FlyBase Gene Report: Dmel\Rb97D

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Rb97D using the Feature Mapper tool.

External Data

Crossreferences

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

Rb97D_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).

1.35

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

(Fisher et al., 2012)

embryonic stage 7 -- 8

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 9 -- 10

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 11 -- 12

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 13 -- 16

organism | ubiquitous

(Fisher et al., 2012)

northern blot

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage -- adult stage

(Karsch-Mizrachi and Haynes, 1993)

Additional Descriptive Data

Rb97D transcripts are observed at most developmental stages. The highest levels are seen in early pupae.

(Karsch-Mizrachi and Haynes, 1993)

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\Rb97D in JBrowse

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

View exonic expression by developmental stage for Dmel\Rb97D

View exonic expression by tissue for Dmel\Rb97D

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

FBgn0004903

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

43231/tissue=All

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

FBgn0004903

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0004903

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

FBgn0004903

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

CG6354

Flygut - An atlas of the Drosophila adult midgut

FBgn0004903

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 8 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 9 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Rb97D

Transgenic constructs containing regulatory region of Rb97D

Aberrations (Deficiencies and Duplications) ( 21 )

Inferred from experimentation ( 21 )

Inferred from location ( 6 )

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

lethal

Rb97D¹

Sterility

Allele

male sterile

Rb97D¹

male sterile | recessive

Phenotype manifest in

Allele

axoneme

Rb97D²

nucleus & spermatid

Rb97D¹

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) (52)

Hsap\HNRNPA1

6 of 14

Yes

Hsap\HNRNPA1L2

6 of 14

Yes

Hsap\HNRNPA2B1

6 of 14

Yes

Hsap\HNRNPA3

6 of 14

Yes

4 of 14

2 of 14

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

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

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

143

Hsap\TIA1

1 of 14

Hsap\U2AF2

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\Hnrnpa1

6 of 14

Yes

Rnor\Hnrnpa2b1

6 of 14

Yes

5 of 14

4 of 14

2 of 14

2 of 14

2 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

1 of 14

1 of 14

Yes

Rnor\Rbms2

1 of 14

Mus musculus (laboratory mouse) (26)

Mmus\Hnrnpa1

6 of 14

Yes

Mmus\Hnrnpa2b1

6 of 14

Yes

5 of 14

3 of 14

2 of 14

2 of 14

2 of 14

1 of 14

Yes

Mmus\Gm21379

1 of 14

Mmus\Hnrnpa1l2-ps2

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

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Mmus\Slirp

1 of 14

Xenopus tropicalis (Western clawed frog) (26)

Xtro\hnrnpa1

5 of 13

Yes

Xtro\hnrnpa3

5 of 13

Yes

4 of 13

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

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

Danio rerio (Zebrafish) (32)

Drer\hnrnpa1b

6 of 14

Yes

5 of 14

5 of 14

3 of 14

2 of 14

2 of 14

2 of 14

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

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (26)

Cele\hrpa-1

6 of 14

Yes

Cele\hrpa-2

2 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

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) (23)

Agam\AgaP_AGAP002374

4 of 12

Yes

2 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (82)

Atha\AT1G01080

2 of 13

Yes

Atha\AT1G60000

2 of 13

Yes

Atha\AT2G22100

2 of 13

Yes

Atha\AT2G35410

2 of 13

Yes

Atha\AT2G37220

2 of 13

Yes

Atha\AT2G41060

2 of 13

Yes

Atha\AT3G13224

2 of 13

Yes

Atha\AT3G15010

2 of 13

Yes

Atha\AT4G09040

2 of 13

Yes

Atha\AT5G40490

2 of 13

Yes

Atha\AT5G47620

2 of 13

Yes

Atha\AT5G55550

2 of 13

Yes

Atha\CP29

2 of 13

Yes

Atha\CP31B

2 of 13

Yes

Atha\CP33

2 of 13

Yes

Atha\NUC-L1

2 of 13

Yes

Atha\NUC-L2

2 of 13

Yes

Atha\PHIP1

2 of 13

Yes

Atha\RBP31

2 of 13

Yes

Atha\UBA1A

2 of 13

Yes

Atha\UBA2A

2 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

1 of 13

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

Yes

Atha\AT5G06210

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

Atha\AT5G53680

1 of 13

Atha\AT5G53700

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

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) (7)

Scer\HRP1

2 of 13

Yes

Scer\NOP12

1 of 13

Scer\NOP13

1 of 13

Yes

Scer\NSR1

1 of 13

Yes

Scer\PAB1

1 of 13

Scer\PUB1

1 of 13

Scer\SGN1

1 of 13

Schizosaccharomyces pombe (Fission yeast) (8)

Spom\gar2

1 of 12

Yes

Spom\nop12

1 of 12

Yes

Spom\pab2

1 of 12

Yes

Spom\pabp

1 of 12

Yes

Spom\rnp24

1 of 12

Yes

Spom\SPAC328.05

1 of 12

Yes

Spom\SPBC365.04c

1 of 12

Yes

Spom\SPBC660.15

1 of 12

Yes

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Rb97D. 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) (35)

9 of 13

9 of 13

4 of 13

2 of 13

2 of 13

2 of 13

msi

2 of 13

Rbp6

2 of 13

SLIRP1

2 of 13

SLIRP2

2 of 13

sqd

2 of 13

Sxl

2 of 13

Syp

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

hfp

1 of 13

LS2

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

ssx

1 of 13

TBPH

1 of 13

trv

1 of 13

U2af50

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 ( 4 )

Human Ortholog

Disease

Evidence

References

HNRNPA1; heterogeneous nuclear ribonucleoprotein A1

model of inclusion body myopathy with early-onset Paget disease of bone with or without frontotemporal dementia 3

IEA

(FlyBase, 2019-)

model of distal myopathy 3

IEA

(FlyBase, 2019-)

model of amyotrophic lateral sclerosis type 20

IEA

(FlyBase, 2019-)

HNRNPA2B1; heterogeneous nuclear ribonucleoprotein A2/B1

model of inclusion body myopathy with early-onset Paget disease of bone with or without frontotemporal dementia 2

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?

HNRNPA1; heterogeneous nuclear ribonucleoprotein A1

6 of 14

164017

HNRNPA1L2; heterogeneous nuclear ribonucleoprotein A1 like 2

6 of 14

HNRNPA2B1; heterogeneous nuclear ribonucleoprotein A2/B1

6 of 14

600124

inclusion body myopathy with early-onset Paget disease of bone with or without frontotemporal dementia 2

HNRNPA3; heterogeneous nuclear ribonucleoprotein A3

6 of 14

605372

HNRNPA1L3; heterogeneous nuclear ribonucleoprotein A1 like 3

4 of 14

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

Rb97D - Tet

experimental knowledge based

(Guruharsha et al., 2011)

Rb97D - ZAP3

experimental knowledge based

(Guruharsha et al., 2011)

Rb97D - mahe

experimental knowledge based

(Guruharsha et al., 2011)

Rb97D - vkg

experimental knowledge based

(Guruharsha et al., 2011)

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

BioGRID - A database of protein and genetic interactions.

68122

DroID - A comprehensive database of gene and protein interactions.

FBgn0004903

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

43231

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

mRNA surveillance pathway

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-92

Cytogenetic map

97D3-97D3

Sequence location

3R:26,872,129..26,875,742 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

97D3-97D3

Limits computationally determined from genome sequence between P{lacW}His2Av^L1602 and P{PZ}sda⁰³⁸⁸⁴

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

97D2-97D3

(determined by in situ hybridisation)

(Ranz et al., 2001)

97D-97D

(Karsch-Mizrachi, 1992)

97D1-97D15

(determined by in situ hybridisation)

(Spradling et al., 1999)

97D-97D

(determined by in situ hybridisation)

(Ranz et al., 1997, Karsch-Mizrachi and Haynes, 1993)

97D1-97D15

(BDGP Project Members, 1994-1999)

Experimentally Determined Recombination Data

Location

3-92

(FlyBase, 2016)

3-89.1

(Comeron et al., 2012)

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

31333

y¹ v¹; P{TRiP.JF01290}attP2

67700

ry⁵⁰⁶ Rb97D²/TM6B, Sb¹

31332

y¹ v¹; P{TRiP.JF01289}attP2/TM3, Ser¹

55662

y¹ sc^* v¹ sev²¹; P{TRiP.HMC03817}attP40

11782

ry⁵⁰⁶ P{PZ}Rb97D¹/TM3, ry^RK Sb¹ Ser¹

NIG-Fly

HMJ21607

y¹ v¹; P{TRiP.HMJ21607}attP40

VDRC

v330450

P{VSH330450}attP40

v102159

P{KK110966}VIE-260B

Genomic Clones (12)

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

cDNA Clones (93)

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

AT15526

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.

FBgn0004903

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0004903

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

The distribution of Rb97D protein in the testes has been examined.

(Heatwole and Haynes, 1996)

Rb97D males are sterile, abnormalities in dynein protein expression render sperm immotile.

(Haynes et al., 1995)

Postmeiotic differentiation defect.

(Castrillon et al., 1993)

Identified by reduced stringency hybridization to the ribonucleoprotein motifs of Hrb98DE. Multiple transcripts are present at varying levels throughout development, but mutant analysis reveals that the Hrb97D product is required for male fertility.

(Karsch-Mizrachi and Haynes, 1993)

Relationship to Other Genes

Source for database merge of

Additional comments

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (10)

Reported As

Symbol Synonym

CG6354

(National Institute of Genetics Fly Stocks, 2023-, Meadows, 2019.11.20, Meadows, 2018.4.4, Çiçek et al., 2016, Horan et al., 2015, Ni et al., 2010.12.1, Keleman et al., 2009.8.5, Ni et al., 2008)

Hrb97D

R16

RBP97D

(Sofola et al., 2007)

Rb97D

(Duncan et al., 2020, Fingerhut et al., 2019, Ustaoglu et al., 2019, Li et al., 2016, Horan et al., 2015, Dubruille et al., 2012, Friedman et al., 2011, Christensen et al., 2008.4.15, Christensen et al., 2008.6.11, Hempel et al., 2006, Raja and Renkawitz-Pohl, 2005)

Rb97D1

(Yasuda et al., 1997)

ms(3)03445

rb97d

(Ramesh et al., 2020, Sofola et al., 2007)

rbf

(Morris et al., 2002)

Name Synonyms

Ribonuclear protein at 97D

Secondary FlyBase IDs

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 68 )

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.

43231

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.

Q02926

UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information

Q02926

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.

Q02926

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0004903

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

43231/tissue=All

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

FBgn0004903

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

FBgn0004903

FlyMine - An integrated database for Drosophila genomics

FBgn0004903

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

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

dme:Dmel_CG6354

MARRVEL_MODEL - MARRVEL (model organism gene)

43231

Linkouts

BioGRID - A database of protein and genetic interactions.

68122

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

FBgn0004903

DroID - A comprehensive database of gene and protein interactions.

FBgn0004903

DRSC - Results frm RNAi screens

FBgn0004903

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

Rb97D_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0004903

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0004903

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

CG6354

Flygut - An atlas of the Drosophila adult midgut

FBgn0004903

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

mRNA surveillance pathway

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

43231

References (68)

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

1.35

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