FlyBase Gene Report: Dmel\Rox8

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Rox8 using the Feature Mapper tool.

External Data

Crossreferences

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

Linkouts

Gene Ontology (6 terms)

Molecular Function (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

mRNA binding

inferred from sequence or structural similarity

(Lasko, 2000)

nucleic acid binding

inferred from electronic annotation with InterPro:IPR000504

(assigned by InterPro )

(FlyBase Curators et al., 2004-)

Biological Process (2 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

regulation of alternative mRNA splicing, via spliceosome

inferred from high throughput mutant phenotype

(Park et al., 2004)

inferred from mutant phenotype

(Katzenberger et al., 2009)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

mRNA splicing, via spliceosome

inferred from sequence or structural similarity with SGD:S000001128

(Mount and Salz, 2000)

Cellular Component (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

nucleus

inferred by curator from GO:0000381

(Park et al., 2004)

U1 snRNP

inferred from sequence or structural similarity with SGD:S000001128

(Mount and Salz, 2000)

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 1 -- 3

organism

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 4 -- 6

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 7 -- 8

organism | ubiquitous

(Fisher et al., 2012)

pole cell

(Fisher et al., 2012)

embryonic stage 9 -- 10

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 11 -- 12

central brain primordium

(Fisher et al., 2012)

germline cell

(Fisher et al., 2012)

organism | faint | ubiquitous

(Fisher et al., 2012)

ventral nerve cord primordium

(Fisher et al., 2012)

embryonic stage 13 -- 16

germline cell

(Fisher et al., 2012)

organism | faint | ubiquitous

(Fisher et al., 2012)

wandering third instar larval stage

wing pouch | restricted

(Molnar et al., 2012)

wing hinge primordium | restricted

(Molnar et al., 2012)

northern blot

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage | female

(Brand and Bourbon, 1993)

larval stage & pupal stage & adult stage

(Brand and Bourbon, 1993)

embryonic stage 1 -- 9

organism

(Brand and Bourbon, 1993)

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

GBrowse - Visual display of RNA-Seq signals

View Dmel\Rox8 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\Rox8

View exonic expression by tissue for Dmel\Rox8

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

FBgn0005649

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

FBgn0005649

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG5422-RD

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

CG5422

Flygut - An atlas of the Drosophila adult midgut

FBgn0005649

Images

FlyExpress - Embryonic expression images (BDGP data)

Show all FlyExpress processed images for Dmel\Rox8

Stages(s) 4-6
Stages(s) 7-8
Stages(s) 9-10
Stages(s) 11-12

FlyBase Wiki

Image Based Resources

Alleles, Insertions, and Transgenic Constructs

Classical and Insertion Alleles ( 13 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 8 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Rox8

Transgenic constructs containing regulatory region of Rox8

Deletions and Duplications ( 2 )

Partially disrupted in

Df(3R)spas^5.75

(Sherwood et al., 2004)

Disrupted in

Df(3R)Exel6197

(Ryder, 2004.4.26)

Phenotypes

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

Lethality

Allele

viable

Rox8^EY04187

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

Rox8^GD11645

viable, with Scer\GAL4^Mef2.PR

Rox8^GD11645

viable, with Scer\GAL4^pnr-MD237

Rox8^GD11645

viable, with Scer\GAL4^tin.CΔ4

Rox8^GD11645

Sterility

Allele

fertile

Rox8^EY04187

Phenotype manifest in

Allele

Orthologs

Downloads

Download All DIOPT Orthologs

Download All OrthoDB Orthologs

Human Orthologs (via DIOPT v7.1)

Homo sapiens (Human) (4)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Hsap\TIAL1

14 of 15

Yes

Hsap\TIA1

11 of 15

Yes

Hsap\SRSF3

1 of 15

Hsap\TRNAU1AP

1 of 15

Model Organism Orthologs (via DIOPT v7.1)

Mus musculus (laboratory mouse) (3)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Tial1

14 of 15

Yes

Mmus\Tia1

11 of 15

Yes

Mmus\Trnau1ap

1 of 15

Rattus norvegicus (Norway rat) (2)

Rnor\Tial1

11 of 13

Yes

Rnor\Tia1

8 of 13

Yes

Xenopus tropicalis (Western clawed frog) (3)

Xtro\tia1

9 of 12

Yes

Xtro\LOC100490872

1 of 12

Yes

Xtro\pick1

1 of 12

Danio rerio (Zebrafish) (4)

Drer\tial1

13 of 15

Yes

Drer\tia1

11 of 15

Yes

Drer\tia1l

11 of 15

Yes

Drer\trnau1apb

1 of 15

Caenorhabditis elegans (Nematode, roundworm) (4)

Cele\tiar-1

11 of 15

Yes

Cele\tiar-2

11 of 15

Yes

Cele\tiar-3

4 of 15

Cele\T07F10.3

1 of 15

Arabidopsis thaliana (thale-cress) (6)

Atha\AT3G14100

7 of 9

Yes

Atha\UBP1A

7 of 9

Yes

Atha\UBP1B

7 of 9

Yes

Atha\UBA2A

2 of 9

Yes

Atha\AT2G41060

1 of 9

Yes

Atha\AT5G19350

1 of 9

Saccharomyces cerevisiae (Brewer's yeast) (4)

Scer\PUB1

11 of 15

Yes

Scer\NAM8

2 of 15

Scer\NGR1

2 of 15

Scer\MRN1

1 of 15

Yes

Schizosaccharomyces pombe (Fission yeast) (4)

Spom\csx1

2 of 12

Yes

Spom\SPBC23E6.01c

2 of 12

Yes

Spom\mug24

1 of 12

Spom\nrd1

1 of 12

Yes

Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG09190B1X )

Organism

Common Name

Gene

AAA Syntenic Ortholog

Multiple Dmel Genes in this Orthologous Group

Drosophila melanogaster

fruit fly

Dmel\Rox8

Drosophila suzukii

Spotted wing Drosophila

Drosophila simulans

Drosophila sechellia

Drosophila erecta

Drosophila yakuba

Drosophila ananassae

Drosophila pseudoobscura pseudoobscura

Dpse\GA32929

Drosophila pseudoobscura pseudoobscura

Dpse\GA18869

Drosophila persimilis

Dper\GL24152

Drosophila willistoni

Dwil\GK11939

Drosophila virilis

Dvir\GJ14540

Drosophila mojavensis

Dmoj\GI22960

Drosophila grimshawi

Dgri\GH19101

Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091506FG )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Musca domestica

House fly

Mdoa\17010056

Glossina morsitans

Tsetse fly

Gmor\GMOY009502

Lucilia cuprina

Australian sheep blowfly

Lcup\FF38_14024

Mayetiola destructor

Hessian fly

Mdes\Mdes000797

Aedes aegypti

Yellow fever mosquito

Aaeg\AAEL006710

Anopheles darlingi

American malaria mosquito

Adar\ADAC000209

Anopheles gambiae

Malaria mosquito

Agam\AGAP002335

Culex quinquefasciatus

Southern house mosquito

Cqui\CPIJ013665

Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W0D4P )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Bombyx mori

Silkmoth

Bmor\BGIBMGA001619

Bombyx mori

Silkmoth

Bmor\BGIBMGA004892

Danaus plexippus

Monarch butterfly

Dple\DPOGS200156-PA

Danaus plexippus

Monarch butterfly

Dple\DPOGS214717-PA

Heliconius melpomene

Postman butterfly

Hmel\HMEL009161

Apis florea

Little honeybee

Aflo\2468482324

Apis florea

Little honeybee

Aflo\2153264516

Apis mellifera

Western honey bee

Amel\Rox8

Apis mellifera

Western honey bee

Amel\GB42292

Bombus impatiens

Common eastern bumble bee

Bimp\BIMP20737

Bombus impatiens

Common eastern bumble bee

Bimp\BIMP25257

Bombus terrestris

Buff-tailed bumblebee

Bter\15216431

Bombus terrestris

Buff-tailed bumblebee

Bter\15205361

Linepithema humile

Argentine ant

Lhum\LH20418

Megachile rotundata

Alfalfa leafcutting bee

Mrot\MROTU:00107d

Megachile rotundata

Alfalfa leafcutting bee

Mrot\MROTU:0026cd

Nasonia vitripennis

Parasitic wasp

Nvit\Nasvi2EG005752

Nasonia vitripennis

Parasitic wasp

Nvit\Nasvi2EG011625

Dendroctonus ponderosae

Mountain pine beetle

Dpod\YQE_11831

Dendroctonus ponderosae

Mountain pine beetle

Dpod\YQE_02488

Tribolium castaneum

Red flour beetle

Tcas\TC031489

Tribolium castaneum

Red flour beetle

Tcas\TC009608

Pediculus humanus

Human body louse

Phum\PHUM511750

Pediculus humanus

Human body louse

Phum\PHUM514840

Rhodnius prolixus

Kissing bug

Rpro\RPRC002783

Cimex lectularius

Bed bug

Clec\CLEC012826

Cimex lectularius

Bed bug

Clec\CLEC003530

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI002888

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI008980

Zootermopsis nevadensis

Nevada dampwood termite

Znev\Znev_13228

Zootermopsis nevadensis

Nevada dampwood termite

Znev\Znev_17487

Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0D2G )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strigamia maritima

European centipede

Smar\SMAR013215

Ixodes scapularis

Black-legged tick

Isca\ISCW016601

Stegodyphus mimosarum

African social velvet spider

Smim\KFM66227.1

Stegodyphus mimosarum

African social velvet spider

Smim\KFM83144.1

Tetranychus urticae

Two-spotted spider mite

Turt\tetur09g01770

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_20224

Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0FH8 )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strongylocentrotus purpuratus

Purple sea urchin

Spur\Sp-Tial1

Ciona intestinalis

Vase tunicate

Cint\ENSCING00000002150

Gallus gallus

Domestic chicken

Ggal\TIAL1

Gallus gallus

Domestic chicken

Ggal\TIA1

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v7.1)

Drosophila melanogaster (Fruit fly) (12)

Gene Symbol

Score

Source

Alignment

5 of 10

trv

3 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

fne

1 of 10

Rbp9

1 of 10

Secp43

1 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 ( 1 )

Allele

Disease

Interaction

References

Rox8^HMS00472

ameliorates amyotrophic lateral sclerosis

modeled by Hsap\TARDBP^UAS.cEa

(Kim et al., 2014)

Disease Associations of Human Orthologs (via DIOPT v7.1 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?

TIAL1; TIA1 cytotoxic granule associated RNA binding protein like 1

14 of 15

603413

TIA1; TIA1 cytotoxic granule associated RNA binding protein

11 of 15

603518

WELANDER DISTAL MYOPATHY; WDM

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

Rox8 - CG44251

two hybrid

(Hu et al., 2017.6.13)

Rox8 - 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

BioGRID - A database of protein and genetic interactions.

67782

DroID - A comprehensive database of gene and protein interactions.

FBgn0005649

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

42848

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-82

Cytogenetic map

95D9-95D10

Sequence location

3R:24,043,056..24,048,265 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

95D9-95D10

Limits computationally determined from genome sequence between P{PZ}l(3)04684⁰⁴⁶⁸⁴ and P{PZ}Atg6⁰⁰⁰⁹⁶

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

95D5-95D9

(Brand, 1993)

95D5-95D9

(determined by in situ hybridisation)

(Ranz et al., 1999, Brand and Bourbon, 1993)

Experimentally Determined Recombination Data

Location

3-82

(FlyBase, 2016)

3-82.5

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (12)

Bloomington

43531

w^*; P{GSV1}Rox8^s-572

84210

y¹ v¹; M{WKO.P5-A4}ZH-86Fb

28035

y¹ v¹; P{TRiP.JF02870}attP2

81798

y¹ v¹; P{TKO.GS04844}attP40

20002

y¹ w^67c23; P{EPgy2}Rox8^EY04187

32472

y¹ sc^* v¹ sev²¹; P{TRiP.HMS00472}attP2

15865

y¹ w^67c23; P{EPgy2}Rox8^EY02351 CG5986^EY02351

Kyoto

103640

w^*; P{GawB}Rox8^NP0528 / TM3, Ser¹

VDRC

v100563

P{KK108120}VIE-260B

v28649

w¹¹¹⁸; P{GD11645}v28649

v41439

w¹¹¹⁸; P{GD11645}v41439

v27415

w¹¹¹⁸; P{GD11645}v27415/CyO

Genomic Clones (20)

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

cDNA Clones (282)

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 sequences

BDGP DGC clones

RE71384

Other clones

FI04408

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.

FBgn0005649

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0005649

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

42848

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Other Information

Relationship to Other Genes

Source for database identify of

Source for identity of: Rox8 CG5422

(Kodira, 1999.11)

Source for database merge of

Source for merge of: Rox8 Rbp12

(Misra, 2000.7.28)

Additional comments

Other Comments

Rox8 is identified as an RRM-type RNA-binding protein that may control important aspects of development.

(Brand et al., 1995)

Rox8 has been cloned and characterised.

(Brand and Bourbon, 1993)

A sequence comparison and numerical analysis of the RRM-containing (RNA recognition motif) proteins suggests that functionally related RRM-containing proteins have significant sequence similarities in their RRMs.

(Kim and Baker, 1993)

Origin and Etymology

Discoverer

Etymology

Identification

External Crossreferences and Linkouts ( 63 )

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.

42848

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

FBgn0005649

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

FBgn0005649

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

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

CG5422

Flygut - An atlas of the Drosophila adult midgut

FBgn0005649

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

42848

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

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

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

Dmel_CG5422

modMine - A data warehouse for the modENCODE project

FBgn0005649

Linkouts

BioGRID - A database of protein and genetic interactions.

67782

DroID - A comprehensive database of gene and protein interactions.

FBgn0005649

DRSC - Results frm RNAi screens

FBgn0005649

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

FBgn0005649

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG5422-RD

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0005649

FlyMine - An integrated database for Drosophila genomics

FBgn0005649

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

42848

Synonyms and Secondary IDs (12)

Reported As

Symbol Synonym

CG5422

(Çiçek et al., 2016, Brooks et al., 2015, Sing et al., 2014, Ni et al., 2010.12.1, Keleman et al., 2009.8.5, Perkins et al., 2009, Haussmann et al., 2008, McIntyre et al., 2006, Mount and Salz, 2000)

DmTIAR

(Brand and Bourbon, 1993)

ROX8

(Li et al., 2016, Brand et al., 1995)

RRM12

(Kim, 1993.3.10)

Rbp12

Rox-8

(Tuxworth et al., 2011)

TIAR

(Brand, 1993, Brand, 1993)

dTIAR

(Venables et al., 2012, Katzenberger et al., 2009)

rox8

(Khalil et al., 2017, Brand and Bourbon, 1993)

rrm12

(Kim and Baker, 1993)

Name Synonyms

RNA-binding protein 12

Rox8

Secondary FlyBase IDs

FBgn0010255
FBgn0010283

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

References (79)

Report Sections

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