FlyBase Gene Report: Dmel\shu

General Information

Symbol

Dmel\shu

Species

D. melanogaster

Name

shutdown

Annotation Symbol

CG4735

Feature Type

protein_coding_gene

FlyBase ID

FBgn0003401

Gene Model Status

Current

Stock Availability

10 publicly available

Enzyme Name (EC)

peptidylprolyl isomerase (5.2.1.8)

Gene Summary

shutdown (shu) encodes an immunophilin cochaperone that collaborates with Hsp90 during piRNA biogenesis and is essential for normal function of germline stem cells. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
UniProtKB
Red Book
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

60A3-60A3

Sequence location

2R:23,841,461..23,843,286 [-]

Recombination map

2-105

RefSeq locus

NT_033778 REGION:23841461..23843286

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 (11 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 Hsp90 protein binding

inferred from biological aspect of ancestor with PANTHER:PTN000828519

(GO Reference Genome Project, 2011-)

enables peptidyl-prolyl cis-trans isomerase activity

inferred from electronic annotation with InterPro:IPR001179, InterPro:IPR046357

(InterPro Project Members, 2004-)

Biological Process (6 terms)

Terms Based on Experimental Evidence (4 terms)

CV Term

Evidence

References

involved_in oogenesis

inferred from high throughput mutant phenotype

(Schupbach and Wieschaus, 1991)

inferred from mutant phenotype

(Munn and Steward, 2000)

involved_in primary piRNA processing

inferred from mutant phenotype

(Olivieri et al., 2012, Preall et al., 2012)

involved_in retrotransposon silencing

inferred from mutant phenotype

(Preall et al., 2012)

involved_in secondary piRNA processing

inferred from mutant phenotype

(Olivieri et al., 2012, Preall et al., 2012)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

involved_in piRNA processing

inferred from biological aspect of ancestor with PANTHER:PTN000828519

(GO Reference Genome Project, 2011-)

involved_in spermatogenesis

inferred from biological aspect of ancestor with PANTHER:PTN000828519

(GO Reference Genome Project, 2011-)

Cellular Component (3 terms)

Terms Based on Experimental Evidence (3 terms)

CV Term

Evidence

References

located_in cytoplasm

inferred from direct assay

(Munn and Steward, 2000)

located_in P granule

inferred from direct assay

(Olivieri et al., 2012)

located_in Yb body

inferred from direct assay

(Olivieri et al., 2012)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

is_active_in cytoplasm

inferred from biological aspect of ancestor with PANTHER:PTN000828519

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

FK506-BINDING PROTEINS

Protein Family (UniProt)

Belongs to the FKBP6 family. (Q9W1I9)

Protein Signatures (InterPro)

Catalytic Activity (EC/Rhea)

peptidyl-prolyl cis-trans isomerase activity

[protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) (5.2.1.8)

RHEA 16237:

Summaries

Gene Snapshot

shutdown (shu) encodes an immunophilin cochaperone that collaborates with Hsp90 during piRNA biogenesis and is essential for normal function of germline stem cells. [Date last reviewed: 2019-03-14]

Gene Group (FlyBase)

FK506-BINDING PROTEINS -: FK506-binding proteins are a class of evolutionary conserved peptidyl prolyl cis/trans isomerases. In vertebrates, they form binary complexes with their ligand, FK506 or rapamycin, and are involved in key biochemical processes including protein folding, receptor signalling, protein trafficking, and transcription. FK506-binding proteins are characterized by the presence of a 'FKBP-type peptidyl-prolyl cis-trans isomerase domain' (IPR001179). (Adapted from PMID:25986569.)

Protein Function (UniProtKB)

Co-chaperone required during oogenesis to repress transposable elements and prevent their mobilization, which is essential for the germline integrity. Acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and govern the methylation and subsequent repression of transposons. Acts as a co-chaperone via its interaction with Hsp83/HSP90 and is required for the biogenesis of all three piRNA major populations.

(UniProt, Q9W1I9)

Phenotypic Description (Red Book; Lindsley and Zimm 1992)

shu: shut down (T. Schupbach)

Female sterile; homozygous females contain few developing egg chambers in their ovaries, which may contain abnormal numbers of nurse cells and usually degenerate before yolk uptake begins. Rarely a few very small and abnormal eggs are produced.

Summary (Interactive Fly)

immunophilin - FK506-binding protein domain and a tetratricopeptide repeat - essential for the normal function of the germline stem cells - a conserved cochaperone that collaborates with Hsp90 during piRNA biogenesis, potentially at the loading step of RNAs into Piwi proteins

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\shu 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 Q9W1I9)

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 5.52

Sequence Ontology: Class of Gene

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

shu-RA

FBtr0072237

NM_137993

1694

455

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

shu-PA

FBpp0072146

51.8

455

5.84

Q9W1I9

NP_611837

AAF47070

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

Subunit Structure (UniProtKB)

Interacts with Hsp83.

(UniProt, Q9W1I9)

Crossreferences

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

Linkouts

Sequences Consistent with the Gene Model

Mapped Features

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

External Data

Crossreferences

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

shu_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).

-0.11

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 3

pole plasm

Comment: maternally deposited

(Fisher et al., 2012)

organism

• pole plasm

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 1 -- 4

Comment: maternally deposited

(Munn and Steward, 2000)

organism | ubiquitous | uniform

(Munn and Steward, 2000)

embryonic stage 4 -- 6

organism

Comment: rapidly degraded

(Fisher et al., 2012)

primordial germ cell

(Fisher et al., 2012)

embryonic stage 5

primordial germ cell

(Munn and Steward, 2000)

embryonic stage 7 -- 8

primordial germ cell

(Fisher et al., 2012)

embryonic stage 9 -- 10

germline cell

(Fisher et al., 2012)

embryonic stage 11 -- 12

germline cell

(Fisher et al., 2012)

embryonic stage 13 -- 16

germline cell

(Fisher et al., 2012)

gonad

(Fisher et al., 2012)

embryonic stage 15

gonad

(Munn and Steward, 2000)

adult stage | female & oogenesis

germarium region 1 | apical

Comment: apical tip

(Munn and Steward, 2000)

germarium region 2b

(Munn and Steward, 2000)

germarium region 3

(Munn and Steward, 2000)

adult stage | female & oogenesis stage S1

egg chamber

(Munn and Steward, 2000)

adult stage | female oogenesis stage S1 -- S4

germarium

(Munn and Steward, 2000)

oogenesis stage S10 & adult stage | female

nurse cell

(Munn and Steward, 2000)

adult stage | male & spermatogenesis

germinal proliferation center

(Munn and Steward, 2000)

Additional Descriptive Data

Expression of shu transcript is high in germ cells during oogenesis stages S1-4. Expression abruptly ceases until oogenesis stage 10, when there are high levels of shu transcript in nurse cells.

(Munn and Steward, 2000)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage | female

ovary

• cytoplasm

(Munn and Steward, 2000)

female germline stem cell

• cytoplasm

(Munn and Steward, 2000)

adult stage | female & oogenesis

cystoblast

• cytoplasm

(Munn and Steward, 2000)

cyst cell of ovary | faint

• cytoplasm | faint

(Munn and Steward, 2000)

adult stage | female & oogenesis stage S1

egg chamber

• cytoplasm

(Munn and Steward, 2000)

oogenesis

egg chamber

(Olivieri et al., 2012)

female germline cell

(Olivieri et al., 2012)

somatic cell of ovariole

(Olivieri et al., 2012)

western blot

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage | female

ovary

(Munn and Steward, 2000)

Additional Descriptive Data

shu protein is localized to the cytoplasm of ovarian germline and somatic cells and is enriched in the nuage. shu protein levels are lower in follicle cells.

(Olivieri et al., 2012)

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in cytoplasm

inferred from direct assay

(Munn and Steward, 2000)

located_in P granule

inferred from direct assay

(Olivieri et al., 2012)

located_in Yb body

inferred from direct assay

(Olivieri et al., 2012)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\shu in JBrowse

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

View exonic expression by developmental stage for Dmel\shu

View exonic expression by tissue for Dmel\shu

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

FBgn0003401

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

45360/tissue=All

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

FBgn0003401

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0003401

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

FBgn0003401

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

CG4735

Flygut - An atlas of the Drosophila adult midgut

FBgn0003401

Images

FlyExpress - Embryonic expression images (BDGP data)

Show all FlyExpress processed images for Dmel\shu

Stages(s) 1-3
Stages(s) 4-6
Stages(s) 7-8
Stages(s) 9-10
Stages(s) 11-12
Stages(s) 13-16

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 ( 12 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of shu

Transgenic constructs containing regulatory region of shu

Aberrations (Deficiencies and Duplications) ( 7 )

Inferred from experimentation ( 7 )

Gene disrupted in

Df(2R)b23

(Munn and Steward, 2000)

Df(2R)BSC600

(Kahsai and Cook, 2018)

Df(2R)BSC665

(Christensen et al., 2008.12.28)

Df(2R)bw-D23

(Schupbach and Wieschaus, 1991)

Df(2R)bw-S46

(Munn and Steward, 2000, Schupbach and Wieschaus, 1991)

Df(2R)OV1

(Munn and Steward, 2000)

Gene not disrupted in

Df(2R)tid

(Munn and Steward, 2000)

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

shu^EY08563

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

shu^GD11412

viable, with Scer\GAL4^Mef2.PR

shu^GD11412

viable, with Scer\GAL4^pnr-MD237

shu^GD11412

viable, with Scer\GAL4^tin.CΔ4

shu^GD11412

Sterility

Allele

female sterile

female sterile, with Scer\GAL4^nanos.PG

female sterile (with Df(2R)BSC600)

shu²

fertile

shu^EY08563

male sterile

male sterile | recessive

Other Phenotypes

Allele

abnormal locomotor behavior | adult stage

shu¹

wild-type

Phenotype manifest in

Allele

dorsal appendage (with shu²)

shu^PB70

dorsal appendage (with shu^PB70)

shu²

egg (with shu²)

shu^PB70

egg (with shu^PB70)

shu²

egg | germline clone

shu^PB70

egg chamber (with Df(2R)b23)

shu¹

egg chamber (with shu²)

shu^PB70

egg chamber (with shu^PB70)

shu²

egg chamber | germline clone

fusome | female (with Df(2R)b23)

shu¹

germline cell | female (with Df(2R)b23)

shu¹

oocyte (with shu²)

shu^PB70

oocyte (with shu^PB70)

shu²

ovariole (with Df(2R)b23)

shu¹

stretch follicle cell

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) (25)

Hsap\FKBP6

13 of 14

Yes

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

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

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

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) (19)

Rnor\Fkbp6

13 of 14

Yes

2 of 14

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

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Mus musculus (laboratory mouse) (21)

Mmus\Fkbp6

12 of 14

Yes

2 of 14

2 of 14

2 of 14

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

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Xenopus tropicalis (Western clawed frog) (11)

Xtro\fkbp6

7 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Danio rerio (Zebrafish) (21)

Drer\fkbp6

13 of 14

Yes

Drer\LOC100537892

6 of 14

Yes

2 of 14

2 of 14

2 of 14

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

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Caenorhabditis elegans (Nematode, roundworm) (11)

Cele\fkb-4

3 of 14

Yes

Cele\fkb-3

2 of 14

Cele\fkb-5

2 of 14

Yes

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Anopheles gambiae (African malaria mosquito) (15)

Agam\AgaP_AGAP011458

12 of 12

Yes

2 of 12

2 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (32)

Atha\TWD1

4 of 13

Yes

Atha\AT3G55520

3 of 13

Yes

2 of 13

2 of 13

2 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

Atha\AT3G52075

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (7)

Scer\FPR2

2 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Schizosaccharomyces pombe (Fission yeast) (3)

Spom\fkh1

2 of 12

Yes

Spom\fkbp39

1 of 12

Spom\SPAC27F1.06c

1 of 12

Escherichia coli (enterobacterium) (2)

Ecol\fklB

1 of 11

Yes

Ecol\fkpA

1 of 11

Yes

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:shu. 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) (15)

CG30075

5 of 13

Fkbp59

3 of 13

zda

3 of 13

2 of 13

2 of 13

2 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Sgt

1 of 13

1 of 13

1 of 13

1 of 13

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?

FKBP6; FKBP prolyl isomerase family member 6 (inactive)

13 of 14

604839

SPERMATOGENIC FAILURE 77; SPGF77

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

Show neighbor-neighbor interactions:

Off

Show/hide secondary interactors
(data from AllianceMine provided by esyN)

Select Layout:

Force Directed

Circle

Concentric

Legend:

Protein

RNA

Selected Interactor(s)

Other Interaction Browsers

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

Please see the Physical Interaction reports below for full details

RNA-protein

Physical Interaction

Assay

References

shu - Hrb98DE

anti bait coimmunoprecipitation, reverse transcription pcr

(Ji and Tulin, 2016)

protein-protein

Physical Interaction

Assay

References

shu - armi

anti bait coimmunoprecipitation, western blot

(Olivieri et al., 2012)

shu - gig

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

shu - piwi

anti bait coimmunoprecipitation, western blot

(Olivieri et al., 2012)

shu - rictor

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

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

Subunit Structure (UniProtKB)

Interacts with Hsp83.

(UniProt, Q9W1I9 )

Linkouts

BioGRID - A database of protein and genetic interactions.

69621

DroID - A comprehensive database of gene and protein interactions.

FBgn0003401

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

45360

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-105

Cytogenetic map

60A3-60A3

Sequence location

2R:23,841,461..23,843,286 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

60A3-60A3

Limits computationally determined from genome sequence between P{EP}egl^EP938 and P{lacW}eIF6^k13214

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

2-105

(FlyBase, 2016)

2-109.6

(Comeron et al., 2012)

Left of (cM)

bgcn

(Munn and Steward, 2000)

Right of (cM)

Notes

Stocks and Reagents

Stocks (10)

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

Bloomington

17473

y¹ w^67c23; P{EPgy2}shu^EY08563

35454

y¹ sc^* v¹ sev²¹; P{TRiP.GL00379}attP2

83499

y¹ sc^* v¹ sev²¹; P{TKO.GS04219}attP40

64591

y¹ sc^* v¹ sev²¹; P{TRiP.HMC05610}attP40/CyO

5109

cn¹ bw¹ shu² speck¹/CyO, l(2)DTS513¹

Kyoto

108046

cn¹ bw¹ shu² speck¹/CyO, l(2)DTS513¹

NIG-Fly

GL00379

y¹ sc^* v¹ sev²¹; P{TRiP.GL00379}attP2

2RG-0099

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

VDRC

v105832

P{KK102092}VIE-260B

v26615

w¹¹¹⁸; P{GD11412}v26615/CyO

Genomic Clones (21)

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

cDNA Clones (36)

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

LD24746

Other clones

DPiM_LD24746

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.

FBgn0003401

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0003401

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Olivieri et al., 2012, Munn and Steward, 2000)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

New stable cell line derived from OSC : Endogenously tagged alleles were established for piwi, shu, Gle1, vir and Nbr in OSC cells.
(Meng et al., 2022)

Other Comments

shu is essential for the biogenesis of all piRNA populations in D. melanogaster.

(Olivieri et al., 2012)

shu is essential for the normal function of the germline stem cells in females and is also required at later stages of oogenesis.

(Munn and Steward, 2000)

The shu locus affects early oogenesis: mutations cause the production of few, defective germ cells.

(Schupbach and Wieschaus, 1991)

Relationship to Other Genes

Source for database merge of

Source for merge of: shu CG4735

(Steward, 2002.9.13)

Additional comments

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (7)

Reported As

Symbol Synonym

CG4735

(National Institute of Genetics Fly Stocks, 2022-, Ibaraki et al., 2021, Ghartey-Kwansah et al., 2018, Chen et al., 2012, Ni et al., 2011.7.19, Zhang et al., 2011, Zhang et al., 2010, Keleman et al., 2009.8.5, Perkins et al., 2009, Asha et al., 2003, Coulier et al., 2000)

Shu

(Meng et al., 2022, Rayford et al., 2021, Ge et al., 2019, Hirakata and Siomi, 2019, Hirakata et al., 2019, Pandey et al., 2017, Yang and Xi, 2017, Hirakata and Siomi, 2016, Czech et al., 2013)

shu

(Nieken et al., 2023, Ibaraki et al., 2021, Ellison et al., 2020, Saint-Leandre et al., 2020, Trcek et al., 2020, Transgenic RNAi Project members, 2017-, Hsu et al., 2015, Van Bortle et al., 2015, Czech et al., 2013, Handler et al., 2013, Muerdter et al., 2013, Olivieri et al., 2012, Preall et al., 2012, Frise et al., 2010, Christensen et al., 2008.12.28, Lindsley and Zimm, 1992)

Name Synonyms

Shut-down

(Ji and Tulin, 2016)

Shutdown

(Ghartey-Kwansah et al., 2018, Yamashiro and Siomi, 2018, Hirakata and Siomi, 2016, Ross et al., 2014, Meister, 2013, Berg, 2005)

shut down

(Lindsley and Zimm, 1992)

shutdown

(Specchia et al., 2017, Han et al., 2015, Hayashi et al., 2014, Handler et al., 2013, Olivieri et al., 2012, Munn and Steward, 1998)

Secondary FlyBase IDs

FBgn0034912

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

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Title

External Crossreferences and Linkouts ( 36 )

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.

45360

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.

Q9W1I9

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

Q9W1I9

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.

Q9W1I9

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0003401

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

45360/tissue=All

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

FBgn0003401

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

FBgn0003401

FlyMine - An integrated database for Drosophila genomics

FBgn0003401

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

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

dme:Dmel_CG4735

MARRVEL_MODEL - MARRVEL (model organism gene)

45360

Linkouts

BioGRID - A database of protein and genetic interactions.

69621

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

FBgn0003401

DroID - A comprehensive database of gene and protein interactions.

FBgn0003401

DRSC - Results frm RNAi screens

FBgn0003401

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

shu_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0003401

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0003401

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

CG4735

Flygut - An atlas of the Drosophila adult midgut

FBgn0003401

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

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

Interactive Fly

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

45360

References (77)

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

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