FlyBase Gene Report: Dmel\Ddx56

General Information

Symbol

Dmel\Ddx56

Species

D. melanogaster

Name

DEAD-box helicase 56

Annotation Symbol

CG1666

Feature Type

protein_coding_gene

FlyBase ID

FBgn0001565

Gene Model Status

Current

Stock Availability

15 publicly available

Enzyme Name (EC)

RNA helicase (3.6.4.13)

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Gene Group
Red Book
Interactive Fly

Also Known As

Hlc, A112, l(1)A112, Helicase, 11P1

Key Links

Genomic Location

Cytogenetic map

20A1-20A1

Sequence location

X:21,385,518..21,387,946 [-]

Recombination map

1-66

RefSeq locus

NC_004354 REGION:21385518..21387946

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 (7 terms)

Molecular Function (3 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

enables ATP binding

inferred from electronic annotation with InterPro:IPR011545

(InterPro Project Members, 2004-)

enables nucleic acid binding

inferred from electronic annotation with InterPro:IPR011545

(InterPro Project Members, 2004-)

enables RNA helicase activity

inferred from electronic annotation with InterPro:IPR014014

(InterPro Project Members, 2004-)

inferred from sequence or structural similarity with SGD:S000004266

(Lasko, 2000)

Biological Process (2 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

involved_in defense response to virus

inferred from direct assay

(Taschuk et al., 2020)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

acts_upstream_of_negative_effect host-mediated perturbation of viral RNA genome replication

inferred from sequence or structural similarity with UniProtKB:Q9NY93

(Taschuk et al., 2020)

Cellular Component (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

located_in cytosol

inferred from sequence or structural similarity with UniProtKB:Q9NY93

(Taschuk et al., 2020)

is_active_in nucleolus

inferred from biological aspect of ancestor with PANTHER:PTN002772752

(GO Reference Genome Project, 2011-)

located_in nucleolus

inferred from sequence or structural similarity with UniProtKB:Q9NY93

(Taschuk et al., 2020)

Gene Group (FlyBase)

DEAD-BOX RNA HELICASES

Protein Family (UniProt)

Protein Signatures (InterPro)

Catalytic Activity (EC/Rhea)

RNA helicase activity

ATP + H2O = ADP + phosphate + H(+) (3.6.4.13)

Summaries

Gene Group (FlyBase)

DEAD-BOX RNA HELICASES -: DEAD-box RNA helicases belong to helicase superfamily 2 (SF2). They are characterized by the presence of nine conserved helicase motifs, including the DEAD sequence in motif II. (Adapted from PMID:21509200.)

Phenotypic Description (Red Book; Lindsley and Zimm 1992)

l(1)19Ff

Mutant embryos have no obvious defects of central nervous system (CNS), peripheral nervous system (PNS), or cuticle. Germ line clones lethal (Perrimon, Smouse, and Miklos, 1989, Genetics 121: 313-31).

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Ddx56 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 Q9VRI0)

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

Gene model reviewed during 5.46

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

Gene model reviewed during 5.53

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Ddx56-RA

FBtr0077221

NM_078710

2116

560

Ddx56-RB

FBtr0343853

NM_001298588

1963

560

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

Ddx56-PA

FBpp0076917

62.9

560

9.67

FBpp0310396

62.9

560

9.67

Q9VRI0

NP_001285517

AHN59987

Polypeptides with Identical Sequences

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

560 aa isoforms: Ddx56-PA, Ddx56-PB

Additional Polypeptide Data and Comments

Reported size (kDa)

560 (aa)

(Maleszka et al., 1998)

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

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Ddx56 using the Feature Mapper tool.

External Data

Crossreferences

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).

-1.10

Transcript Expression

northern blot

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage -- adult stage

(Maleszka et al., 1998)

larval stage

imaginal disc

(Maleszka et al., 1998)

embryonic/larval fat body

(Maleszka et al., 1998)

larval brain

(Maleszka et al., 1998)

embryonic/larval salivary gland

(Maleszka et al., 1998)

adult stage

adult brain

(Maleszka et al., 1998)

adult stage & oogenesis

ovary

(Maleszka et al., 1998)

RT-PCR

Stage

Tissue/Position (including subcellular localization)

Reference

pharate adult stage

brain

(Maleszka et al., 1998)

mature adult stage

adult brain

(Maleszka et al., 1998)

Additional Descriptive Data

Ddx56 transcripts are detected in embryos, larvae, pupae, and adults on northern blots. They are observed in ovaries, salivary gland, larval fat body, imaginal discs, and in larval, late pupal and adult brain by RT-PCR.

(Maleszka et al., 1998)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Ddx56 in JBrowse

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

View exonic expression by developmental stage for Dmel\Ddx56

View exonic expression by tissue for Dmel\Ddx56

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

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

33118/tissue=All

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

FBgn0001565

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0001565

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

FBgn0001565

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

CG1666

Flygut - An atlas of the Drosophila adult midgut

FBgn0001565

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 15 )

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 Ddx56

Transgenic constructs containing regulatory region of Ddx56

Aberrations (Deficiencies and Duplications) ( 190 )

Inferred from experimentation ( 190 )

Gene disrupted in

Df(1)2/19B

(Maleszka et al., 1996, Miklos and de Couet, 1990, Perrimon et al., 1989)

Df(1)14-11

(Munoz, 2003.12.10)

Df(1)16-1-88

(Munoz, 2004.1.5)

Df(1)16-3-22

(Miklos et al., 1987)

(Munoz, 2004.1.5)

(Munoz, 2004.1.5)

(Munoz, 2004.1.5)

(Munoz, 2004.1.5)

(Schalet and Lefevre, 1973)

Df(1)17-241

(Munoz, 2003.12.10)

Df(1)17-244

(Munoz, 2004.1.5)

Df(1)17-257

(Maleszka et al., 1996, Russell et al., 1992, Miklos and de Couet, 1990, Perrimon et al., 1989, Miklos et al., 1987)

Df(1)17-322

(Munoz, 2004.1.5)

Df(1)17-351

(Miklos and de Couet, 1990, Perrimon et al., 1989, Miklos et al., 1987)

Df(1)17-412

(Munoz, 2004.1.5)

Df(1)17-489

(Perrimon et al., 1989, Miklos et al., 1987)

Df(1)18-36

(Munoz, 2004.1.5)

Df(1)19-2

(Munoz, 2004.1.5)

Df(1)19-18

(Munoz, 2004.1.5, Munoz, 2003.12.10)

Df(1)26B

(Perrimon et al., 1989)

Df(1)A53

(Perrimon et al., 1989)

Df(1)A58

(Lifschytz and Falk, 1968)

Df(1)B12

(Prud'homme et al., 1995, Lifschytz and Yakobovitz, 1978, Lifschytz and Falk, 1969, Lifschytz and Falk, 1968)

Df(1)B82

(Lifschytz and Falk, 1969)

Df(1)C74

(Miklos and de Couet, 1990, Perrimon et al., 1989)

Df(1)D5

(Eeken et al., 1985)

Df(1)D43L1

(Kramers et al., 1991, Perrimon et al., 1989, Eeken et al., 1985, Rahman and Lindsley, 1981)

Df(1)DCB1-35b

(Prud'homme et al., 1995, Perrimon et al., 1989)

Df(1)GA33

(Perrimon et al., 1989)

Df(1)GA37

(Perrimon et al., 1989)

Df(1)GA40

(Perrimon et al., 1989)

Df(1)GA104

(Maleszka et al., 1996, Miklos and de Couet, 1990, Perrimon et al., 1989, Miklos et al., 1987)

Df(1)GE263

(Miklos and de Couet, 1990, Perrimon et al., 1989, Miklos et al., 1987)

Df(1)HM44

(Miklos et al., 1997, Miklos and de Couet, 1990, Perrimon et al., 1989, Miklos et al., 1987, Miklos et al., 1986)

Df(1)JA117

(Miklos et al., 1997, Miklos and de Couet, 1990, Perrimon et al., 1989, Miklos et al., 1987)

Df(1)JC77

(Miklos et al., 1997, Miklos and de Couet, 1990, Perrimon et al., 1989, Miklos et al., 1987)

Df(1)LB6

(Prud'homme et al., 1995, Perrimon et al., 1989)

Df(1)LB7

(Perrimon et al., 1989)

Df(1)LB23

(Perrimon et al., 1989)

Df(1)mal3

(Kramers et al., 1991, Rahman and Lindsley, 1981)

Df(1)mal6

(Kramers et al., 1991)

Df(1)mal12

(Rahman and Lindsley, 1981, Rahman and Lindsley, 1980)

Df(1)n17-8

(Munoz, 2004.1.5)

Df(1)N77

(Perrimon et al., 1989)

Df(1)Q38

(Lifschytz and Falk, 1969)

Df(1)Q219

(Lifschytz and Falk, 1969)

Df(1)Q408

(Lifschytz and Falk, 1969)

Df(1)Q539

(Miklos et al., 1997, Prud'homme et al., 1995, Miklos and de Couet, 1990, Perrimon et al., 1989, Miklos et al., 1987, Schalet and Lefevre, 1973, Lifschytz and Falk, 1969)

Df(1)R1

(Rahman and Lindsley, 1981)

Df(1)R4

(Rahman and Lindsley, 1981)

Df(1)R5

(Rahman and Lindsley, 1981)

Df(1)R-9-1

(Lifschytz and Falk, 1969)

Df(1)R9

(Rahman and Lindsley, 1981)

Df(1)R-10-5

(Lifschytz and Falk, 1969)

Df(1)R11

(Rahman and Lindsley, 1981)

Df(1)R34

(Rahman and Lindsley, 1981)

Df(1)R39

(Rahman and Lindsley, 1981)

Df(1)S54

(Miklos and de Couet, 1990, Perrimon et al., 1989, Miklos et al., 1987)

Df(1)su(f)7085

(Lifschytz and Yakobovitz, 1978)

Df(1)su(f)9122

(Lifschytz and Yakobovitz, 1978)

Df(1)wl-2

(Lifschytz and Falk, 1969)

Df(1)yl-1

(Lifschytz and Falk, 1969)

Gene not disrupted in

Df(1)16-2-13

(Prud'homme et al., 1995, Miklos et al., 1987)

Df(1)16-3-35

(Kramers et al., 1991, Perrimon et al., 1989, Miklos et al., 1987, Eeken et al., 1985)

Df(1)16-3-53

(Munoz, 2004.1.5)

Df(1)16-129

(Maleszka et al., 1996, Miklos and de Couet, 1990, Perrimon et al., 1989, Miklos et al., 1987, Eeken et al., 1985)

Df(1)16-185

(Rahman and Lindsley, 1981)

Df(1)17-87

(Rahman and Lindsley, 1981, Rahman and Lindsley, 1980)

Df(1)17-137

(Rahman and Lindsley, 1981, Schalet and Lefevre, 1973)

Df(1)17-148

(Prud'homme et al., 1995, Rahman and Lindsley, 1981)

Df(1)17-228

(Munoz, 2004.1.5)

Df(1)17-369

(Munoz, 2004.1.5)

Df(1)17-408

(Rahman and Lindsley, 1981)

Df(1)17-456

(Munoz, 2004.1.5)

Df(1)18-80

(Munoz, 2004.1.5, Schalet and Lefevre, 1973)

Df(1)A19

(Lifschytz and Falk, 1969, Lifschytz and Falk, 1968)

Df(1)A33

(Lifschytz and Falk, 1969, Lifschytz and Falk, 1968)

Df(1)A58

(Lifschytz and Falk, 1969)

Df(1)A118

(Kramers et al., 1991, Perrimon et al., 1989, Miklos et al., 1987, Eeken et al., 1985, Lifschytz and Yakobovitz, 1978, Lifschytz and Falk, 1969, Lifschytz and Falk, 1968)

Df(1)A122

(Lifschytz and Falk, 1969, Lifschytz and Falk, 1968)

Df(1)A129

(Lifschytz and Falk, 1968)

Df(1)A161

(Lifschytz and Falk, 1968)

Df(1)A200

(Lifschytz and Falk, 1968)

Df(1)A209

(Rahman and Lindsley, 1981, Rahman and Lindsley, 1980, Lifschytz and Falk, 1969, Lifschytz and Falk, 1968)

Df(1)A211

(Lifschytz and Falk, 1968)

Df(1)B18

(Lifschytz and Falk, 1968)

Df(1)B47

(Lifschytz and Falk, 1968)

Df(1)B56

(Lifschytz and Falk, 1969, Lifschytz and Falk, 1968)

Df(1)B57

(Miklos and de Couet, 1990, Perrimon et al., 1989, Miklos et al., 1987, Lifschytz and Yakobovitz, 1978, Lifschytz and Falk, 1969, Lifschytz and Falk, 1968)

Df(1)B82

(Lifschytz and Falk, 1968)

Df(1)B85

(Lifschytz and Falk, 1968)

Df(1)B99

(Lifschytz and Falk, 1968)

Df(1)B111

(Lifschytz and Falk, 1969, Lifschytz and Falk, 1968)

Df(1)B155

(Lifschytz and Falk, 1969, Lifschytz and Falk, 1968)

Df(1)B179

(Lifschytz and Falk, 1968)

Df(1)B182

(Lifschytz and Falk, 1968)

Df(1)B199

(Lifschytz and Falk, 1968)

Df(1)B214

(Lifschytz and Falk, 1969, Lifschytz and Falk, 1968)

Df(1)B225

(Lifschytz and Falk, 1968)

Df(1)B240

(Lifschytz and Falk, 1968)

Df(1)B255

(Lifschytz and Falk, 1968)

Df(1)B264

(Lifschytz and Falk, 1969, Lifschytz and Falk, 1968)

Df(1)DCB1-35c

(Prud'homme et al., 1995, Miklos et al., 1987)

Df(1)EA113

(Miklos et al., 1987)

Df(1)GA22

(Miklos et al., 1987)

Df(1)GA42

(Rahman and Lindsley, 1981, Rahman and Lindsley, 1980)

Df(1)GA90

(Rahman and Lindsley, 1981, Rahman and Lindsley, 1980)

Df(1)GA131

(Miklos et al., 1987)

Df(1)HC279

(Perrimon et al., 1989)

Df(1)HF359

(Miklos et al., 1987)

Df(1)JA21

(Miklos et al., 1987)

Df(1)JC4

(Miklos and de Couet, 1990, Miklos et al., 1987)

Df(1)K5

(Rahman and Lindsley, 1981)

Df(1)M31

(Lifschytz and Yakobovitz, 1978)

Df(1)M158

(Lifschytz and Yakobovitz, 1978)

Df(1)M171

(Lifschytz and Yakobovitz, 1978)

Df(1)M176

(Lifschytz and Yakobovitz, 1978)

Df(1)mal8

(Kramers et al., 1991)

Df(1)mal10

(Perrimon et al., 1989)

Df(1)mal17

(Perrimon et al., 1989)

Df(1)Q539

(Kramers et al., 1991)

Df(1)R2

(Rahman and Lindsley, 1981)

Df(1)R3

(Rahman and Lindsley, 1981)

Df(1)R6

(Rahman and Lindsley, 1981)

Df(1)R7

(Prud'homme et al., 1995, Rahman and Lindsley, 1981)

Df(1)R8A

(Rahman and Lindsley, 1981)

Df(1)R8

(Rahman and Lindsley, 1981)

Df(1)R10

(Rahman and Lindsley, 1981)

Df(1)R12

(Rahman and Lindsley, 1981)

Df(1)R13

(Rahman and Lindsley, 1981)

Df(1)R14

(Rahman and Lindsley, 1981)

Df(1)R15

(Rahman and Lindsley, 1981)

Df(1)R16

(Rahman and Lindsley, 1981)

Df(1)R17

(Rahman and Lindsley, 1981)

Df(1)R18

(Rahman and Lindsley, 1981)

Df(1)R19

(Rahman and Lindsley, 1981)

Df(1)R20

(Prud'homme et al., 1995, Rahman and Lindsley, 1981)

Df(1)R21

(Prud'homme et al., 1995, Rahman and Lindsley, 1981)

Df(1)R22

(Rahman and Lindsley, 1981)

Df(1)R23

(Rahman and Lindsley, 1981)

Df(1)R24

(Rahman and Lindsley, 1981)

Df(1)R25

(Rahman and Lindsley, 1981, Rahman and Lindsley, 1980)

Df(1)R26

(Rahman and Lindsley, 1981)

Df(1)R27

(Rahman and Lindsley, 1981)

Df(1)R28

(Rahman and Lindsley, 1981)

Df(1)R29

(Rahman and Lindsley, 1981)

Df(1)R30

(Rahman and Lindsley, 1981)

Df(1)R31

(Rahman and Lindsley, 1981)

Df(1)R32

(Rahman and Lindsley, 1981)

Df(1)R33

(Rahman and Lindsley, 1981)

Df(1)R35

(Rahman and Lindsley, 1981)

Df(1)R36

(Rahman and Lindsley, 1981)

Df(1)R37

(Rahman and Lindsley, 1981)

Df(1)R38

(Rahman and Lindsley, 1981)

Df(1)R40

(Rahman and Lindsley, 1981)

Df(1)R41

(Rahman and Lindsley, 1981)

Df(1)R42

(Rahman and Lindsley, 1981)

Df(1)R43

(Rahman and Lindsley, 1981)

Df(1)R44

(Prud'homme et al., 1995, Rahman and Lindsley, 1981, Rahman and Lindsley, 1980)

Df(1)R45

(Rahman and Lindsley, 1981)

Df(1)R46

(Prud'homme et al., 1995, Rahman and Lindsley, 1981)

Df(1)R47

(Rahman and Lindsley, 1981)

Df(1)R48

(Rahman and Lindsley, 1981)

Df(1)run1112

(Perrimon et al., 1989)

Df(1)Sp20A-F

(Schalet, 1986)

Df(1)su(f)4B

(Kramers et al., 1991)

Df(1)su(f)724

(Prud'homme et al., 1995, Lifschytz and Yakobovitz, 1978)

Df(1)su(f)733

(Lifschytz and Yakobovitz, 1978)

Df(1)su(f)754

(Lifschytz and Yakobovitz, 1978)

Df(1)su(f)795

(Lifschytz and Yakobovitz, 1978)

Df(1)su(f)7009

(Lifschytz and Yakobovitz, 1978)

Df(1)T2-14A

(Perrimon et al., 1989, Miklos et al., 1987)

Df(1)X-1

(Rahman and Lindsley, 1981, Rahman and Lindsley, 1980, Lifschytz and Falk, 1969, Lifschytz and Falk, 1968)

Df(1)y-X5

(Rahman and Lindsley, 1981)

Df(1)y-X15

(Kramers et al., 1991, Rahman and Lindsley, 1981, Rahman and Lindsley, 1980)

Dp(1;Y)y⁺mal¹²⁶

(Lifschytz and Yakobovitz, 1978)

Gene not duplicated in

Dp(1;f)3

(Rahman and Lindsley, 1981)

Dp(1;Y)Bar^S

(Prud'homme et al., 1995, Kramers et al., 1991)

Dp(1;Y)Bar^SYy⁺

(Rahman and Lindsley, 1981)

Dp(1;Y)y²67g19.1

(Eeken et al., 1985)

Dp(1;Y)y⁺mal¹¹⁸

(Prud'homme et al., 1995)

Dp(1;Y)y⁺mal¹²⁶

(Miklos and de Couet, 1990, Rahman and Lindsley, 1981, Schalet and Lefevre, 1973)

Dp(1;Y)y⁺mal^N152

(Prud'homme et al., 1995)

Inferred from location ( 22 )

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

cell lethal | germline clone

lethal

Ddx56^19Ff-6

lethal, with Scer\GAL4^insc-Mz1407

Ddx56^GD9183

lethal | recessive

lethal - all die before end of larval stage | recessive

Ddx56^19Ff-2

partially lethal - majority die, with Scer\GAL4^pnr-MD237

Ddx56^GD9183

viable

Ddx56^f06483

viable, with Scer\GAL4^pnr-MD237

Ddx56^GD16441

viable, with Scer\GAL4^tin.CΔ4

Ddx56^GD9183

Sterility

Allele

fertile

Ddx56^f06483

Other Phenotypes

Allele

abnormal neuroanatomy | larval stage, with Scer\GAL4^insc-Mz1407

Ddx56^GD9183

some die during larval stage | recessive

Ddx56^19Ff-2

some die during pupal stage, with Scer\GAL4^pnr-MD237

Ddx56^GD9183

visible, with Scer\GAL4^pnr-MD237

Ddx56^GD9183

wild-type

Phenotype manifest in

Allele

central nervous system

ganglion mother cell | larval stage, with Scer\GAL4^insc-Mz1407

Ddx56^GD9183

larval neuroblast | larval stage, with Scer\GAL4^insc-Mz1407

Ddx56^GD9183

mesonotum, with Scer\GAL4^pnr-MD237

Ddx56^GD9183

peripheral nervous system

trichogen cell, with Scer\GAL4^pnr-MD237

Ddx56^GD9183

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) (18)

Hsap\DDX56

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

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

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\Ddx56

14 of 14

Yes

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) (15)

Mmus\Ddx56

14 of 14

Yes

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) (14)

Xtro\ddx56

11 of 13

Yes

2 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

Danio rerio (Zebrafish) (15)

Drer\ddx56

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

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (18)

Cele\C24H12.4

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

Anopheles gambiae (African malaria mosquito) (18)

Agam\AgaP_AGAP011145

12 of 12

Yes

Agam\AgaP_AGAP011147

12 of 12

Yes

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

1 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (34)

Atha\AT4G34910

13 of 13

Yes

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

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

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (10)

Scer\DBP9

13 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

Schizosaccharomyces pombe (Fission yeast) (8)

Spom\SPCC1494.06c

12 of 12

Yes

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

Escherichia coli (enterobacterium) (3)

Ecol\dbpA

1 of 11

Yes

Ecol\deaD

1 of 11

Yes

Ecol\rhlE

1 of 11

Yes

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Ddx56. 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) (31)

4 of 13

4 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

pit

3 of 13

pths

3 of 13

Rs1

3 of 13

ais

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

vas

2 of 13

abs

1 of 13

bel

1 of 13

1 of 13

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 ( 2 )

Allele

Disease

Interaction

References

Ddx56^HMS01424

ameliorates high grade glioma

modeled by Egfr^Act.cUa.UAS, Pi3K92E^CAAX.UAS

(Pryszlak et al., 2021)

Ddx56^GD9183

ameliorates high grade glioma

modeled by Egfr^Act.cUa.UAS, Pi3K92E^CAAX.UAS

(Pryszlak et al., 2021)

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?

DDX56; DEAD-box helicase 56

14 of 14

608023

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

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0001565

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

1-66

Cytogenetic map

20A1-20A1

Sequence location

X:21,385,518..21,387,946 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

20A1-20A1

Limits computationally determined from genome sequence between P{EP}CG1702^EP1525 and P{EP}EP1465&P{EP}CG1486^EP1192

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

1-66

(FlyBase, 2016)

1-66.0

(Comeron et al., 2012)

Left of (cM)

slgA

(Hayward et al., 1993)

(Schalet, 1972)

Right of (cM)

(Schalet, 1972)

Notes

Stocks and Reagents

Stocks (15)

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

Bloomington

4731

Ddx56^19Ff-7/FM6

6889

Ddx56^19Ff-1/FM6

18982

w¹¹¹⁸ PBac{WH}Ddx56^f06483

7485

Ddx56^19Ff-2/FM6/Dp(1;Y)mal⁺

7423

Ddx56^17-62/Binsn/Dp(1;Y)mal⁺

28991

y¹ v¹; P{TRiP.JF02921}attP2 e^*

35308

y¹ sc^* v¹ sev²¹; P{TRiP.HMS01424}attP2

NIG-Fly

1666R-2

P{NIG.1666R}2

VDRC

v32693

w¹¹¹⁸; P{GD9183}v32693

v32694

w¹¹¹⁸; P{GD9183}v32694

v318807

PBac{fTRG01225.sfGFP-TVPTBF}VK00002

v50144

w¹¹¹⁸; P{GD16441}v50144/CyO

More stocks available...

Genomic Clones (11)

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

cDNA Clones (130)

Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see JBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA clones, fully sequenced

BDGP DGC clones

Other clones

Drosophila Genomics Resource Center cDNA clones

For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

FBgn0001565

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0001565

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Su et al., 2024, Jia et al., 2022)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

New stable cell line derived from S2-unspecified : S2 cell lines expressing circCG32369, circMCPH1, circeIF5B, circrl, circPde11, circCG17715, circzfh2, circTao, circcrol, circdrn, circMeltrin, circpxb, circfru, circdati, circstw, circSarm, circStim, circCG2991, circPvr, circHil, circmub, circsxc, circbnl, and circCG9743 were created. The author reports new stable cell lines S2-circMCPH1, S2-circCG32369, S2-Flag-Ddx56 , and S2-Flag-gw.
(Su et al., 2024)
New stable cell line derived from S2-unspecified : Stable S2 cell lines were generated containing FLAG-tagged Ddx56 or a FLAG-tagged mutant of Ddx56, in which the DNA-binding domain has been deleted. The S2 cells were obtained from the laboratory of Qingfa Wu.
(Jia et al., 2022)

Other Comments

snoRNA:Z30 is an intronic RNA encoded in the first intron of Hlc.

(Zhou et al., 2002)

Mutant embryos have no obvious defects of central nervous system, peripheral nervous system, or cuticle. Germ line clones lethal (Perrimon, Smouse, and Miklos, 1989).

Relationship to Other Genes

Source for database merge of

Additional comments

Nomenclature History

Source for database identify of

Source for identity of: Hlc CG1666

(Li, 1999.11)

Source for identity of: Ddx56 Hlc

(Taschuk et al., 2020)

Nomenclature comments

Etymology

Named 'DEAD-box helicase 56' after the human ortholog.

(Taschuk et al., 2020)

Synonyms and Secondary IDs (26)

Reported As

Symbol Synonym

11P1

(Kramers et al., 1991, Schalet, 1986)

(Lifschytz and Falk, 1969)

(Lifschytz and Falk, 1968)

A112

(Bergman et al., 2006, Miklos et al., 1997, Maleszka et al., 1996, Prud'homme et al., 1995, Hayward et al., 1993, Miklos and Cotsell, 1990, Miklos and de Couet, 1990, Perrimon et al., 1989, Miklos et al., 1987, Lefevre and Watkins, 1986, Eeken et al., 1985, Lefevre, 1981, Rahman and Lindsley, 1981, Lifschytz, 1978)

CG1666

(Çiçek et al., 2016, Hosono et al., 2015, Haelterman et al., 2014, Ni et al., 2011.7.19, Perkins et al., 2009, Huang et al., 2005)

Ddx56

DmRH10

(Boudet et al., 2001)

HLC

(Boudet et al., 2001)

HM-44

(Kramers et al., 1991)

Hlc

(Ohhara et al., 2021, Pryszlak et al., 2021, Sureka and Mishra, 2021, Taschuk et al., 2020, Gene Disruption Project members, 2018-, Lee et al., 2016, Sarov et al., 2016, Angrisani et al., 2015, Moy et al., 2014, Thomae et al., 2013, Yamamoto et al., 2013-, Japanese National Institute of Genetics, 2012.5.21, Friedman et al., 2011, Neumüller et al., 2011, Ulvila et al., 2010)

dDDX56

(Taschuk et al., 2020)

hlc

(Hyun et al., 2005, Miklos, 1997.8.4)

l(1)11P1

(Rahman and Lindsley, 1980)

l(1)19Ff

l(1)8-1

l(1)A112

(Miklos et al., 1987, Schalet, 1972)

l(1)S-19F6

l11P1

(Schalet and Singer, 1971)

lA112

(Schalet and Singer, 1971)

Name Synonyms

DEAD-box helicase 56

Helicase

(Meiklejohn et al., 2011)

RNA helicase gene

(Zhou et al., 2002)

helicase

(Maleszka et al., 1998)

lethal(1)19Ff

section 14

(Lifschytz and Falk, 1969)

section 7

(Lifschytz and Falk, 1968)

Secondary FlyBase IDs

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 41 )

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.

33118

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.

Q9VRI0

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.

Q9VRI0

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

33118/tissue=All

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

FBgn0001565

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

FBgn0001565

FlyMine - An integrated database for Drosophila genomics

FBgn0001565

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

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

dme:Dmel_CG1666

MARRVEL_MODEL - MARRVEL (model organism gene)

33118

Linkouts

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

FBgn0001565

DroID - A comprehensive database of gene and protein interactions.

FBgn0001565

DRSC - Results frm RNAi screens

FBgn0001565

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0001565

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0001565

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

CG1666

Flygut - An atlas of the Drosophila adult midgut

FBgn0001565

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

TC001089

References (90)

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

-1.10

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