FlyBase Gene Report: Dmel\Prtl99C

General Information

Symbol

Dmel\Prtl99C

Species

D. melanogaster

Name

Protamine-like 99C

Annotation Symbol

CG15510

Feature Type

protein_coding_gene

FlyBase ID

FBgn0039707

Gene Model Status

Current

Stock Availability

2 publicly available

Gene Summary

Protamine-like 99C (Prtl99C) encodes a sperm chromatin-associated protein that is essential for male fertility. It acts additively together with the products of Mst77F, ProtA and ProtB to compact the paternal chromatin. [Date last reviewed: 2019-03-21] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
UniProtKB
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

99C2-99C3

Sequence location

3R:29,835,950..29,837,447 [+]

Recombination map

3-99

RefSeq locus

NT_033777 REGION:29835950..29837447

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 (4 terms)

Molecular Function (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Biological Process (2 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

involved_in sperm DNA condensation

inferred from mutant phenotype

(Eren-Ghiani et al., 2015)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

involved_in sperm DNA condensation

inferred from electronic annotation with InterPro:IPR024460

(InterPro Project Members, 2004-)

involved_in spermatogenesis

inferred from electronic annotation with InterPro:IPR024460

(InterPro Project Members, 2004-)

Cellular Component (2 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

located_in nucleus

inferred from direct assay

(Eren-Ghiani et al., 2015)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

located_in chromosome

inferred from experiment

(Eren-Ghiani et al., 2015)

Gene Group (FlyBase)

Protein Family (UniProt)

Belongs to the UPF0771 family. (Q9VAF7)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

Protein Function (UniProtKB)

Regulates chromatin compaction in spermatid nuclei and is essential for male fertility. Functions in parallel with other chromatin-condensing proteins such as ProtA, ProtB and Mst77F.

(UniProt, Q9VAF7)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Prtl99C 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 Q9VAF7)

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 5.49

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Prtl99C-RB

FBtr0301745

NM_143478

1053

201

Prtl99C-RC

FBtr0301746

NM_001170300

745

193

Prtl99C-RD

FBtr0339143

NM_001300665

769

201

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

Prtl99C-PB

FBpp0290959

23.6

201

11.48

FBpp0290960

22.7

193

11.45

FBpp0308288

23.6

201

11.48

Q9VAF7

NP_001287594

AHN57593

Polypeptides with Identical Sequences

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

201 aa isoforms: Prtl99C-PB, Prtl99C-PD

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Domain

The C-terminal part (169-201) is essential for male fertility and correct chromatin compaction in mature sperm.

(UniProt, Q9VAF7)

Crossreferences

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

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Q9VAF7

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Prtl99C using the Feature Mapper tool.

External Data

Crossreferences

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

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).

5.05

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage | male

spermatocyte

(Eren-Ghiani et al., 2015)

spermatid

(Eren-Ghiani et al., 2015)

RT-PCR

Stage

Tissue/Position (including subcellular localization)

Reference

larval stage

testis

(Eren-Ghiani et al., 2015)

adult stage | male

testis

(Eren-Ghiani et al., 2015)

Additional Descriptive Data

Prtl99C-RD is detected by RT-PCR in testis at all stages of spermatogenesis. In situ hybridization shows transcripts distributed from early spermatocytes to late spermatids, but not in the hub region or in seminal vesicles.

(Eren-Ghiani et al., 2015)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage | male

mid-late elongation-stage spermatid

(Eren-Ghiani et al., 2015)

western blot

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage | male

testis

(Eren-Ghiani et al., 2015)

seminal vesicle

(Eren-Ghiani et al., 2015)

Additional Descriptive Data

Prtl99C protein is detected in late canoe stage spermatids but not in mature sperm by immunolocalization.

(Eren-Ghiani et al., 2015)

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in nucleus

inferred from direct assay

(Eren-Ghiani et al., 2015)

Expression Deduced from Reporters

Reporter: P{Prtl99C-EGFP.386}

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage | male

mid-late elongation-stage spermatid

(Eren-Ghiani et al., 2015)

spermatozoon

(Eren-Ghiani et al., 2015)

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Prtl99C in JBrowse

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

View exonic expression by developmental stage for Dmel\Prtl99C

View exonic expression by tissue for Dmel\Prtl99C

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

FBgn0039707

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

43526/tissue=All

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

FBgn0039707

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0039707

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

FBgn0039707

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

CG15510

Flygut - An atlas of the Drosophila adult midgut

FBgn0039707

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 ( 5 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Prtl99C

Transgenic constructs containing regulatory region of Prtl99C

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 2 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

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

Sterility

Allele

male semi-sterile

Prtl99C^MI10224

male semi-sterile, with Scer\GAL4^VP16.bam

Prtl99C^KK109686

Phenotype manifest in

Allele

spermatid

Prtl99C^MI10224

spermatid, with Scer\GAL4^VP16.bam

Prtl99C^KK109686

spermatozoon

Prtl99C^MI10224

spermatozoon, with Scer\GAL4^VP16.bam

Prtl99C^KK109686

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) (0)

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (0)

Mus musculus (laboratory mouse) (0)

Xenopus tropicalis (Western clawed frog) (0)

Danio rerio (Zebrafish) (0)

Caenorhabditis elegans (Nematode, roundworm) (0)

Anopheles gambiae (African malaria mosquito) (0)

Arabidopsis thaliana (thale-cress) (0)

Saccharomyces cerevisiae (Brewer's yeast) (0)

Schizosaccharomyces pombe (Fission yeast) (0)

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Prtl99C. 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) (5)

2 of 13

2 of 13

2 of 13

2 of 13

2 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?

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

Interaction Browsers

Summary of Genetic Interactions

Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

Please look at the allele data for full details of the genetic interactions

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Cad99C

suppressible

Prtl99C

(Eren-Ghiani et al., 2015)

External Data

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0039707

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

3-99

Cytogenetic map

99C2-99C3

Sequence location

3R:29,835,950..29,837,447 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

99C2-99C3

Limits computationally determined from genome sequence between P{PZ}ncd⁰⁵⁸⁸⁴ and P{lacW}l(3)s2500^s2500

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-99

(FlyBase, 2016)

3-97.0

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (2)

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

Bloomington

53232

y¹ w^*; Mi{MIC}Prtl99C^MI10224

VDRC

v106856

P{KK109686}VIE-260B

Genomic Clones (16)

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.

FBgn0039707

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0039707

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Eren-Ghiani et al., 2015)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Relationship to Other Genes

Source for database merge of

Source for merge of: CG15510 BcDNA:AT14346

(FlyBase, 1996-)

Additional comments

Source for merge of CG15510 BcDNA:AT14346 was a shared cDNA ( date:030728 ).

(FlyBase, 1996-)

Nomenclature History

Source for database identify of

Source for identity of: Prtl99C CG15510

(Eren-Ghiani et al., 2015)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (4)

Reported As

Symbol Synonym

BcDNA:AT14346

CG15510

(Doyen et al., 2015, Eren-Ghiani et al., 2015, Gärtner et al., 2015, Keleman et al., 2009.8.5, Rathke et al., 2007)

Prtl99C

(Eren-Ghiani et al., 2015)

Name Synonyms

Protamine-like 99C

(Eren-Ghiani et al., 2015)

Secondary FlyBase IDs

FBgn0063334

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 34 )

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.

43526

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.

Q9VAF7

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

Q9VAF7

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.

Q9VAF7

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0039707

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

43526/tissue=All

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

FBgn0039707

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

FBgn0039707

FlyMine - An integrated database for Drosophila genomics

FBgn0039707

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

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

dme:Dmel_CG15510

MARRVEL_MODEL - MARRVEL (model organism gene)

43526

Linkouts

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

FBgn0039707

DroID - A comprehensive database of gene and protein interactions.

FBgn0039707

DRSC - Results frm RNAi screens

FBgn0039707

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

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0039707

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0039707

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

CG15510

Flygut - An atlas of the Drosophila adult midgut

FBgn0039707

References (16)

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

5.05

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