FlyBase Gene Report: Dmel\tplus3a

General Information

Symbol

Dmel\tplus3a

Species

D. melanogaster

Name

testis-specific Plus3 domain a

Annotation Symbol

CG31702

Feature Type

protein_coding_gene

FlyBase ID

FBgn0051702

Gene Model Status

Current

Stock Availability

4 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

40E1-40E1

Sequence location

2L:22,071,144..22,072,902 [+]

Recombination map

2-54

RefSeq locus

NT_033779 REGION:22071144..22072902

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 (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 DNA binding

inferred from electronic annotation with InterPro:IPR004343, InterPro:IPR036128

(InterPro Project Members, 2004-)

enables RNA polymerase II C-terminal domain phosphoserine binding

inferred from biological aspect of ancestor with PANTHER:PTN000319032

(GO Reference Genome Project, 2011-)

Biological Process (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Cellular Component (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

part_of Cdc73/Paf1 complex

inferred from biological aspect of ancestor with PANTHER:PTN000319032

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\tplus3a 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 Q8IME8)

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 5.51

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

tplus3a-RA

FBtr0085934

NM_165405

1710

441

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

tplus3a-PA

FBpp0085288

50.4

441

8.87

Q8IME8

NP_724373

AAN11142

Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

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

Q8IME8

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\tplus3a using the Feature Mapper tool.

External Data

Crossreferences

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

CG31702_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).

3.42

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

spermatogenesis

spermatocyte

(Hundertmark et al., 2019)

spermatid

Comment: early spermatid stages

(Hundertmark et al., 2019)

Additional Descriptive Data

tplus3a transcripts are detected from the spermatocyte stage onward into early spermatid stages but are not detected at late stages of spermatogenesis.

(Hundertmark et al., 2019)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

spermatogenesis

spermatocyte

• nucleus

(Hundertmark et al., 2019)

Additional Descriptive Data

tplus3a protein localizes mainly to the nuclei of spermatocytes.

(Hundertmark et al., 2019)

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\tplus3a in JBrowse

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

View exonic expression by developmental stage for Dmel\tplus3a

View exonic expression by tissue for Dmel\tplus3a

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

FBgn0051702

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

318904/tissue=All

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

FBgn0051702

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0051702

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

FBgn0051702

Flygut - An atlas of the Drosophila adult midgut

FBgn0051702

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 1 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 3 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of tplus3a

Transgenic constructs containing regulatory region of tplus3a

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(2L)BSC151

(Hundertmark et al., 2019)

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.

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\RTF1

4 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) (1)

Rnor\Rtf1

3 of 14

Yes

Mus musculus (laboratory mouse) (1)

Mmus\Rtf1

4 of 14

Yes

Xenopus tropicalis (Western clawed frog) (1)

Xtro\LOC101732341

1 of 13

Yes

Danio rerio (Zebrafish) (1)

Drer\rtf1

4 of 14

Yes

Caenorhabditis elegans (Nematode, roundworm) (1)

Cele\rtfo-1

3 of 14

Yes

Anopheles gambiae (African malaria mosquito) (1)

Agam\AgaP_AGAP012057

3 of 12

Yes

Arabidopsis thaliana (thale-cress) (5)

Atha\VIP5

6 of 13

Yes

Atha\NERD

3 of 13

Yes

Atha\AT3G51120

1 of 13

Atha\AT5G08430

1 of 13

Atha\TZP

1 of 13

Yes

Saccharomyces cerevisiae (Brewer's yeast) (1)

Scer\RTF1

2 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (1)

Spom\SPBC651.09c

3 of 12

Yes

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:tplus3a. 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) (3)

tplus3b

6 of 13

Rtf1

5 of 13

CG12498

4 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?

RTF1; RTF1 homolog, Paf1/RNA polymerase II complex component

4 of 14

611633

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

DroID - A comprehensive database of gene and protein interactions.

FBgn0051702

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-54

Cytogenetic map

40E1-40E1

Sequence location

2L:22,071,144..22,072,902 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

40E1-40E1

Limits computationally determined from genome sequence between P{lacW}Df31^k05815 and P{PZ}cul-2⁰²⁰⁷⁴&P{lacW}l(2)k08110^k08110

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

2-54

(FlyBase, 2016)

2-54.6

(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

Bloomington

61323

y¹ v¹; P{TRiP.HMJ23158}attP40/CyO

NIG-Fly

31702R-1

P{NIG.31702R}1

HMJ23158

y¹ v¹; P{TRiP.HMJ23158}attP40/CyO

VDRC

v109981

P{KK115200}VIE-260B

Genomic Clones (7)

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

cDNA Clones (5)

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

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.

FBgn0051702

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0051702

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Hundertmark et al., 2019)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

New annotation (CG31702) in release 3 of the genome annotation.

(FlyBase Genome Annotators, 2002-2003)

Relationship to Other Genes

Source for database merge of

Additional comments

Nomenclature History

Source for database identify of

Source for identity of: tplus3a CG31702

(Hundertmark et al., 2019)

Nomenclature comments

Etymology

Named 'tPlus' based on its testis-specific transcription and its encoded Plus3 domain.

(Hundertmark et al., 2019)

Synonyms and Secondary IDs (5)

Reported As

Symbol Synonym

CG31702

(Japanese National Institute of Genetics, 2012.5.21, Perkins et al., 2009)

tPlus3a

(Hundertmark et al., 2019)

tplus3a

(Lawlor et al., 2021, Hundertmark et al., 2019)

Name Synonyms

testis-specific Plus3 domain a

testis-specifically transcribed plus3 a

(Hundertmark et al., 2019)

Secondary FlyBase IDs

FBan0031702

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 23 )

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.

318904

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.

AAN11142

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.

Q8IME8

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

Q8IME8

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.

Q8IME8

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0051702

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

318904/tissue=All

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

FBgn0051702

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

FBgn0051702

FlyMine - An integrated database for Drosophila genomics

FBgn0051702

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

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

dme:Dmel_CG31702

MARRVEL_MODEL - MARRVEL (model organism gene)

318904

Linkouts

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

FBgn0051702

DroID - A comprehensive database of gene and protein interactions.

FBgn0051702

DRSC - Results frm RNAi screens

FBgn0051702

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

CG31702_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0051702

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0051702

Flygut - An atlas of the Drosophila adult midgut

FBgn0051702

References (11)

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

3.42

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