FlyBase Gene Report: Dmel\XNP

General Information

Symbol

Dmel\XNP

Species

D. melanogaster

Name

XNP

Annotation Symbol

CG4548

Feature Type

protein_coding_gene

FlyBase ID

FBgn0039338

Gene Model Status

Stock Availability

15 publicly available

Gene Summary

XNP (XNP) encodes two protein isoforms that participate in the maintenance of heterochromatin and chromosomal stability. They interact with heterochromatin proteins such as those encoded by Su(var)205 and ADD1. [Date last reviewed: 2018-11-08] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
UniProtKB
Interactive Fly

Also Known As

dATRX, dXNP

Key Links

Genomic Location

Cytogenetic map

Sequence location

3R:25,477,868..25,482,834 [-]

Recombination map

3-88

RefSeq locus

NT_033777 REGION:25477868..25482834

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse GBrowse

Other Genome Views

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

Function

GO Summary Ribbons

Gene Ontology (GO) Annotations (17 terms)

Molecular Function (4 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

enables ATP hydrolysis activity

inferred from direct assay

(Emelyanov et al., 2010)

enables DNA translocase activity

inferred from direct assay

(Emelyanov et al., 2010)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

enables ATP binding

inferred from electronic annotation with InterPro:IPR000330

(assigned by InterPro )

(FlyBase Curators et al., 2004-)

enables DNA translocase activity

inferred from sequence or structural similarity with UniProtKB:P46100

(FlyBase Curators, 2008--)

enables nucleosome-dependent ATPase activity

inferred from electronic annotation with InterPro:IPR000330

(assigned by InterPro )

(FlyBase Curators et al., 2004-)

Biological Process (8 terms)

Terms Based on Experimental Evidence (8 terms)

CV Term

Evidence

References

involved_in axon guidance

inferred from mutant phenotype

(Sun et al., 2006)

involved_in chromosome organization

inferred from mutant phenotype

(Bassett et al., 2008)

involved_in DNA replication-independent nucleosome assembly

inferred from mutant phenotype

(Schneiderman et al., 2012)

involved_in glial cell migration

inferred from mutant phenotype

(Sun et al., 2006)

involved_in heterochromatin organization involved in chromatin silencing

inferred from mutant phenotype

(Emelyanov et al., 2010)

involved_in intrinsic apoptotic signaling pathway

inferred from mutant phenotype

(Lee et al., 2007)

involved_in nervous system development

inferred from mutant phenotype

(Koizumi et al., 2007)

involved_in regulation of JNK cascade

inferred from genetic interaction with FLYBASE:hep; FB:FBgn0010303

(Lee et al., 2007)

Terms Based on Predictions or Assertions (0 terms)

Cellular Component (5 terms)

Terms Based on Experimental Evidence (5 terms)

CV Term

Evidence

References

colocalizes_with beta-heterochromatin

inferred from direct assay

(Emelyanov et al., 2010)

colocalizes_with chromosome, centromeric region

inferred from direct assay

(Bassett et al., 2008)

located_in germinal vesicle

inferred from direct assay

(Orsi et al., 2013)

colocalizes_with heterochromatin

inferred from direct assay

(Swenson et al., 2016)

located_in nucleus

inferred from direct assay

(Orsi et al., 2013)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

is_active_in nucleus

inferred from biological aspect of ancestor with PANTHER:PTN000847877

(assigned by GO_Central )

(Gaudet et al., 2011)

Gene Group (FlyBase)

SNF2-LIKE CHROMATIN REMODELERS

Protein Family (UniProt)

Belongs to the SNF2/RAD54 helicase family. (Q9GQN5)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

XNP (XNP) encodes two protein isoforms that participate in the maintenance of heterochromatin and chromosomal stability. They interact with heterochromatin proteins such as those encoded by Su(var)205 and ADD1. [Date last reviewed: 2018-11-08]

Gene Group (FlyBase)

SNF2-LIKE CHROMATIN REMODELERS -: Snf2-like chromatin remodelers are a family of helicase-like proteins that direct energy derived from ATP hydrolysis into the mechanical remodelling of chromatin structure. They are so-called due to the presence of a domain homologous to the helicase-like ATPase domain of the S. cerevisiae Snf2 protein. This domain, the Snf2 domain, consists of two tandem RecA-like folds and contains seven conserved helicase-related sequence motifs that classify it as part of the helicase superfamily 2 (SF2). However, Snf2 proteins are not bona fide helicases, lacking the ability to separate nucleic acid strands. Instead, Snf2 proteins are DNA translocases that apply an ATP-dependent torsional strain to DNA, which provides the necessary force to remodel nucleosomes or in some cases other DNA-protein complexes. (Adapted from PMID:21862382.)

Protein Function (UniProtKB)

Global transcriptional regulator. Modifies gene expression by affecting chromatin.

(UniProt, Q9GQN5)

Summary (Interactive Fly)

DEAD-like helicases superfamily - complements HIRA in recognizing exposed DNA and serving as a binding platform for the efficient recruitment of H3.3 predeposition complexes to chromatin gaps

Interactive Fly

Gene Model and Products

Number of Transcripts

4

Number of Unique Polypeptides

2

Please see the JBrowse view of Dmel\XNP 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

Comments on Gene Model

Gene model reviewed during 5.48

Gene model reviewed during 5.43

Gene model reviewed during 5.55

Sequence Ontology: Class of Gene

gene_with_edited_transcript

(Graveley et al., 2011)

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

FBtr0084837

4493

1311

FBtr0084838

4557

1311

FBtr0344718

4493

1046

FBtr0344719

4557

1046

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

RefSeq ID

GenBank

FBpp0084212

148.2

1311

8.66

FBpp0084213

148.2

1311

8.66

FBpp0311051

119.5

1046

6.87

FBpp0311052

119.5

1046

6.87

Polypeptides with Identical Sequences

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

1311 aa isoforms: XNP-PA, XNP-PB

1046 aa isoforms: XNP-PC, XNP-PD

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

Mapped Features

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

External Data

Crossreferences

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

XNP_1
XNP_2

Linkouts

Expression Data

Expression Summary Ribbons

Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.

For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 3

organism | ubiquitous

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 4 -- 6

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 7 -- 8

antennal anlage

Comment: reported as procephalic ectoderm anlage

(Fisher et al., 2012)

central brain anlage

Comment: reported as procephalic ectoderm anlage

(Fisher et al., 2012)

dorsal head epidermis anlage

Comment: reported as procephalic ectoderm anlage

(Fisher et al., 2012)

Comment: reported as procephalic ectoderm anlage

(Fisher et al., 2012)

organism | ubiquitous

(Fisher et al., 2012)

posterior endoderm

(Fisher et al., 2012)

ventral ectoderm

(Fisher et al., 2012)

embryonic stage 9 -- 10

antennal primordium

Comment: reported as procephalic ectoderm primordium

(Fisher et al., 2012)

central brain primordium

Comment: reported as procephalic ectoderm primordium

(Fisher et al., 2012)

visual primordium

Comment: reported as procephalic ectoderm primordium

(Fisher et al., 2012)

dorsal head epidermis primordium

Comment: reported as procephalic ectoderm primordium

(Fisher et al., 2012)

lateral head epidermis primordium

Comment: reported as procephalic ectoderm primordium

(Fisher et al., 2012)

ventral head epidermis primordium

Comment: reported as procephalic ectoderm primordium

(Fisher et al., 2012)

organism | ubiquitous

(Fisher et al., 2012)

posterior endoderm

(Fisher et al., 2012)

ventral nerve cord primordium

(Fisher et al., 2012)

embryonic stage 11 -- 12

central brain primordium

(Fisher et al., 2012)

embryonic central brain neuron

(Fisher et al., 2012)

lateral cord neuron

(Fisher et al., 2012)

organism | ubiquitous

(Fisher et al., 2012)

ventral nerve cord primordium

(Fisher et al., 2012)

embryonic stage 13 -- 16

embryonic brain

(Fisher et al., 2012)

embryonic central brain neuron

(Fisher et al., 2012)

embryonic/larval nervous system

(Fisher et al., 2012)

larval ventral nerve cord

(Fisher et al., 2012)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

blastoderm stage

(Orsi et al., 2013)

oogenesis stage S10 & adult stage | female

• germinal vesicle

(Orsi et al., 2013)

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

day 5 of adulthood & male -- day 7 of adulthood & male

(Dorus et al., 2006)

western blot

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage -- adult stage

(Emelyanov et al., 2010)

Additional Descriptive Data

Both XNP isoforms are detected at all stages of development on western blots with the highest levels in embryos and pupae.

(Emelyanov et al., 2010)

Marker for

Subcellular Localization

CV Term

Evidence

References

colocalizes_with beta-heterochromatin

inferred from direct assay

(Emelyanov et al., 2010)

colocalizes_with chromosome, centromeric region

inferred from direct assay

(Bassett et al., 2008)

located_in germinal vesicle

inferred from direct assay

(Orsi et al., 2013)

colocalizes_with heterochromatin

inferred from direct assay

(Swenson et al., 2016)

located_in nucleus

inferred from direct assay

(Orsi et al., 2013)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\XNP in GBrowse 2

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

View exonic expression by developmental stage for Dmel\XNP

View exonic expression by tissue for Dmel\XNP

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

FBgn0039338

DRscDB

43080/tissue=All

EMBL-EBI Single Cell Expression Atlas

FBgn0039338

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG4548-RA

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

CG4548

Flygut - An atlas of the Drosophila adult midgut

FBgn0039338

Images

FlyExpress - Embryonic expression images (BDGP data)

Show all FlyExpress processed images for Dmel\XNP

Stages(s) 1-3
Stages(s) 4-6
Stages(s) 7-8
Stages(s) 11-12
Stages(s) 13-16

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 17 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 11 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of XNP

Transgenic constructs containing regulatory region of XNP

Aberrations (Deficiencies and Duplications) ( 2 )

Inferred from experimentation ( 2 )

Gene disrupted in

(Ryder, 2004.4.26)

(Bassett et al., 2008)

Inferred from location ( 0 )

Alleles Representing Disease-Implicated Variants

Phenotypes

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

Lethality

Allele

lethal, with Scer\GAL4^Act5C.PI

XNP^EP635

partially lethal - majority die

partially lethal - majority die, with Scer\GAL4^Act5C.PU

XNP^UY3132

partially lethal - majority die (with XNP¹)

partially lethal - majority die (with XNP²)

XNP¹

partially lethal - majority die (with XNP³)

XNP¹

partially lethal - majority die | recessive

XNP⁵

partially lethal - majority live (with XNP²)

XNP³

partially lethal - majority live (with XNP³)

XNP²

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

XNP^GD4562

viable, with Scer\GAL4^Mef2.PR

XNP^GD4562

viable, with Scer\GAL4^pnr-MD237

XNP^GD4562

viable, with Scer\GAL4^tin.CΔ4

XNP^GD4562

Sterility

Allele

Other Phenotypes

Allele

abnormal neuroanatomy

XNP^{dsRNA.UAS.WIZ}

abnormal neuroanatomy, with Scer\GAL4^7B

XNP^UY3132

abnormal neuroanatomy, with Scer\GAL4^elav.PLu

suppressor of variegation, with Dp(?;2)bw^D, Scer\GAL4^GMR.PF

XNP^EP635

suppressor of variegation, with In(3L)BL1

XNP³

suppressor of variegation, with P{hsp26-pt-T}39C-12

XNP³

suppressor of variegation (with XNP⁴⁰³), with Dp(?;2)bw^D

XNP⁴⁰⁶

suppressor of variegation (with XNP⁴⁰³), with In(1)w^m4

XNP⁴⁰⁶

suppressor of variegation (with XNP⁴⁰⁶), with Dp(?;2)bw^D

XNP⁴⁰³

suppressor of variegation (with XNP⁴⁰⁶), with In(1)w^m4

XNP⁴⁰³

suppressor of variegation | dominant, with Dp(?;2)bw^D

suppressor of variegation | dominant, with In(1)w^m4

XNP⁴⁰³

suppressor of variegation | dominant, with In(1)w^m4h

suppressor of variegation | dominant, with P{hsp26-pt-T}39C-12

XNP¹

suppressor of variegation | recessive

visible, with Scer\GAL4^ap-md544

XNP^EP635

Phenotype manifest in

Allele

adult mushroom body, with Scer\GAL4^7B

XNP^UY3132

adult thorax, with Scer\GAL4^ap-md544

XNP^EP635

embryonic/larval glial cell

XNP^{dsRNA.UAS.WIZ}

interface glial cell

XNP^{dsRNA.UAS.WIZ}

Kenyon cell, with Scer\GAL4^7B

XNP^UY3132

larval anterior commissure, with Scer\GAL4^elav.PLu

XNP^EP635

larval longitudinal connective, with Scer\GAL4^elav.PLu

larval posterior commissure, with Scer\GAL4^elav.PLu

XNP^EP635

microchaeta, with Scer\GAL4^ap-md544

XNP^EP635

scutellum, with Scer\GAL4^ap-md544

XNP^EP635

Orthologs

Downloads

Download All DIOPT Orthologs

Download All OrthoDB Orthologs

Human Orthologs (via DIOPT v8.0)

Homo sapiens (Human) (4)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

10 of 15

Yes

Yes

1 of 15

No

No

1 of 15

No

No

1 of 15

No

Yes

Model Organism Orthologs (via DIOPT v8.0)

Mus musculus (laboratory mouse) (1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

10 of 15

Yes

Yes

Rattus norvegicus (Norway rat) (4)

3 of 13

Yes

Yes

Rnor\LOC102552166

2 of 13

No

No

Rnor\LOC103690008

2 of 13

No

Yes

1 of 13

No

No

Xenopus tropicalis (Western clawed frog) (2)

5 of 12

Yes

Yes

2 of 12

No

No

Danio rerio (Zebrafish) (3)

8 of 15

Yes

Yes

2 of 15

No

No

1 of 15

No

Yes

Caenorhabditis elegans (Nematode, roundworm) (2)

15 of 15

Yes

Yes

1 of 15

No

No

Arabidopsis thaliana (thale-cress) (1)

4 of 9

Yes

Yes

Saccharomyces cerevisiae (Brewer's yeast) (0)

No records found.

Schizosaccharomyces pombe (Fission yeast) (0)

No records found.

Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG091901YQ )

Organism

Common Name

Gene

AAA Syntenic Ortholog

Multiple Dmel Genes in this Orthologous Group

Drosophila suzukii

Spotted wing Drosophila

Dsuz\DS10_00013148

Drosophila simulans

Drosophila sechellia

Drosophila erecta

Drosophila yakuba

Drosophila ananassae

Drosophila pseudoobscura pseudoobscura

Drosophila persimilis

Drosophila willistoni

Drosophila virilis

Drosophila mojavensis

Drosophila grimshawi

Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091500GI )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Musca domestica

House fly

Glossina morsitans

Tsetse fly

Gmor\GMOY010542

Lucilia cuprina

Australian sheep blowfly

Lcup\FF38_01191

Mayetiola destructor

Hessian fly

Mdes\Mdes006491

Aedes aegypti

Yellow fever mosquito

Aaeg\AAEL001141

Anopheles darlingi

American malaria mosquito

Adar\ADAC004772

Anopheles gambiae

Malaria mosquito

Agam\AGAP002490

Culex quinquefasciatus

Southern house mosquito

Cqui\CPIJ009998

Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W00D6 )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Bombyx mori

Silkmoth

Bmor\BGIBMGA008314

Danaus plexippus

Monarch butterfly

Dple\DPOGS202629-PA

Apis florea

Little honeybee

Aflo\4583331316

Apis florea

Little honeybee

Aflo\2147758099

Apis mellifera

Western honey bee

Bombus impatiens

Common eastern bumble bee

Bombus terrestris

Buff-tailed bumblebee

Linepithema humile

Argentine ant

Linepithema humile

Argentine ant

Megachile rotundata

Alfalfa leafcutting bee

Mrot\MROTU:002600

Nasonia vitripennis

Parasitic wasp

Nvit\Nasvi2EG010833

Nasonia vitripennis

Parasitic wasp

Nvit\Nasvi2EG010834

Dendroctonus ponderosae

Mountain pine beetle

Tribolium castaneum

Red flour beetle

Pediculus humanus

Human body louse

Phum\PHUM456670

Rhodnius prolixus

Kissing bug

Rpro\RPRC009731

Cimex lectularius

Bed bug

Clec\CLEC011668

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI005035

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI000690

Zootermopsis nevadensis

Nevada dampwood termite

Znev\Znev_15331

Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X00CE )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strigamia maritima

European centipede

Smar\SMAR005694

Ixodes scapularis

Black-legged tick

Isca\ISCW009437

Ixodes scapularis

Black-legged tick

Isca\ISCW007361

Stegodyphus mimosarum

African social velvet spider

Smim\KFM57756.1

Tetranychus urticae

Two-spotted spider mite

Turt\tetur07g03670

Tetranychus urticae

Two-spotted spider mite

Turt\tetur10g01600

Tetranychus urticae

Two-spotted spider mite

Turt\tetur80g00040

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_188325

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_101480

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_319936

Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G01G9 )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strongylocentrotus purpuratus

Purple sea urchin

Strongylocentrotus purpuratus

Purple sea urchin

Strongylocentrotus purpuratus

Purple sea urchin

Spur\Sp-AtrxL_2

Ciona intestinalis

Vase tunicate

Cint\ENSCING00000009208

Ciona intestinalis

Vase tunicate

Cint\ENSCING00000003076

Gallus gallus

Domestic chicken

Gallus gallus

Domestic chicken

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v8.0)

Drosophila melanogaster (Fruit fly) (17)

Gene Symbol

Score

Source

Alignment

3 of 10

3 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

Human Disease Associations

FlyBase Human Disease Model Reports

Disease Model Summary Ribbon

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 0 )

Allele

Disease

Evidence

References

Potential Models Based on Orthology ( 2 )

Human Ortholog

Disease

Evidence

References

ATRX; ATRX chromatin remodeler

model of alpha thalassemia-X-linked intellectual disability syndrome

IEA

(FlyBase, 2019-)

model of alpha-thalassemia myelodysplasia syndrome

IEA

(FlyBase, 2019-)

Modifiers Based on Experimental Evidence ( 0 )

Allele

Disease

Interaction

References

Disease Associations of Human Orthologs (via DIOPT v8.0 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?

ATRX; ATRX chromatin remodeler

10 of 15

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

Interactions Browser

View in Interactions Browser

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

anti bait coimmunoprecipitation, western blot, anti tag coimmunoprecipitation, anti tag western blot, pull down, autoradiography

(López-Falcón et al., 2014)

anti bait coimmunoprecipitation, western blot, two hybrid, pull down, autoradiography

(Valadez-Graham et al., 2012)

(Hu et al., 2017.6.13)

XNP - Su(var)205

anti tag coimmunoprecipitation, molecular sieving, western blot, ion exchange chromatography, anti bait coimmunoprecipitation, pull down, autoradiography, peptide massfingerprinting, anti tag western blot, enzymatic study

(Alekseyenko et al., 2014, Emelyanov et al., 2010, Bassett et al., 2008)

Summary of Genetic Interactions

esyN Network Diagram

esyN Network Key:

Suppression

Enhancement

View in Interactions Browser

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

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

enhanceable

(López-Falcón et al., 2014)

enhanceable

(Sun et al., 2006)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

enhanceable

(López-Falcón et al., 2014)

suppressible

(Chen et al., 2015)

suppressible

(Schneiderman et al., 2010)

enhanceable

(Ellis et al., 2015)

suppressible

(Valadez-Graham et al., 2012)

enhanceable

(Sun et al., 2006)

enhanceable

(Sun et al., 2006)

enhanceable

(Sun et al., 2006)

enhanceable

(Valadez-Graham et al., 2012, Pena-Rangel et al., 2002)

suppressible

(Valadez-Graham et al., 2012)

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

67994

DroID - A comprehensive database of gene and protein interactions.

FBgn0039338

MIST (genetic) - An integrated Molecular Interaction Database

XNP

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

XNP

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

Genomic Location and Detailed Mapping Data

Chromosome (arm)

3R

Recombination map

3-88

Cytogenetic map

Sequence location

3R:25,477,868..25,482,834 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

96E1-96E2

Limits computationally determined from genome sequence between P{PZ}Aats-gln⁰⁵⁴⁶¹ and P{EP}EP3354

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

96C-96D

(Cardoso, 1999.12.20)

Experimentally Determined Recombination Data

Location

3-88

(FlyBase, 2016)

3-86.3

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (15)

26645

w^*; P{UAS-XNP.HA}3

26646

w^*; P{UAS-XNP.K495R.HA}3

17188

w¹¹¹⁸; P{EP}XNP^EP635

26644

w^*; XNP³/TM6B, Tb⁺

29444

y¹ v¹; P{TRiP.JF03380}attP2

43425

w^*; P{GSV1}XNP^EP-51/TM3, Sb¹

26643

w^*; XNP²/TM3, Sb¹ Ser¹

7355

y¹ w^67c23; P{Mae-UAS.6.11}XNP^UY3132

26642

w^*; Df(3R)XNP¹, XNP¹/TM6B, Tb¹

v101568

P{KK103859}VIE-260B

v10618

w¹¹¹⁸; P{GD4562}v10618

v318736

PBac{fTRG01055.sfGFP-TVPTBF}VK00002

More stocks available...

Genomic Clones (20)

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

cDNA Clones (107)

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 GBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA clones, fully sequenced

BDGP DGC clones

Other clones

DPiM_LD28477

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.

FBgn0039338

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0039338

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

43080

Antibody Information

Laboratory Generated Antibodies

monoclonal

(Fromental-Ramain et al., 2017)

polyclonal

(Valadez-Graham et al., 2012, Emelyanov et al., 2010, Schneiderman et al., 2009, Bassett et al., 2008)

Commercially Available Antibodies

Other Information

Relationship to Other Genes

Source for database identify of

Source for identity of: XNP CG4548

(FlyBase, 1996-)

Source for database merge of

Source for merge of: XNP EP635

(FlyBase, 1996-)

Additional comments

Source for merge of XNP EP635 was that EP635 insertion is within XNP (and in the right orientation) ( date:040519 ).

(FlyBase, 1996-)

Source for identity of XNP CG4548 was sequence comparison ( date:001220 ).

(FlyBase, 1996-)

Other Comments

One of 42 Drosophila genes identified as being most likely to reveal molecular and cellular mechanisms of nervous system development or plasticity relevant to human Mental Retardation disorders.

(Inlow and Restifo, 2004)

Origin and Etymology

Discoverer

Etymology

Identification

External Crossreferences and Linkouts ( 55 )

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.

43080

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

Q9GQN5

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

Other crossreferences

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0039338

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

FBgn0039338

DRscDB

43080/tissue=All

EMBL-EBI Single Cell Expression Atlas

FBgn0039338

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

XNP_1
XNP_2

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

CG4548

Flygut - An atlas of the Drosophila adult midgut

FBgn0039338

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

43080

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

TC009794

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

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

Dmel_CG4548

MARRVEL_MODEL

43080

modMine - A data warehouse for the modENCODE project

FBgn0039338

Linkouts

BioGRID - A database of protein and genetic interactions.

67994

DroID - A comprehensive database of gene and protein interactions.

FBgn0039338

DRSC - Results frm RNAi screens

FBgn0039338

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG4548-RA

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0039338

FlyMine - An integrated database for Drosophila genomics

FBgn0039338

Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution

Interactive Fly

MIST (genetic) - An integrated Molecular Interaction Database

XNP

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

XNP

Synonyms and Secondary IDs (16)

Reported As

Symbol Synonym

ATR-X/XNP

(Sun et al., 2006)

ATRX

(Jin et al., 2020)

CG4548

(Hosono et al., 2015, Ni et al., 2010.12.1, Schneiderman et al., 2010, Keleman et al., 2009.8.5, Perkins et al., 2009, Schneiderman et al., 2009, Lee et al., 2007, Molnar et al., 2006, Sun et al., 2006, Wang et al., 2004)

DATR-X

(Sun et al., 2006)

DATRX

(Hong et al., 2009)

EP(3)0635

(Pena-Rangel et al., 2002)

EP635

XNP/dATRX

(Meyer-Nava et al., 2020)

Xnp

(Kwon et al., 2018, Nikalayevich and Ohkura, 2015)

atrx

(López-Falcón et al., 2014)

dATRX

(Yadav et al., 2019, Tue et al., 2017, Valadez-Graham et al., 2012, Bassett et al., 2008)

dXNP

(Chavez et al., 2017, Hong et al., 2009, Lee et al., 2007)

datrx

(Chavez et al., 2017)

xnp

(Fromental-Ramain et al., 2017, Orsi et al., 2013, Schneiderman et al., 2012, Emelyanov et al., 2010, Schneiderman et al., 2010, Schneiderman et al., 2009)

xnp/atr-x

(Cardoso, 1999.12.20)

Name Synonyms

XNP

(Davis et al., 2011, Lee et al., 2007)

Secondary FlyBase IDs

FBgn0062645

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

References (75)

Report Sections