FlyBase Gene Report: Dmel\lark

General Information

Symbol

Dmel\lark

Species

D. melanogaster

Name

lark

Annotation Symbol

CG8597

Feature Type

protein_coding_gene

FlyBase ID

FBgn0011640

Gene Model Status

Stock Availability

5 publicly available

Gene Summary

lark (lark) encodes an essential RNA-binding protein of the RNA recognition motif (RRM) class. It is implicated in both RNA splicing and translational control. It contributes to oogenesis, tissue development and circadian behavior. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
UniProtKB
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

Sequence location

3L:7,339,266..7,341,893 [+]

Recombination map

3-20

RefSeq locus

NT_037436 REGION:7339266..7341893

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 (22 terms)

Molecular Function (3 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

enables RNA binding

inferred from direct assay

(Huang et al., 2014)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

enables mRNA binding

inferred from biological aspect of ancestor with PANTHER:PTN002751717

(assigned by GO_Central )

(Gaudet et al., 2011)

inferred from sequence or structural similarity

(Lasko, 2000)

enables RNA binding

inferred from biological aspect of ancestor with PANTHER:PTN000567445

(assigned by GO_Central )

(Gaudet et al., 2011)

non-traceable author statement

(assigned by UniProt )

(McNeil et al., 2004)

enables zinc ion binding

inferred from electronic annotation with InterPro:IPR001878

(assigned by InterPro )

(FlyBase Curators et al., 2004-)

Biological Process (15 terms)

Terms Based on Experimental Evidence (12 terms)

CV Term

Evidence

References

involved_in actin cytoskeleton organization

inferred from mutant phenotype

(assigned by UniProt )

(McNeil et al., 2004)

involved_in circadian rhythm

inferred from mutant phenotype

(Newby and Jackson, 1993)

involved_in cytoplasmic transport, nurse cell to oocyte

inferred from mutant phenotype

(assigned by UniProt )

(McNeil et al., 2004)

involved_in eclosion rhythm

inferred from mutant phenotype

(Newby and Jackson, 1993)

inferred from mutant phenotype

(assigned by UniProt )

(Newby and Jackson, 1996)

involved_in embryo development ending in birth or egg hatching

inferred from mutant phenotype

(assigned by UniProt )

(Newby and Jackson, 1993)

involved_in locomotor rhythm

inferred from mutant phenotype

(Sundram et al., 2012)

involved_in mitotic cell cycle

inferred from high throughput mutant phenotype

(Ducat et al., 2008)

involved_in negative regulation of eclosion

inferred from mutant phenotype

(Newby and Jackson, 1993)

inferred from mutant phenotype

(assigned by UniProt )

(Newby and Jackson, 1996)

involved_in positive regulation of cytoplasmic translation

inferred from mutant phenotype

(Huang et al., 2014)

involved_in protein localization

inferred from mutant phenotype

(assigned by UniProt )

(McNeil et al., 2004)

involved_in regulation of circadian rhythm

inferred from mutant phenotype

(Huang et al., 2014)

inferred from genetic interaction with FLYBASE:dco; FB:FBgn0002413

(Huang et al., 2014)

involved_in regulation of embryonic development

inferred from mutant phenotype

(Newby and Jackson, 1993)

Terms Based on Predictions or Assertions (6 terms)

CV Term

Evidence

References

involved_in circadian rhythm

non-traceable author statement

(Sokolowski, 2001)

involved_in eclosion rhythm

traceable author statement

(Stanewsky, 2003, Panda et al., 2002)

non-traceable author statement

(Sokolowski, 2001)

involved_in eclosion

traceable author statement

(Hendricks, 2003)

involved_in locomotor rhythm

traceable author statement

(Panda et al., 2002)

involved_in mRNA splicing, via spliceosome

inferred by curator from GO:0071011,GO:0071013

(Herold et al., 2009)

inferred from biological aspect of ancestor with PANTHER:PTN000567445

(assigned by GO_Central )

(Gaudet et al., 2011)

NOT involved_in locomotion

traceable author statement

(Hendricks, 2003)

Cellular Component (4 terms)

Terms Based on Experimental Evidence (3 terms)

CV Term

Evidence

References

part_of catalytic step 2 spliceosome

inferred from high throughput direct assay

(Herold et al., 2009)

located_in cytoplasm

inferred from direct assay

(assigned by UniProt )

(McNeil et al., 1998)

located_in nucleus

inferred from direct assay

(assigned by UniProt )

(McNeil et al., 2001, McNeil et al., 1998)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

is_active_in nuclear speck

inferred from biological aspect of ancestor with PANTHER:PTN000567445

(assigned by GO_Central )

(Gaudet et al., 2011)

Gene Group (FlyBase)

Protein Family (UniProt)

-

Protein Signatures (InterPro)

Summaries

Gene Snapshot

lark (lark) encodes an essential RNA-binding protein of the RNA recognition motif (RRM) class. It is implicated in both RNA splicing and translational control. It contributes to oogenesis, tissue development and circadian behavior. [Date last reviewed: 2019-03-14]

Protein Function (UniProtKB)

Essential RNA-binding protein. May be required for circadian repression of eclosion. Also essential for nurse cell dumping during oogenesis, the process whereby the cytoplasmic contents of nurse cells are transferred to the oocyte late in it's development.

(UniProt, Q94901)

Gene Model and Products

Number of Transcripts

5

Number of Unique Polypeptides

1

Please see the JBrowse view of Dmel\lark 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

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

Gene model reviewed during 5.45

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)

FBtr0076841

1837

352

FBtr0076842

1650

352

FBtr0076843

1784

352

FBtr0076844

1758

352

FBtr0076845

2087

352

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

FBpp0076552

39.9

352

9.30

FBpp0076553

39.9

352

9.30

FBpp0076554

39.9

352

9.30

FBpp0076555

39.9

352

9.30

FBpp0076556

39.9

352

9.30

Polypeptides with Identical Sequences

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

352 aa isoforms: lark-PA, lark-PB, lark-PC, lark-PD, lark-PE

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

Q94901

Mapped Features

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

External Data

Crossreferences

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

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

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 1 -- 6

organism | ubiquitous | uniform

(McNeil et al., 1999)

embryonic stage 4 -- 6

(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

embryonic brain

(Fisher et al., 2012)

organism | ubiquitous

(Fisher et al., 2012)

larval ventral nerve cord

(Fisher et al., 2012)

northern blot

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 4

Comment: reference stages 0-2 hr AEL

(McNeil et al., 1999)

embryonic stage 17

Comment: reference stages 16-18 hr AEL

(McNeil et al., 1999)

(McNeil et al., 1999)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 4

embryonic cortex

(McNeil et al., 1999)

embryonic stage 4 -- 11

organism | ubiquitous

(McNeil et al., 1999)

embryonic stage 5 -- 11

(McNeil et al., 1999)

adult stage | female & oogenesis

egg chamber | ubiquitous

(McNeil et al., 1999)

(McNeil et al., 1999)

oogenesis & adult stage | female

(McNeil et al., 1999)

(McNeil et al., 1999)

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

• membrane

(Aradska et al., 2015)

day 7 of adulthood -- day 49 of adulthood

(Cammarato et al., 2011)

western blot

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 8

Comment: 0-3.5 hr AEL

(McNeil et al., 1999)

unfertilized egg stage

unfertilized egg

(McNeil et al., 1999)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

part_of catalytic step 2 spliceosome

inferred from high throughput direct assay

(Herold et al., 2009)

located_in cytoplasm

inferred from direct assay

(assigned by UniProt )

(McNeil et al., 1998)

located_in nucleus

inferred from direct assay

(assigned by UniProt )

(McNeil et al., 2001, McNeil et al., 1998)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\lark 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\lark

View exonic expression by tissue for Dmel\lark

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

FBgn0011640

DRscDB

38811/tissue=All

EMBL-EBI Single Cell Expression Atlas

FBgn0011640

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG8597-RA

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

CG8597

Flygut - An atlas of the Drosophila adult midgut

FBgn0011640

Images

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 ( 18 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of lark

Transgenic constructs containing regulatory region of lark

Aberrations (Deficiencies and Duplications) ( 2 )

Inferred from experimentation ( 2 )

Gene duplicated in

(Newby and Jackson, 1996)

Gene disrupted in

(Cook, 2015.11.25)

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

lark¹

lethal (with Df(3L)BSC33)

lark^EY23084

lethal | recessive

lethal - all die before end of P-stage, with Scer\GAL4^elav-C155

lark^UAS.Tag:HA

lethal - all die before end of pupal stage, with Scer\GAL4^Act5C.PHb

lark^UAS.Tag:HA

lethal - all die before end of pupal stage, with Scer\GAL4^Act5C.PU

lark^{dsRNA.UAS.cSb}

lethal - all die during embryonic stage | recessive

lark¹

partially lethal - majority die, with Scer\GAL4^386Y

lark^UAS.Tag:HA

partially lethal - majority die, with Scer\GAL4^dimm-929

lark^UAS.Tag:HA

viable, with Scer\GAL4^Act5C.PU

lark^{dsRNA.UAS.cSa}

viable, with Scer\GAL4^CCAP.PP

lark^UAS.Tag:HA

viable, with Scer\GAL4^P2.4.Pdf

lark^UAS.Tag:HA

viable, with Scer\GAL4^ple.PF

lark^UAS.Tag:HA

viable, with Scer\GAL4^tim.PE

lark^UAS.Tag:HA

Sterility

Allele

female fertile, with lark¹

female fertile, with lark^cMa.Tag:HA

lark¹

female fertile, with lark^{RRM1.RNP2.Tag:HA}

lark¹

female sterile, with lark¹

female sterile, with lark^{RRM1+RTZF.Tag:HA}

lark¹

female sterile, with lark^{RRM2.RNP2.Tag:HA}

lark¹

female sterile, with lark^{RRM2+RTZF.Tag:HA}

lark¹

male fertile, with lark¹

male fertile, with lark^cMa.Tag:HA

lark¹

male fertile, with lark^{RRM1.RNP2.Tag:HA}

lark¹

male fertile, with lark^{RRM1+RTZF.Tag:HA}

lark¹

male fertile, with lark^{RRM2.RNP2.Tag:HA}

lark¹

male fertile, with lark^{RRM2+RTZF.Tag:HA}

lark¹

Other Phenotypes

Allele

abnormal behavior | dominant

lark¹

abnormal eclosion | dominant

lark¹

abnormal eclosion rhythm, with Scer\GAL4^CCAP.PP

lark^UAS.Tag:HA

abnormal eclosion rhythm, with Scer\GAL4^Eh.2.4

lark^UAS.Tag:HA

abnormal eclosion rhythm, with Scer\GAL4^phm.PO

abnormal eclosion rhythm, with Scer\GAL4^tim.PE

lark^UAS.Tag:HA

abnormal eclosion rhythm, with Scer\GAL4^tim.UAS

lark^{dsRNA.UAS.cSb}

abnormal flight, with lark¹

lark^{RRM2.RNP2.Tag:HA}

abnormal flight, with lark^{RRM2.RNP2.Tag:HA}

lark¹

abnormal locomotor rhythm, with Scer\GAL4^P2.4.Pdf

lark^UAS.Tag:HA

abnormal locomotor rhythm, with Scer\GAL4^P2.4.Pdf, lark¹

lark^{dsRNA.UAS.cSb}

abnormal locomotor rhythm, with Scer\GAL4^P2.4.Pdf, lark^{dsRNA.UAS.cSb}

lark¹

abnormal locomotor rhythm, with Scer\GAL4^tim.PE

lark^UAS.Tag:HA

abnormal locomotor rhythm | heat sensitive, with Scer\GAL4^dimm-929

lark^{dsRNA.UAS.cSb}

abnormal locomotor rhythm | heat sensitive, with Scer\GAL4^dimm-929, lark¹

lark^{dsRNA.UAS.cSb}

abnormal locomotor rhythm | heat sensitive, with Scer\GAL4^dimm-929, lark^{dsRNA.UAS.cSb}

lark¹

abnormal locomotor rhythm | heat sensitive, with Scer\GAL4^elav-C155

lark^{dsRNA.UAS.cSb}

abnormal locomotor rhythm | heat sensitive, with Scer\GAL4^elav-C155, lark¹

lark^{dsRNA.UAS.cSb}

abnormal locomotor rhythm | heat sensitive, with Scer\GAL4^elav-C155, lark^{dsRNA.UAS.cSb}

lark¹

abnormal locomotor rhythm | heat sensitive, with Scer\GAL4^Mai179

lark^{dsRNA.UAS.cSb}

abnormal locomotor rhythm | heat sensitive, with Scer\GAL4^Mai179, lark¹

lark^{dsRNA.UAS.cSb}

abnormal locomotor rhythm | heat sensitive, with Scer\GAL4^Mai179, lark^{dsRNA.UAS.cSb}

lark¹

abnormal locomotor rhythm | heat sensitive, with Scer\GAL4^nrv2.PS

lark^{dsRNA.UAS.cSb}

abnormal locomotor rhythm | heat sensitive, with Scer\GAL4^nrv2.PS, lark¹

lark^{dsRNA.UAS.cSb}

abnormal locomotor rhythm | heat sensitive, with Scer\GAL4^nrv2.PS, lark^{dsRNA.UAS.cSb}

lark¹

abnormal locomotor rhythm | heat sensitive, with Scer\GAL4^P2.4.Pdf, lark¹

lark^{dsRNA.UAS.cSb}

abnormal locomotor rhythm | heat sensitive, with Scer\GAL4^P2.4.Pdf, lark^{dsRNA.UAS.cSb}

lark¹

abnormal locomotor rhythm | heat sensitive, with Scer\GAL4^tim.UAS

lark^{dsRNA.UAS.cSb}

abnormal locomotor rhythm | heat sensitive, with Scer\GAL4^tim.UAS, lark¹

lark^{dsRNA.UAS.cSb}

abnormal locomotor rhythm | heat sensitive, with Scer\GAL4^tim.UAS, lark^{dsRNA.UAS.cSb}

lark¹

flightless, with lark¹

flightless, with lark^{RRM1+RTZF.Tag:HA}

lark¹

flightless, with lark^{RRM2+RTZF.Tag:HA}

lark¹

flightless, with lark^ZF.Tag:HA

lark¹

some die during embryonic stage | recessive

lark¹

some die during pharate adult stage, with Scer\GAL4^386Y

lark^UAS.Tag:HA

some die during pharate adult stage, with Scer\GAL4^dimm-929

lark^UAS.Tag:HA

some die during pharate adult stage, with Scer\GAL4^elav-C155

lark^UAS.Tag:HA

some die during pupal stage, with Scer\GAL4^Act5C.PHb

lark^UAS.Tag:HA

some die during pupal stage, with Scer\GAL4^Act5C.PU

lark^{dsRNA.UAS.cSb}

visible, with lark¹

visible, with lark^{RRM2.RNP2.Tag:HA}

lark¹

visible, with lark^{RRM2+RTZF.Tag:HA}

lark¹

visible, with lark^ZF.Tag:HA

lark¹

visible, with Scer\GAL4^386Y

lark^UAS.Tag:HA

visible, with Scer\GAL4^bbg-C96

lark^d04807

visible, with Scer\GAL4^CCAP.PP

lark^UAS.Tag:HA

visible, with Scer\GAL4^Eh.2.4

lark^UAS.Tag:HA

Phenotype manifest in

Allele

adult cuticle, with Scer\GAL4^386Y

lark^UAS.Tag:HA

adult cuticle, with Scer\GAL4^CCAP.PP

lark^UAS.Tag:HA

adult cuticle, with Scer\GAL4^Eh.2.4

lark^UAS.Tag:HA

adult cuticle, with Scer\GAL4^elav-C155

lark^UAS.Tag:HA

embryo | germline clone

lark¹

posterior scutellar bristle, with lark¹

lark^ZF.Tag:HA

posterior scutellar bristle, with lark^ZF.Tag:HA

lark¹

scutellar bristle, with lark¹

scutellar bristle, with lark^{RRM2.RNP2.Tag:HA}

lark¹

scutellar bristle, with lark^{RRM2+RTZF.Tag:HA}

lark¹

scutellar bristle, with lark^ZF.Tag:HA

lark¹

scutellar bristle | ectopic, with lark¹

lark^ZF.Tag:HA

scutellar bristle | ectopic, with lark^ZF.Tag:HA

lark¹

wing, with lark¹

wing, with lark^{RRM2.RNP2.Tag:HA}

lark¹

wing, with lark^{RRM2+RTZF.Tag:HA}

lark¹

wing, with lark^ZF.Tag:HA

lark¹

wing, with Scer\GAL4^386Y

lark^UAS.Tag:HA

wing, with Scer\GAL4^bbg-C96

lark^d04807

wing, with Scer\GAL4^CCAP.PP

lark^UAS.Tag:HA

wing, with Scer\GAL4^Eh.2.4

lark^UAS.Tag:HA

wing, with Scer\GAL4^elav-C155

lark^UAS.Tag:HA

Orthologs

Downloads

Download All DIOPT Orthologs

Download All OrthoDB Orthologs

Human Orthologs (via DIOPT v8.0)

Homo sapiens (Human) (24)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

10 of 15

Yes

Yes

1

9 of 15

No

Yes

4 of 15

No

Yes

Hsap\RBM14-RBM4

3 of 15

No

Yes

1 of 15

No

No

2

1 of 15

No

No

3

1 of 15

No

No

2

1 of 15

No

No

1 of 15

No

No

1 of 15

No

Yes

1 of 15

No

Yes

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

Yes

1 of 15

No

No

1 of 15

No

Yes

1 of 15

No

No

1

1 of 15

No

No

1 of 15

No

No

1

Model Organism Orthologs (via DIOPT v8.0)

Mus musculus (laboratory mouse) (22)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

11 of 15

Yes

Yes

9 of 15

No

Yes

3 of 15

No

Yes

3 of 15

No

Yes

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

Yes

1 of 15

No

No

1 of 15

No

Yes

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

Rattus norvegicus (Norway rat) (20)

6 of 13

Yes

Yes

4 of 13

No

Yes

4 of 13

No

Yes

1 of 13

No

No

1 of 13

No

No

1 of 13

No

No

1 of 13

No

No

1 of 13

No

No

1 of 13

No

No

1 of 13

No

No

1 of 13

No

No

1 of 13

No

No

1 of 13

No

No

1 of 13

No

No

1 of 13

No

No

1 of 13

No

Yes

1 of 13

No

No

1 of 13

No

No

1 of 13

No

No

1 of 13

No

No

Xenopus tropicalis (Western clawed frog) (16)

8 of 12

Yes

Yes

5 of 12

No

Yes

2 of 12

No

Yes

1 of 12

No

No

1 of 12

No

No

1 of 12

No

No

1 of 12

No

No

1 of 12

No

No

1 of 12

No

No

1 of 12

No

No

1 of 12

No

Yes

1 of 12

No

No

1 of 12

No

Yes

1 of 12

No

No

1 of 12

No

No

1 of 12

No

No

Danio rerio (Zebrafish) (25)

11 of 15

Yes

Yes

10 of 15

No

Yes

9 of 15

No

Yes

8 of 15

No

Yes

5 of 15

No

Yes

4 of 15

No

Yes

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

Yes

1 of 15

No

No

1 of 15

No

Yes

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

1 of 15

No

No

Caenorhabditis elegans (Nematode, roundworm) (3)

9 of 15

Yes

Yes

1 of 15

No

No

1 of 15

No

Yes

Arabidopsis thaliana (thale-cress) (13)

1 of 9

Yes

Yes

1 of 9

Yes

Yes

1 of 9

Yes

No

1 of 9

Yes

Yes

1 of 9

Yes

No

1 of 9

Yes

Yes

1 of 9

Yes

Yes

1 of 9

Yes

Yes

1 of 9

Yes

Yes

1 of 9

Yes

Yes

1 of 9

Yes

No

1 of 9

Yes

No

1 of 9

Yes

No

Saccharomyces cerevisiae (Brewer's yeast) (0)

No records found.

Schizosaccharomyces pombe (Fission yeast) (2)

Spom\SPBC1861.04c

1 of 12

Yes

No

1 of 12

Yes

Yes

Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG09190CB2 )

Organism

Common Name

Gene

AAA Syntenic Ortholog

Multiple Dmel Genes in this Orthologous Group

Drosophila suzukii

Spotted wing Drosophila

Dsuz\DS10_00007243

Drosophila simulans

Drosophila erecta

Drosophila yakuba

Drosophila ananassae

Drosophila pseudoobscura pseudoobscura

Drosophila willistoni

Drosophila virilis

Drosophila mojavensis

Drosophila mojavensis

Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG09150AV9 )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Musca domestica

House fly

Glossina morsitans

Tsetse fly

Gmor\GMOY003846

Lucilia cuprina

Australian sheep blowfly

Lcup\FF38_03467

Mayetiola destructor

Hessian fly

Mdes\Mdes002638

Aedes aegypti

Yellow fever mosquito

Aaeg\AAEL013982

Anopheles darlingi

American malaria mosquito

Adar\ADAC001514

Culex quinquefasciatus

Southern house mosquito

Cqui\CPIJ009028

Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W0CGH )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Bombyx mori

Silkmoth

Bmor\BGIBMGA007410

Bombyx mori

Silkmoth

Bmor\BGIBMGA007418

Danaus plexippus

Monarch butterfly

Dple\DPOGS213215-PA

Danaus plexippus

Monarch butterfly

Dple\DPOGS213222-PA

Heliconius melpomene

Postman butterfly

Hmel\HMEL017088

Heliconius melpomene

Postman butterfly

Hmel\HMEL017077

Apis florea

Little honeybee

Aflo\2985342964

Apis florea

Little honeybee

Aflo\2985342900

Apis mellifera

Western honey bee

Apis mellifera

Western honey bee

Bombus impatiens

Common eastern bumble bee

Bombus impatiens

Common eastern bumble bee

Bombus terrestris

Buff-tailed bumblebee

Bombus terrestris

Buff-tailed bumblebee

Linepithema humile

Argentine ant

Linepithema humile

Argentine ant

Megachile rotundata

Alfalfa leafcutting bee

Mrot\MROTU:002d47

Megachile rotundata

Alfalfa leafcutting bee

Mrot\MROTU:002d48

Nasonia vitripennis

Parasitic wasp

Nvit\Nasvi2EG002440

Nasonia vitripennis

Parasitic wasp

Nvit\Nasvi2EG002443

Dendroctonus ponderosae

Mountain pine beetle

Dendroctonus ponderosae

Mountain pine beetle

Tribolium castaneum

Red flour beetle

Tribolium castaneum

Red flour beetle

Tribolium castaneum

Red flour beetle

Pediculus humanus

Human body louse

Phum\PHUM127280

Pediculus humanus

Human body louse

Phum\PHUM127250

Rhodnius prolixus

Kissing bug

Rpro\RPRC004065

Rhodnius prolixus

Kissing bug

Rpro\RPRC014260

Cimex lectularius

Bed bug

Clec\CLEC012360

Cimex lectularius

Bed bug

Clec\CLEC012359

Cimex lectularius

Bed bug

Clec\CLEC008070

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI003989

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI003756

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI008316

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI060559

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI010087

Zootermopsis nevadensis

Nevada dampwood termite

Znev\Znev_17217

Zootermopsis nevadensis

Nevada dampwood termite

Znev\Znev_04523

Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0CE9 )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strigamia maritima

European centipede

Smar\SMAR004399

Ixodes scapularis

Black-legged tick

Isca\ISCW021148

Stegodyphus mimosarum

African social velvet spider

Smim\KFM60217.1

Stegodyphus mimosarum

African social velvet spider

Smim\KFM71389.1

Stegodyphus mimosarum

African social velvet spider

Smim\KFM58991.1

Tetranychus urticae

Two-spotted spider mite

Turt\tetur07g05720

Tetranychus urticae

Two-spotted spider mite

Turt\tetur32g01790

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_45130

Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0JQC )

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

Strongylocentrotus purpuratus

Purple sea urchin

Ciona intestinalis

Vase tunicate

Cint\ENSCING00000004452

Ciona intestinalis

Vase tunicate

Cint\ENSCING00000008757

Gallus gallus

Domestic chicken

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v8.0)

Drosophila melanogaster (Fruit fly) (23)

Gene Symbol

Score

Source

Alignment

2 of 10

2 of 10

2 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

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 ( 0 )

Human Ortholog

Disease

Evidence

References

Modifiers Based on Experimental Evidence ( 1 )

Allele

Disease

Interaction

References

ameliorates frontotemporal dementia and/or amyotrophic lateral sclerosis-1

modeled by Zzzz\poly-GR^50.UAS.EGFP

(Lee et al., 2016)

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?

RBM4; RNA binding motif protein 4

10 of 15

RBM4B; RNA binding motif protein 4B

9 of 15

RBM14; RNA binding motif protein 14

4 of 15

RBM14-RBM4; RBM14-RBM4 readthrough

3 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

(Sofola et al., 2008)

lark - Nipped-B

anti bait coimmunoprecipitation, western blot, pull down

(Swain et al., 2016)

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based

(Rhee et al., 2014)

anti tag coimmunoprecipitation, peptide massfingerprinting

(Friedman et al., 2011)

anti tag coimmunoprecipitation, peptide massfingerprinting

(Friedman et al., 2011)

lark - qkr58E-1

anti tag coimmunoprecipitation, anti tag western blot

(Stoiber et al., 2015)

pull down, western blot

(Swain et al., 2016)

RNA-protein

Physical Interaction

Assay

References

pull down, quantitative reverse transcription pcr

(Swain et al., 2016)

pull down, quantitative reverse transcription pcr

(Swain et al., 2016)

nucleic acid uv cross-linking assay, autoradiography, anti bait coimmunoprecipitation, primer specific pcr

(Huang et al., 2014)

pull down, quantitative reverse transcription pcr

(Swain et al., 2016)

pull down, quantitative reverse transcription pcr

(Swain et al., 2016)

pull down, quantitative reverse transcription pcr

(Swain et al., 2016)

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

suppressible

(Huang et al., 2014)

enhanceable

(Huang et al., 2014)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

enhanceable

(Kankel et al., 2007)

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

64251

DroID - A comprehensive database of gene and protein interactions.

FBgn0011640

MIST (genetic) - An integrated Molecular Interaction Database

lark

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

lark

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

Genomic Location and Detailed Mapping Data

Chromosome (arm)

3L

Recombination map

3-20

Cytogenetic map

Sequence location

3L:7,339,266..7,341,893 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

65F5-65F5

Limits computationally determined from genome sequence between P{lacW}Cdc27^L7123 and P{EP}lark^EP3259&P{lacW}l(3)j1D5^j1D5

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

65E-65F

(Newby, 1996.5.29)

Experimentally Determined Recombination Data

Location

3-20

(FlyBase, 2016)

3-17.1

(Comeron et al., 2012)

3-

(Newby, 1996.5.29)

3-17.8

(Newby and Jackson, 1993)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (5)

7125

w¹¹¹⁸; P{UAS-lark-3HA}23A

27703

y¹ v¹; P{TRiP.JF02783}attP2

15287

y¹ w^67c23; P{EPgy2}lark^EY00297 eco^EY00297

22604

y¹ w^67c23; P{EPgy2}lark^EY23084/TM3, Sb¹ Ser¹

v108993

P{KK107711}VIE-260B

Genomic Clones (14)

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

cDNA Clones (103)

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

LD40792

Other clones

DPiM_LD40792

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.

FBgn0011640

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0011640

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

38811

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Swain et al., 2016, Newby and Jackson, 1996)

Commercially Available Antibodies

Other Information

Relationship to Other Genes

Source for database identify of

Source for database merge of

Additional comments

Other Comments

The lark RNA-binding protein oscillates in abundance during the circadian cycle.

(McNeil et al., 1998)

Results from mRNA expression pattern studies and gene dosage experiments suggest lark is required for the posttranscriptional repression of genes encoding other elements of the clock output pathway.

(Newby and Jackson, 1996)

The lark gene encodes an essential embryonic product which is also required later in development for the daily timing of adult eclosion. The lark protein is a repressor, a member of the RNP (RMM) class of RNA-binding proteins, which mediates inhibition of eclosion until an appropriate time of day.

(Newby and Jackson, 1995)

Mutants of lark alter the timing of eclosion but do not perturb circadian period or the expression of the activity rhythm. lark gene product has an essential function and is one element of the output pathway mediating the pacemaker control of eclosion.

(Newby and Jackson, 1993)

Origin and Etymology

Discoverer

Etymology

Identification

External Crossreferences and Linkouts ( 60 )

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.

38811

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

Q94901

Other crossreferences

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0011640

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

FBgn0011640

DRscDB

38811/tissue=All

EMBL-EBI Single Cell Expression Atlas

FBgn0011640

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

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

CG8597

Flygut - An atlas of the Drosophila adult midgut

FBgn0011640

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

38811

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

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

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

Dmel_CG8597

MARRVEL_MODEL

38811

modMine - A data warehouse for the modENCODE project

FBgn0011640

Linkouts

BioGRID - A database of protein and genetic interactions.

64251

DroID - A comprehensive database of gene and protein interactions.

FBgn0011640

DRSC - Results frm RNAi screens

FBgn0011640

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG8597-RA

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0011640

FlyMine - An integrated database for Drosophila genomics

FBgn0011640

MIST (genetic) - An integrated Molecular Interaction Database

lark

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

lark

Synonyms and Secondary IDs (5)

Reported As

Symbol Synonym

CG8597

(Kolkhof et al., 2017, Rosa-Ferreira et al., 2015, Cammarato et al., 2011, Herold et al., 2009, Keleman et al., 2009.8.5, Perkins et al., 2009, Ducat et al., 2008)

LARK

(Niu et al., 2019, Tataroglu and Emery, 2015, Huang et al., 2014, Lim and Allada, 2013, Staiger and Koster, 2011, Sofola et al., 2007, Levine, 2004)

Lark

(Kochanova et al., 2020, Swain et al., 2016, Lu et al., 2013, Ducat et al., 2008, Lai et al., 2003)

dLARK

(Huang et al., 2007)

lark

(Sapiro et al., 2020, Lee et al., 2016, Stoiber et al., 2015, Kwon et al., 2013, Japanese National Institute of Genetics, 2012.5.21, Sundram et al., 2012, Friedman et al., 2011, Arancio et al., 2010, Kallappagoudar et al., 2010, Herold et al., 2009, Huang et al., 2009, McNeil et al., 2008, Sofola et al., 2008, Kankel et al., 2007, Sofola et al., 2007, Martin et al., 2005, Schroeder et al., 2003, Newby and Jackson, 1996)

Name Synonyms

lark

(Cammarato et al., 2011, McNeil et al., 2009, Newby and Jackson, 1995)

Secondary FlyBase IDs

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

References (114)

Report Sections