FlyBase Gene Report: Dmel\RpL34b

General Information

Symbol

Dmel\RpL34b

Species

D. melanogaster

Name

Ribosomal protein L34b

Annotation Symbol

CG9354

Feature Type

protein_coding_gene

FlyBase ID

FBgn0037686

Gene Model Status

Current

Stock Availability

4 publicly available

Gene Summary

Ribosomal protein L34b (RpL34b) encodes a ribosomal structural constituent. [Date last reviewed: 2019-07-11] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
Interactive Fly

Also Known As

RpL34

Key Links

Genomic Location

Cytogenetic map

85D15-85D15

Sequence location

3R:9,400,237..9,401,226 [-]

Recombination map

3-48

RefSeq locus

NT_033777 REGION:9400237..9401226

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 (7 terms)

Molecular Function (1 term)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

enables structural constituent of ribosome

inferred from high throughput direct assay

(Alonso and Santaren, 2006)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

enables structural constituent of ribosome

traceable author statement

(Marygold et al., 2007)

inferred from electronic annotation with InterPro:IPR008195, InterPro:IPR047868

(InterPro Project Members, 2004-)

inferred from biological aspect of ancestor with PANTHER:PTN000079601

(GO Reference Genome Project, 2011-)

Biological Process (3 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

involved_in cytoplasmic translation

inferred by curator from GO:0022626

(Alonso and Santaren, 2006)

traceable author statement

(Marygold et al., 2007)

involved_in ribosome biogenesis

inferred from biological aspect of ancestor with PANTHER:PTN000079601

(GO Reference Genome Project, 2011-)

involved_in translation

inferred from electronic annotation with InterPro:IPR008195, InterPro:IPR047868

(InterPro Project Members, 2004-)

Cellular Component (3 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

located_in cytosolic ribosome

inferred from high throughput direct assay

(Alonso and Santaren, 2006)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

part_of cytosolic large ribosomal subunit

traceable author statement

(Marygold et al., 2007)

inferred from biological aspect of ancestor with PANTHER:PTN000079601

(GO Reference Genome Project, 2011-)

located_in ribosome

inferred from electronic annotation with InterPro:IPR008195, InterPro:IPR047868

(InterPro Project Members, 2004-)

Gene Group (FlyBase)

CYTOPLASMIC LARGE RIBOSOMAL PROTEINS

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

Ribosomal protein L34b (RpL34b) encodes a ribosomal structural constituent. [Date last reviewed: 2019-07-11]

Gene Group (FlyBase)

CYTOPLASMIC LARGE RIBOSOMAL PROTEINS -: Cytoplasmic ribosomes are found on the endoplasmic reticulum and in the cytoplasm. They translate all mRNAs produced from nuclear genes and perform the majority of cellular protein synthesis. Ribosomes are formed by two ribonucleoprotein subunits, large and small. The principle function of the large subunit is to bind tRNA during the synthesis of polypeptides. (Adapted from FBrf0205398).

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\RpL34b 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 Q9VHE5)

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

PDB - An information portal to biological macromolecular structures

Comments on Gene Model

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

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

Gene model reviewed during 5.49

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

RpL34b-RA

FBtr0082050

NM_141630

771

168

RpL34b-RB

FBtr0082049

NM_169277

754

168

RpL34b-RC

FBtr0339176

NM_001300320

589

168

RpL34b-RD

FBtr0339177

NM_001300321

622

168

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

RpL34b-PA

FBpp0081528

18.4

168

12.07

FBpp0081527

18.4

168

12.07

FBpp0308318

18.4

168

12.07

FBpp0308319

18.4

168

12.07

Q9VHE5

NP_001287250

AHN57249

Polypeptides with Identical Sequences

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

168 aa isoforms: RpL34b-PA, RpL34b-PB, RpL34b-PC, RpL34b-PD

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Crossreferences

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

PDB - An information portal to biological macromolecular structures

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Q9VHE5

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\RpL34b using the Feature Mapper tool.

External Data

Crossreferences

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

RpL34b_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).

-0.35

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)

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)

day 7 of adulthood -- day 49 of adulthood

adult heart

(Cammarato et al., 2011)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in cytosolic ribosome

inferred from high throughput direct assay

(Alonso and Santaren, 2006)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\RpL34b in JBrowse

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

View exonic expression by developmental stage for Dmel\RpL34b

View exonic expression by tissue for Dmel\RpL34b

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

FBgn0037686

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

41120/tissue=All

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

FBgn0037686

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0037686

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

FBgn0037686

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

CG9354

Flygut - An atlas of the Drosophila adult midgut

FBgn0037686

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 0 )

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 RpL34b

Transgenic constructs containing regulatory region of RpL34b

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 3 )

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

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

RpL34b^GD17856

viable, with Scer\GAL4^Mef2.PR

RpL34b^GD17856

viable, with Scer\GAL4^pnr-MD237

RpL34b^GD17856

viable, with Scer\GAL4^tin.CΔ4

RpL34b^GD17856

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) (1)

Hsap\RPL34

11 of 14

Yes

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\Rpl34

12 of 14

Yes

Rnor\Rpl34-ps1

9 of 14

Yes

Mus musculus (laboratory mouse) (3)

Mmus\Rpl34

11 of 14

Yes

Mmus\Rpl34-ps1

11 of 14

Yes

Mmus\Gm4705

2 of 14

Yes

Xenopus tropicalis (Western clawed frog) (3)

Xtro\rpl34

10 of 13

Yes

Xtro\rpl34p

7 of 13

Yes

Xtro\gins2

6 of 13

Danio rerio (Zebrafish) (1)

Drer\rpl34

12 of 14

Yes

Caenorhabditis elegans (Nematode, roundworm) (1)

Cele\rpl-34

14 of 14

Yes

Anopheles gambiae (African malaria mosquito) (1)

Agam\AgaP_AGAP009324

12 of 12

Yes

Arabidopsis thaliana (thale-cress) (3)

Atha\AT1G26880

13 of 13

Yes

Atha\AT3G28900

13 of 13

Yes

Atha\RPL34

13 of 13

Yes

Saccharomyces cerevisiae (Brewer's yeast) (2)

Scer\RPL34A

13 of 13

Yes

Scer\RPL34B

13 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (2)

Spom\rpl3401

12 of 12

Yes

Spom\rpl3402

12 of 12

Yes

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:RpL34b. 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) (1)

RpL34a

12 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?

RPL34; ribosomal protein L34

11 of 14

616862

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

Other Interaction Browsers

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.

66285

DroID - A comprehensive database of gene and protein interactions.

FBgn0037686

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.

Ribosome

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-48

Cytogenetic map

85D15-85D15

Sequence location

3R:9,400,237..9,401,226 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

85D15-85D15

Limits computationally determined from genome sequence between P{lacW}l(3)L4092^L4092 and P{PZ}ps¹⁰⁶¹⁵&P{PZ}Ras85D⁰⁶⁶⁷⁷

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-48

(FlyBase, 2016)

3-46.1

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (4)

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

FlyORF

F001573

M{UAS-RpL34b.ORF}ZH-86Fb

F001069

M{UAS-RpL34b.ORF.3xHA}ZH-86Fb

VDRC

v109138

P{KK115858}VIE-260B

v49901

w¹¹¹⁸; P{GD17856}v49901

Genomic Clones (14)

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

cDNA Clones (596)

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

RH48056

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.

FBgn0037686

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0037686

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Haploinsufficient locus.

(Cook et al., 2012)

Nonsense-mediated mRNA decay (NMD) down-regulates a distinct splice isoform(s) of this gene.

(Hansen et al., 2009)

Likely Minute gene.

(Marygold et al., 2007)

RpL34b lies in a gap in deletion coverage.

(Marygold et al., 2007)

Relationship to Other Genes

Source for database merge of

Source for merge of: CG9354 anon- EST:fe1C10 anon- EST:fe1E8

(Bayraktaroglu, 2000.11.2)

Additional comments

Nomenclature History

Source for database identify of

Source for identity of: RpL34b CG9354

(Ashburner and Marygold, 2004.7.2)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (10)

Reported As

Symbol Synonym

CG9354

(Schertel et al., 2013, Cammarato et al., 2011, Zhang et al., 2010, Hansen et al., 2009, Keleman et al., 2009.8.5, Pflieger et al., 2008, Huang et al., 2007, Marygold et al., 2007)

L34b

(Carpenter et al., 2009)

Rp L34b

(Alonso and Santaren, 2006)

RpL34

(Wang and DiMario, 2017, He et al., 2015, Huang et al., 2007)

RpL34b

(Hopes et al., 2022, Loganathan et al., 2022, Baumgartner et al., 2021, Jin et al., 2020, Crofton et al., 2018, Zolotarev et al., 2017, Handler et al., 2013, Kwon et al., 2013, Schertel et al., 2013, Cook et al., 2012, Friedman et al., 2011, Cook et al., 2010.2.12, Hansen et al., 2009, Marygold et al., 2007)

anon-EST:fe1C10

anon-EST:fe1E8

Name Synonyms

Ribosomal protein L34b

RpL34b

(Cammarato et al., 2011)

anon-fast-evolving-1C10

anon-fast-evolving-1E8

Secondary FlyBase IDs

FBgn0025253
FBgn0025263

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 46 )

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.

41120

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.

Q9VHE5

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

Q9VHE5

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.

Q9VHE5

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0037686

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

41120/tissue=All

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

FBgn0037686

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

FBgn0037686

FlyMine - An integrated database for Drosophila genomics

FBgn0037686

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

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

dme:Dmel_CG9354

MARRVEL_MODEL - MARRVEL (model organism gene)

41120

PDB - An information portal to biological macromolecular structures

Linkouts

BioGRID - A database of protein and genetic interactions.

66285

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

FBgn0037686

DroID - A comprehensive database of gene and protein interactions.

FBgn0037686

DRSC - Results frm RNAi screens

FBgn0037686

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

RpL34b_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0037686

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0037686

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

CG9354

Flygut - An atlas of the Drosophila adult midgut

FBgn0037686

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

TC005648

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

Ribosome

References (50)

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

-0.35

Report Sections