

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI003600

Zootermopsis nevadensis

Nevada dampwood termite

Znev\Znev_00050

Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0FOD )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strigamia maritima

European centipede

Smar\SMAR004193

Stegodyphus mimosarum

African social velvet spider

Smim\KFM74596.1

Stegodyphus mimosarum

African social velvet spider

Smim\KFM72883.1

Tetranychus urticae

Two-spotted spider mite

Turt\tetur08g03540

Tetranychus urticae

Two-spotted spider mite

Turt\tetur02g10880

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_313092

Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0P6B )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strongylocentrotus purpuratus

Purple sea urchin

Spur\Sp-Rpusd2

Ciona intestinalis

Vase tunicate

Cint\ENSCING00000018276

Ciona intestinalis

Vase tunicate

Cint\ENSCING00000023201

Gallus gallus

Domestic chicken

Ggal\RPUSD2

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v8.0)

Drosophila melanogaster (Fruit fly) (1)

Gene Symbol

Score

Source

Alignment

8 of 10

Human Disease Associations

FlyBase Human Disease Model Reports

Disease Model Summary Ribbon

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 v8.0 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?

RPUSD2; RNA pseudouridine synthase domain containing 2

12 of 15

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

View in Interactions Browser

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

RluA-1 - trv

two hybrid

(Hu et al., 2017.6.13)

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.

FBgn0051719

InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.

34438

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-42

Cytogenetic map

31E6-31F1

Sequence location

2L:10,463,340..10,474,349 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

31E6-31F1

Limits computationally determined from genome sequence between P{lacW}KdelR^k00311 and P{lacW}l(2)k09116^k09116&P{lacW}Fatp^k10307

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

2-42

(FlyBase, 2016)

2-35.5

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (6)

Bloomington

42194

y¹ w^*; Mi{MIC}RluA-1^MI06897

61043

y¹ w^*; Mi{MIC}RluA-1^MI15411

21409

y¹ w^67c23; P{EPgy2}RluA-1^EY13178

VDRC

v109586

P{KK107880}VIE-260B

v41757

w¹¹¹⁸; P{GD10341}v41757

v41758

w¹¹¹⁸; P{GD10341}v41758

Genomic Clones (20)

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

cDNA Clones (63)

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 GBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA clones, fully sequenced

BDGP DGC clones

RH45372

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.

FBgn0051719

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0051719

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

34438

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Wang et al., 2011)

Commercially Available Antibodies

Other Information

Relationship to Other Genes

Source for database identify of

Source for identity of: RluA-1 CG31719

(Chien, 2003.3.19)

Source for database merge of

Source for merge of: CG13143 CG7475

(FlyBase Genome Annotators, 2002-2003)

Additional comments

Annotations CG13143 and CG7475 merged as CG31719 in release 3 of the genome annotation.

(Chien, 2003.3.19, FlyBase Genome Annotators, 2002-2003)

"CG13143" may correspond to "Scim16". Sequence analysis off ends of P{SUPor-P} in Scim insertion mutant places "Scim16" near/in "CG13143" or "CG6187".

(Dobie and Karpen, 2001.4.18)

Other Comments

Mutations in RluA-1 do not affect the morphology of multiple dendritic neurons. Misexpression of RluA-1 results in abnormal bristles on the adult notum.

(Huang et al., 2003)

Origin and Etymology

Discoverer

Etymology

Identification

External Crossreferences and Linkouts ( 42 )

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.

34438

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

Other crossreferences

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0051719

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

FBgn0051719

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

RluA-1_1

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

CG31719

Flygut - An atlas of the Drosophila adult midgut

FBgn0051719

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

34438

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

TC014142

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

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

Dmel_CG31719

modMine - A data warehouse for the modENCODE project

FBgn0051719

Linkouts

DPiM - Drosophila Protein interaction map

FBgn0051719

DroID - A comprehensive database of gene and protein interactions.

FBgn0051719

DRSC - Results frm RNAi screens

FBgn0051719

FLIGHT - Cell culture data for RNAi and other high-throughput technologies

FBgn0051719

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG31719-RA

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0051719

FlyMine - An integrated database for Drosophila genomics

FBgn0051719

InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.

34438

Synonyms and Secondary IDs (7)

Reported As

Symbol Synonym

CG13143

CG31719

(Hosono et al., 2015, Keleman et al., 2009.8.5, Metaxakis et al., 2005, Chien, 2003.3.19, FlyBase Genome Annotators, 2002-2003, Dobie and Karpen, 2001.4.18)

CG7475

RluA-1

(Hall et al., 2019, Wang et al., 2018, Hu et al., 2017.6.13, Dezi et al., 2016, Cole et al., 2012.7.6, Izutsu et al., 2012, Japanese National Institute of Genetics, 2012.5.21, Takahashi et al., 2012, Wang et al., 2011, Nicholson et al., 2008, Greene et al., 2005)

RluA1

(Yalgin et al., 2015, Blanchard et al., 2014)

Name Synonyms

RluA pseudouridine synthase 1

RluA-1

multiple

(Chien, 2003.3.19, Huang et al., 2003)

Secondary FlyBase IDs

FBgn0032254
FBgn0032255

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

References (48)

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

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