FlyBase Gene Report: Dmel\mil

General Information

Symbol

Dmel\mil

Species

D. melanogaster

Name

milkah

Annotation Symbol

CG5017

Feature Type

protein_coding_gene

FlyBase ID

FBgn0267366

Gene Model Status

Current

Stock Availability

23 publicly available

Gene Summary

milkah (mil) encodes a nucleosome assembly factor of the Nap family. It is involved in spermatogenesis, long-term memory formation and male courtship. [Date last reviewed: 2019-09-12] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Interactive Fly

Also Known As

hanabi

Key Links

Genomic Location

Cytogenetic map

98B5-98B5

Sequence location

3R:27,912,447..27,913,785 [+]

Recombination map

3-94

RefSeq locus

NT_033777 REGION:27912447..27913785

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 (10 terms)

Molecular Function (2 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

enables histone binding

inferred from direct assay

(Kimura, 2013)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

enables chromatin binding

inferred from biological aspect of ancestor with PANTHER:PTN000221934

(GO Reference Genome Project, 2011-)

enables histone binding

inferred from biological aspect of ancestor with PANTHER:PTN000221934

(GO Reference Genome Project, 2011-)

Biological Process (4 terms)

Terms Based on Experimental Evidence (4 terms)

CV Term

Evidence

References

involved_in male courtship behavior

inferred from mutant phenotype

(Kuzin et al., 2014)

involved_in memory

inferred from mutant phenotype

(Kuzin et al., 2014)

involved_in nucleosome assembly

inferred from direct assay

(Kimura, 2013)

involved_in spermatogenesis

inferred from mutant phenotype

(Kimura, 2013)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

involved_in nucleosome assembly

inferred from biological aspect of ancestor with PANTHER:PTN000221935

(GO Reference Genome Project, 2011-)

inferred from electronic annotation with InterPro:IPR002164

(InterPro Project Members, 2004-)

Cellular Component (4 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

located_in cytosol

inferred from direct assay

(Kimura, 2013)

located_in Nebenkern

inferred from direct assay

(Kimura, 2013)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

is_active_in chromatin

inferred from biological aspect of ancestor with PANTHER:PTN000221934

(GO Reference Genome Project, 2011-)

is_active_in nucleus

inferred from biological aspect of ancestor with PANTHER:PTN000221934

(GO Reference Genome Project, 2011-)

located_in nucleus

inferred from electronic annotation with InterPro:IPR002164

(InterPro Project Members, 2004-)

Gene Group (FlyBase)

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

milkah (mil) encodes a nucleosome assembly factor of the Nap family. It is involved in spermatogenesis, long-term memory formation and male courtship. [Date last reviewed: 2019-09-12]

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\mil 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 Q9VAZ1)

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

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

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

mil-RA

FBtr0085246

NM_143335

1097

283

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

mil-PA

FBpp0084615

33.2

283

4.28

Q9VAZ1

NP_651592

AAF56755

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

Q9VAZ1

Mapped Features

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

External Data

Crossreferences

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

mil_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).

4.09

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage | male

testis

(Doyen et al., 2015)

spermatozoon

Comment: apical tip

(Doyen et al., 2015)

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

adult head

• membrane

(Aradska et al., 2015)

Additional Descriptive Data

mil localizes to the apical tip of mature sperm cells.

(Doyen et al., 2015)

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in cytosol

inferred from direct assay

(Kimura, 2013)

located_in Nebenkern

inferred from direct assay

(Kimura, 2013)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\mil in JBrowse

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

View exonic expression by developmental stage for Dmel\mil

View exonic expression by tissue for Dmel\mil

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

FBgn0267366

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

43343/tissue=All

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

FBgn0267366

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0039553

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

FBgn0267366

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

CG5017

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 5 )

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 mil

Transgenic constructs containing regulatory region of mil

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 0 )

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

mil^GD10622

viable, with Scer\GAL4^Mef2.PR

mil^GD10622

viable, with Scer\GAL4^pnr-MD237

mil^GD10622

viable, with Scer\GAL4^tin.CΔ4

mil^GD10622

Sterility

Allele

female fertile

mil^hanabi-1

male sterile

mil^hanabi-1

Other Phenotypes

Allele

abnormal courtship behavior

mil¹

abnormal memory

Phenotype manifest in

Allele

elongation stage spermatid

mil^hanabi-1

investment cone

mil^hanabi-1

male germ cell nucleus, with Scer\GAL4^path-c135

mil^GD10622

spermatid, with Scer\GAL4^path-c135

mil^GD10622

spermatid | spermatogenesis

mil^hanabi-1

spermatid cyst | spermatogenesis

mil^hanabi-1

spermatozoon, with Scer\GAL4^path-c135

mil^GD10622

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) (20)

Hsap\NAP1L1

6 of 14

Yes

Hsap\NAP1L2

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

2 of 14

2 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

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (16)

Rnor\Nap1l1

6 of 14

Yes

5 of 14

5 of 14

4 of 14

2 of 14

2 of 14

2 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

Yes

Rnor\RGD1563307

1 of 14

Mus musculus (laboratory mouse) (11)

Mmus\Nap1l2

6 of 14

Yes

5 of 14

5 of 14

4 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

Xenopus tropicalis (Western clawed frog) (5)

Xtro\nap1l1

5 of 13

Yes

2 of 13

1 of 13

1 of 13

1 of 13

Danio rerio (Zebrafish) (6)

Drer\nap1l4a

6 of 14

Yes

5 of 14

5 of 14

2 of 14

1 of 14

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (2)

Cele\nap-1

6 of 14

Yes

Cele\spr-2

1 of 14

Anopheles gambiae (African malaria mosquito) (3)

Agam\AgaP_AGAP001928

6 of 12

Yes

Agam\AgaP_AGAP009639

4 of 12

Yes

Agam\AgaP_AGAP003598

1 of 12

Arabidopsis thaliana (thale-cress) (6)

Atha\NAP1;1

7 of 13

Yes

Atha\NAP1;2

7 of 13

Yes

Atha\NAP1;3

7 of 13

Yes

Atha\NAP1;4

7 of 13

Yes

Atha\NRP1

1 of 13

Atha\NRP2

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (2)

Scer\NAP1

7 of 13

Yes

Scer\VPS75

1 of 13

Schizosaccharomyces pombe (Fission yeast) (3)

Spom\nap1

5 of 12

Yes

Spom\nap2

5 of 12

Yes

Spom\SPBC36B7.08c

1 of 12

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:mil. 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)

CG3708

7 of 13

Nap1

7 of 13

Set

3 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?

NAP1L1; nucleosome assembly protein 1 like 1

6 of 14

164060

NAP1L2; nucleosome assembly protein 1 like 2

6 of 14

300026

NAP1L3; nucleosome assembly protein 1 like 3

5 of 14

300117

NAP1L4; nucleosome assembly protein 1 like 4

5 of 14

601651

NAP1L5; nucleosome assembly protein 1 like 5

3 of 14

612203

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

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

mil - Mst77F

pull down, western blot, anti bait coimmunoprecipitation, peptide massfingerprinting

(Doyen et al., 2015)

Summary of Genetic Interactions

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.

FBgn0267366

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

43343

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-94

Cytogenetic map

98B5-98B5

Sequence location

3R:27,912,447..27,913,785 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

98B5-98B5

Limits computationally determined from genome sequence between P{PZ}btz^rL203 and P{PZ}l(3)06487⁰⁶⁴⁸⁷

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-94

(FlyBase, 2016)

3-92.4

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (23)

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

Bloomington

68473

w¹¹¹⁸; P{VT048582-p65.AD}attP40

73194

w¹¹¹⁸; P{VT048579-p65.AD}attP40

73386

w¹¹¹⁸; P{VT048572-p65.AD}attP40

Korea

11967

P{VT048572-GAL4}attP2

12213

P{VT048573-GAL4}attP2

12214

P{VT048581-GAL4}attP2

13315

P{VT048582-GAL4}attP2

13545

P{VT048577-GAL4}attP2

15280

P{VT048579-GAL4}attP2

15281

P{VT048580-GAL4}attP2

VDRC

v106545

P{KK112260}VIE-260B

v21583

w¹¹¹⁸; P{GD10622}v21583

More stocks available...

Genomic Clones (19)

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

cDNA Clones (10)

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

AT14585

Other clones

DPiM_AT14585

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.

FBgn0267366

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Kimura, 2013)

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: mil hanabi

(Kuzin et al., 2014)

Additional comments

Nomenclature History

Source for database identify of

Source for identity of: hanabi CG5017

(Kimura, 2013)

Nomenclature comments

Etymology

The gene is named "Hanabi", the Japanese term for "fireworks" based on the mutant phenotype of scattered nuclei during spermatid elongation.

(Kimura, 2013)

Given the name "milkah", after one of Pavlov's dogs.

(Dubnau et al., 2003)

Synonyms and Secondary IDs (9)

Reported As

Symbol Synonym

CG5017

(National Institute of Genetics Fly Stocks, 2023-, Raun et al., 2021, Akishina et al., 2018, Doyen et al., 2015, Hosono et al., 2015, Kuzin et al., 2014, Kimura, 2013, Keleman et al., 2009.8.5, Pan and Zhang, 2009)

Hanabi

(Xiao et al., 2025)

Mil

(Sen and Cox, 2022)

hanabi

mil

(Zheng et al., 2023, Adashev et al., 2022, Lee et al., 2017)

milkah

(Kuzin et al., 2014)

tNAP

(Doyen et al., 2015)

Name Synonyms

Milkah

(Ganguly-Fitzgerald et al., 2006)

hanabi

(Kimura, 2013)

milkah

(Berger et al., 2008, Dubnau et al., 2003, Tully and Dubnau, 2003)

milkah-1

(Berger et al., 2008)

Secondary FlyBase IDs

FBgn0066342
FBgn0039553

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 28 )

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.

43343

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.

Q9VAZ1

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

Q9VAZ1

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.

Q9VAZ1

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0267366

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

43343/tissue=All

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

FBgn0267366

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

FBgn0267366

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

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

dme:Dmel_CG5017

MARRVEL_MODEL - MARRVEL (model organism gene)

43343

Linkouts

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

FBgn0267366

DroID - A comprehensive database of gene and protein interactions.

FBgn0267366

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

mil_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0039553

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0267366

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

CG5017

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

43343

References (42)

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

4.09

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