FlyBase Gene Report: Dmel\Ndf

General Information

Symbol

Dmel\Ndf

Species

D. melanogaster

Name

Nucleosome-destabilizing factor

Annotation Symbol

CG4747

Feature Type

protein_coding_gene

FlyBase ID

FBgn0043456

Gene Model Status

Current

Stock Availability

10 publicly available

Gene Summary

Nucleosome-destabilizing factor (Ndf) encodes a putative H3K36me3 binding protein, which binds active gene bodies. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
UniProtKB
Interactive Fly

Also Known As

BEST:LD22483

Key Links

Genomic Location

Cytogenetic map

30F5-30F5

Sequence location

2L:10,003,832..10,008,889 [+]

Recombination map

2-38

RefSeq locus

NT_033779 REGION:10003832..10008889

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 (5 terms)

Terms Based on Experimental Evidence (3 terms)

CV Term

Evidence

References

enables chromatin binding

inferred from direct assay

(Fei et al., 2018)

enables DNA binding

inferred from direct assay

(Fei et al., 2018)

enables nucleosome binding

inferred from direct assay

(Fei et al., 2018)

Terms Based on Predictions or Assertions (4 terms)

CV Term

Evidence

References

enables DNA binding

inferred from biological aspect of ancestor with PANTHER:PTN000541396

(GO Reference Genome Project, 2011-)

enables NAD binding

inferred from electronic annotation with InterPro:IPR029154

(InterPro Project Members, 2004-)

enables NADP binding

inferred from electronic annotation with InterPro:IPR006115

(InterPro Project Members, 2004-)

enables nucleosome binding

inferred from biological aspect of ancestor with PANTHER:PTN000541396

(GO Reference Genome Project, 2011-)

Biological Process (2 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

involved_in dosage compensation by hyperactivation of X chromosome

inferred from mutant phenotype

(Wang et al., 2013)

involved_in transcription elongation-coupled chromatin remodeling

inferred from direct assay

(Fei et al., 2018)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

involved_in transcription elongation-coupled chromatin remodeling

inferred from biological aspect of ancestor with PANTHER:PTN000541396

(GO Reference Genome Project, 2011-)

Cellular Component (3 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

located_in polytene chromosome interband

inferred from direct assay

(Wang et al., 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:PTN000541396

(GO Reference Genome Project, 2011-)

located_in chromosome

inferred from experiment

(Fei et al., 2018, Wang et al., 2013)

Gene Group (FlyBase)

Protein Family (UniProt)

Belongs to the HIBADH-related family. NP60 subfamily. (Q8T079)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

Nucleosome-destabilizing factor (Ndf) encodes a putative H3K36me3 binding protein, which binds active gene bodies. [Date last reviewed: 2019-03-14]

Protein Function (UniProtKB)

Nucleosome-destabilizing factor that is recruited to genes during transcriptional activation and colocalizes with a subset of trimethylated 'Lys-36' histone H3 (H3K36me3)-enriched regions (PubMed:23295261, PubMed:29759984). Binds DNA (in vitro) (PubMed:29759984). Facilitates Pol II transcription through nucleosomes (PubMed:29759984). Facilitates male-specific lethal (MSL) histone acetyltransferase complex targeting to active genes on the X chromosome (PubMed:23295261). Stimulates the acetylation of 'Lys-56' of nucleosomal histone H3 (H3K56ac) by nej (PubMed:29759984). May have oxidoreductase activity (By similarity).

(UniProt, Q8T079)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Ndf 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 Q8T079)

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

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

Gene model reviewed during 5.52

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Ndf-RA

FBtr0079930

NM_135492

3147

602

Ndf-RB

FBtr0303902

NM_001201838

3150

603

Ndf-RC

FBtr0343740

NM_001298862

2119

602

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

Ndf-PA

FBpp0079520

65.3

602

5.93

FBpp0292905

65.4

603

5.76

FBpp0310306

65.3

602

5.93

Q8T079

NP_001285791

AHN54305

Polypeptides with Identical Sequences

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

602 aa isoforms: Ndf-PA, Ndf-PC

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Subunit Structure (UniProtKB)

Binds to mononucleosomes (PubMed:29759984). Interacts with male-specific lethal (MSL) histone acetyltransferase complex at least composed of mof, msl-1, msl-2 and msl-3 (PubMed:23295261).

(UniProt, Q8T079)

Domain

The PWWP domain is a H3 reader and strongly binds DNA.

In the dehydrogenase domain, the conserved NAD(P)H-binding sites and sequence similarity to plant dehydrogenases suggest that this protein may have oxidoreductase activity. However, since the active site is not conserved, the dehydrogenase domain seems to serve as a catalytically inert oligomerization module.

(UniProt, Q8T079)

Crossreferences

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

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Mapped Features

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

External Data

Crossreferences

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

CG4747_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).

-0.60

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 | ubiquitous

(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 polytene chromosome interband

inferred from direct assay

(Wang et al., 2013)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Ndf in JBrowse

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

View exonic expression by developmental stage for Dmel\Ndf

View exonic expression by tissue for Dmel\Ndf

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

FBgn0043456

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

192507/tissue=All

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

FBgn0043456

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0043456

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

FBgn0043456

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

CG4747

Flygut - An atlas of the Drosophila adult midgut

FBgn0043456

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 6 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 8 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Ndf

Transgenic constructs containing regulatory region of Ndf

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene partially disrupted in

Df(2L)Ndf³

(Wang et al., 2013)

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.

Other Phenotypes

Allele

visible, with Scer\GAL4^sca-537.4

Ndf^EP594

Phenotype manifest in

Allele

dorsocentral bristle, with Scer\GAL4^sca-537.4

Ndf^EP594

scutellar bristle, with Scer\GAL4^sca-537.4

Ndf^EP594

tormogen cell, with Scer\GAL4^sca-537.4

Ndf^EP594

trichogen cell, with Scer\GAL4^sca-537.4

Ndf^EP594

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) (10)

Hsap\GLYR1

14 of 14

Yes

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Hsap\PWWP2B

1 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) (7)

Rnor\Glyr1

14 of 14

Yes

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Mus musculus (laboratory mouse) (10)

Mmus\Glyr1

13 of 14

Yes

2 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\Pwwp2b

1 of 14

Yes

Xenopus tropicalis (Western clawed frog) (7)

Xtro\glyr1

11 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

Xtro\trak2

1 of 13

Danio rerio (Zebrafish) (11)

Drer\glyr1

13 of 14

Yes

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

Yes

Caenorhabditis elegans (Nematode, roundworm) (3)

Cele\B0250.5

2 of 14

Yes

Cele\C06A5.3

1 of 14

Cele\T25B9.9

1 of 14

Anopheles gambiae (African malaria mosquito) (4)

Agam\GLYR1_ANOGA

12 of 12

Yes

Agam\AgaP_AGAP005581

2 of 12

Agam\AgaP_AGAP002983

1 of 12

Agam\AgaP_AGAP004197

1 of 12

Arabidopsis thaliana (thale-cress) (20)

Atha\GLYR1

11 of 13

Yes

Atha\GLYR2

10 of 13

Yes

Atha\AT4G29120

4 of 13

Yes

3 of 13

3 of 13

2 of 13

2 of 13

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

Yes

Atha\AT3G27860

1 of 13

Yes

Atha\AT5G02950

1 of 13

Yes

Atha\AT5G08230

1 of 13

Atha\AT5G40340

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (3)

Scer\GND1

1 of 13

Yes

Scer\GND2

1 of 13

Yes

Scer\PDP3

1 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (1)

Spom\SPAC23D3.01

1 of 12

Yes

Escherichia coli (enterobacterium) (5)

Ecol\glxR

4 of 11

Yes

Ecol\ygbJ

3 of 11

Yes

Ecol\garR

2 of 11

Ecol\yihU

2 of 11

Ecol\gnd

1 of 11

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Ndf. 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) (6)

3 of 13

1 of 13

1 of 13

1 of 13

sba

1 of 13

Zmynd8

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 ( 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?

GLYR1; glyoxylate reductase 1 homolog

14 of 14

610660

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

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Subunit Structure (UniProtKB)

Binds to mononucleosomes (PubMed:29759984). Interacts with male-specific lethal (MSL) histone acetyltransferase complex at least composed of mof, msl-1, msl-2 and msl-3 (PubMed:23295261).

(UniProt, Q8T079 )

Linkouts

BioGRID - A database of protein and genetic interactions.

72969

DroID - A comprehensive database of gene and protein interactions.

FBgn0043456

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

192507

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

2-38

Cytogenetic map

30F5-30F5

Sequence location

2L:10,003,832..10,008,889 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

30F5-30F5

Limits computationally determined from genome sequence between P{EP}CG5899^EP701 and P{EP}CG4747^EP594&P{lacW}l(2)k13305^k13305

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

30F5-30F6

(determined by in situ hybridisation)

(Abdelilah-Seyfried et al., 2000)

Experimentally Determined Recombination Data

Location

2-38

(FlyBase, 2016)

2-33.2

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (10)

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

Bloomington

17183

w¹¹¹⁸; P{EP}Ndf^EP594

33696

y¹ v¹; P{TRiP.HMS00568}attP2

41698

y¹ sc^* v¹ sev²¹; P{TRiP.HMS02263}attP40

42838

y¹ sc^* v¹ sev²¹; P{TRiP.HMS02530}attP40

83233

y¹ w^*; TI{CRIMIC.TG4.2}Ndf^{CR00981-TG4.2} asRNA:CR44873^{CR00981-TG4.2-X}/SM6a

NIG-Fly

M2L-0840

y¹ w¹¹¹⁸; Ndf^SK3 P{neoFRT}40A/CyO-Tb

HMS00568

y¹ sc^* v¹ sev²¹; P{TRiP.HMS00568}attP2

2LG-0668

y² VhaAC39-1^cho-1 v¹; P{U6-Ndf.NIG.sgRNA}attP40/CyO

VDRC

v330116

P{VSH330116}attP40

v100783

P{KK108595}VIE-260B

Genomic Clones (13)

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

cDNA Clones (212)

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

LD22344

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.

FBgn0043456

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0043456

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Fei et al., 2018)

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: BEST:LD29743 CG4747

(Bayraktaroglu, 2000.11.2)

Source for merge of: CG4747 BEST:GH19401

(Rana, 2004.7.8)

Additional comments

Nomenclature History

Source for database identify of

Source for identity of: Ndf CG4747

(Fei et al., 2018)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (11)

Reported As

Symbol Synonym

BEST:GH19401

BEST:LD22483

(Giot et al., 2003, Abdelilah-Seyfried et al., 2000)

BEST:LD29743

CG4747

(National Institute of Genetics Fly Stocks, 2022-, Fei et al., 2018, Marcogliese et al., 2017, Meadows, 2017.1.11, Kwon et al., 2013, Wang et al., 2013, Cammarato et al., 2011, Friedman et al., 2011, Varma and Mishra, 2011, Ni et al., 2010.12.1, Keleman et al., 2009.8.5, Akdemir et al., 2007, Quinones-Coello, 2007)

Dm_AI388468

(Stec et al., 2000)

LD29743

(Toba et al., 1999)

NDF

(Fei et al., 2018)

Ndf

(GenetiVision Corporation, 2026-, Gene Disruption Project members, 2018-)

dNDF

(Fei et al., 2018)

Name Synonyms

Nucleosome-destabilizing factor

nucleosome-destabilizing factor

(Fei et al., 2018)

Secondary FlyBase IDs

FBgn0026572
FBgn0032174
FBgn0041705

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 48 )

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.

192507

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.

Q8T079

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

Q8T079

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.

Q8T079

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0043456

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

192507/tissue=All

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

FBgn0043456

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

FBgn0043456

FlyMine - An integrated database for Drosophila genomics

FBgn0043456

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

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

dme:Dmel_CG4747

MARRVEL_MODEL - MARRVEL (model organism gene)

192507

Linkouts

BioGRID - A database of protein and genetic interactions.

72969

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

FBgn0043456

DroID - A comprehensive database of gene and protein interactions.

FBgn0043456

DRSC - Results frm RNAi screens

FBgn0043456

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

CG4747_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0043456

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0043456

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

CG4747

Flygut - An atlas of the Drosophila adult midgut

FBgn0043456

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

TC007359

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

192507

References (46)

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

-0.60

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