FlyBase Gene Report: Dmel\Clk

adult head

(Kadener et al., 2006)

adult brain

Comment: Clk mRNA expression is lower in ZT16 than in ZT4.

(Kadener et al., 2006)

adult fat body

Comment: cyclical, peak ZT1-4

(Xu et al., 2011)

RT-PCR

Stage

Tissue/Position (including subcellular localization)

Reference

adult head

(Zheng et al., 2009)

adult oenocyte

Comment: displays circadian cycling

(Krupp et al., 2008)

adult stage | male

organism

Comment: circadian oscillating expression

(Rakshit et al., 2012)

Additional Descriptive Data

Expression oscillates with the circadian cycle and peaks at ZT0. The relative amount of mRNA is less in bodies compared to heads.

(Rakshit et al., 2012)

Expressed cyclically in the adult fat body.

(Xu et al., 2011)

RT-PCR analysis indicates that the levels of the Clk transcript cycle when in light:dark conditions, in anti-phase with the levels of the per transcript. Clk transcript levels decrease gradually from ZT02 to ZT14, and increase after that until ZT20. In conditions of constant darkness the cycling behaviour is abolished. Clk transcript levels gradually increase from CT02 until CT14 and are maintained after that until CT20.

(Zheng et al., 2009)

Clk is expressed in adult oenocytes and shows a sinusoidal expression pattern with a peak during the day and a trough at night.

(Krupp et al., 2008)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

LP neuron

(Liu et al., 2015)

(Liu et al., 2015)

larval LNd neuron

(Liu et al., 2015)

(Liu et al., 2015)

LNd neuron

Comment: at CT09

(Zheng et al., 2009)

LNv neuron

Comment: at CT09

(Zheng et al., 2009)

DN1 neuron

Comment: at ZT11

(Zheng et al., 2009)

western blot

Stage

Tissue/Position (including subcellular localization)

Reference

adult head

(Zheng et al., 2009)

adult fat body

Comment: displays circadian cycling

(Xu et al., 2008)

Additional Descriptive Data

Expression of Clk protein was analyzed at zeitgeber time 12 and 22.

(Liu et al., 2015)

The Clk protein is detected in the dorsal and ventral lateral (LNd and LNv) and dorsal (DN1) clock neurons in the adult brain. Western blot analysis in adult head extracts indicates that in light:dark conditions, Clk protein shows a cycling behaviour, with its peak level at ZT08. In conditions of constant darkness, cycling is dampened.

(Zheng et al., 2009)

Clk protein levels undergo circadian cycling. In adult heads, protein levels reach a peak between (zeitgeber times) ZT23.5 and ZT4 and a minimum between ZT11.5 and ZT16. The time course for the accumulation of Clk mRNA and Clk protein is similar. Circadian cycling of Clk protein levels continues for at least 2 days under dark conditions.

(Lee et al., 1998)

Marker for

Subcellular Localization

CV Term

Evidence

References

part_of CLOCK-BMAL transcription complex

inferred from direct assay

(Lee et al., 2016)

Expression Deduced from Reporters

Reporter: P{Clk-GAL4.1.5}

Stage

Tissue/Position (including subcellular localization)

Reference

DN1p neuron | subset

(Zhang et al., 2010)

DN1p neuron

(Cavanaugh et al., 2014)

DN1 neuron

(Guo et al., 2016)

Reporter: P{Clk-GAL4.8.0}

Stage

Tissue/Position (including subcellular localization)

Reference

LNv neuron

(Lear et al., 2005)

LNd neuron | subset

(Lear et al., 2005)

DN1 neuron | subset

(Lear et al., 2005)

DN3 neuron | subset

(Lear et al., 2005)

Reporter: P{Clk-GAL4.-84}

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic/larval brain | restricted

Bolwig nerve

(Gummadova et al., 2009)

(Gummadova et al., 2009)

larval DN period neuron | subset

(Gummadova et al., 2009)

larval LN period neuron | subset

(Gummadova et al., 2009)

DN1a neuron

(Gummadova et al., 2009)

DN2 neuron

(Gummadova et al., 2009)

LNd neuron | subset

(Gummadova et al., 2009)

l-LNv neuron | subset

(Gummadova et al., 2009)

Reporter: P{Clk-GAL4.-206}

Stage

Tissue/Position (including subcellular localization)

Reference

larval DN period neuron | subset

(Gummadova et al., 2009)

larval LN period neuron | subset

(Gummadova et al., 2009)

s-LNv neuron

(Gummadova et al., 2009)

DN1a neuron

(Gummadova et al., 2009)

DN2 neuron

(Gummadova et al., 2009)

LNd neuron

(Gummadova et al., 2009)

l-LNv neuron | subset

(Gummadova et al., 2009)

Reporter: P{Clk-GAL4.-856}

Stage

Tissue/Position (including subcellular localization)

Reference

LN period neuron

(Gummadova et al., 2009)

adult DN period neuron

(Gummadova et al., 2009)

LP neuron | faint

(Gummadova et al., 2009)

s-LNv neuron

(Fujiwara et al., 2018)

l-LNv neuron

(Fujiwara et al., 2018)

Reporter: P{Clk-GAL4.-1982}

Stage

Tissue/Position (including subcellular localization)

Reference

local interneuron of adult antennal lobe | subset

LN period neuron

(Gummadova et al., 2009)

adult DN period neuron

(Gummadova et al., 2009)

eye photoreceptor cell

• neuron projection terminus

(Gummadova et al., 2009)

Kenyon cell

(Gummadova et al., 2009)

(Gummadova et al., 2009)

adult brain | restricted

(Gummadova et al., 2009)

Reporter: P{Clk-GAL4.-6939}

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 16

(Gummadova et al., 2009)

first instar larval stage

(Gummadova et al., 2009)

(Gummadova et al., 2009)

(Gummadova et al., 2009)

(Gummadova et al., 2009)

(Gummadova et al., 2009)

Reporter: P{Clk-GAL4.int1-3}

Stage

Tissue/Position (including subcellular localization)

Reference

DN2 neuron

(Kaneko et al., 2012)

s-LNv Pdf neuron

(Kaneko et al., 2012)

Reporter: P{Clk-lexA.4.1M}

Stage

Tissue/Position (including subcellular localization)

Reference

DN1p neuron

(Cavanaugh et al., 2014)

DN1 neuron

(Guo et al., 2016)

Reporter: P{GMR43D05-GAL4}

Stage

Tissue/Position (including subcellular localization)

Reference

first instar larval stage

adult pacemaker neuron

(Kunst et al., 2014)

Reporter: PBac{Clk-V5-GFP}

Stage

Tissue/Position (including subcellular localization)

Reference

larval DN1 neuron

Comment: 48h AEL

(Liu et al., 2015)

larval DN2 neuron

Comment: 48h AEL

(Liu et al., 2015)

second instar larval stage

Comment: 48h AEL

(Liu et al., 2015)

larval DN1 neuron

Comment: 60h AEL

(Liu et al., 2015)

larval DN2 neuron

Comment: 60h AEL

(Liu et al., 2015)

larval LNd neuron

Comment: 72h AEL

(Liu et al., 2015)

Comment: 60h AEL

(Liu et al., 2015)

LP neuron

(Liu et al., 2015)

(Liu et al., 2015)

larval LNd neuron

(Liu et al., 2015)

View Dmel\Clk in GBrowse 2

(Liu et al., 2015)

pupal stage P6 -- P7

LP neuron

(Liu et al., 2015)

s-LNv neuron

(Liu et al., 2015)

pupal DN period neuron

(Liu et al., 2015)

pupal stage P7

LNv neuron

(Liu et al., 2015)

pharate adult stage P8 -- adult stage

(Liu et al., 2015)

(Liu et al., 2015)

(Liu et al., 2015)

(Liu et al., 2015)

(Liu et al., 2015)

(Liu et al., 2015)

(Liu et al., 2015)

High-Throughput Expression Data

Associated Tools

GBrowse - Visual display of RNA-Seq signals

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

View exonic expression by developmental stage for Dmel\Clk

View exonic expression by tissue for Dmel\Clk

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

FBgn0023076

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

38872/tissue=All

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

FBgn0023076

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0023076

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

FBgn0023076

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

CG7391

Flygut - An atlas of the Drosophila adult midgut

FBgn0023076

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 7 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 39 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Clk

Transgenic constructs containing regulatory region of Clk

Aberrations (Deficiencies and Duplications) ( 8 )

Inferred from experimentation ( 8 )

Gene disrupted in

Df(3L)HnD-1

(Allada et al., 2003, Allada et al., 1998)

Df(3L)pbl-X1

(Allada et al., 1998)

Df(3L)RM5-2

(Allada et al., 1998)

Gene not disrupted in

Df(3L)29A6

(Allada et al., 1998)

Df(3L)AC1

(Allada et al., 1998)

Df(3L)h-i22

(Allada et al., 1998)

Df(3L)HnD-2

(Allada et al., 1998)

Df(3L)lxd6

(Allada et al., 1998)

Inferred from location ( 0 )

Alleles Representing Disease-Implicated Variants

Phenotypes

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

Lethality

Allele

lethal, with Scer\GAL4^unspecified

Clk^UAS.cZa

viable

Clk^out

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

Clk^GD1297

viable, with Scer\GAL4^cry.PE

Clk^UAS.cZa

viable, with Scer\GAL4^cry.PZ

Clk^UAS.cZa

viable, with Scer\GAL4^Mef2.PR

Clk^GD1297

viable, with Scer\GAL4^MJ162A

Clk^UAS.cZa

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

Clk^UAS.cZa

viable, with Scer\GAL4^pnr-MD237

Clk^GD1297

viable, with Scer\GAL4^tin.CΔ4

Clk^GD1297

Other Phenotypes

Allele

abnormal behavior

abnormal circadian behavior, with Scer\GAL4^P2.4.Pdf

abnormal circadian rhythm

abnormal circadian rhythm, with Scer\GAL4^cry.PE

Clk^UAS.cZa

abnormal circadian rhythm, with Scer\GAL4^cry.PZ

Clk^UAS.cZa

abnormal circadian rhythm, with Scer\GAL4^Or22a.8197

Clk^{Δ.UAS.Tag:HA}

abnormal circadian rhythm, with Scer\GAL4^{Orco.2.642.Hsim\VP22}

Clk^{Δ.UAS.Tag:HA}

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

Clk^{Δ.UAS.Tag:HA}

abnormal circadian rhythm, with Scer\GAL4^to.PD

Clk^DN.UAS

abnormal circadian rhythm, with Scer\GAL4^yolk

Clk^DN.UAS

abnormal circadian rhythm (with Clk^out)

abnormal circadian rhythm (with Clk^S258A.Tag:V5)

Clk^out

abnormal circadian rhythm (with Clk^{S476A.S482A.S487A.Tag:V5})

Clk^out

abnormal circadian rhythm (with Clk^{S476A.S482A.Tag:V5})

Clk^out

abnormal circadian rhythm (with Clk^S487A.Tag:V5)

Clk^out

abnormal circadian rhythm (with Clk^S525A.Tag:V5)

Clk^out

abnormal circadian rhythm (with Clk^S859A.Tag:V5)

Clk^out

abnormal circadian rhythm (with Clk^S912A.Tag:V5)

Clk^out

abnormal circadian rhythm (with Df(3L)BSC631)

Clk^out

abnormal circadian rhythm | adult stage

abnormal circadian rhythm | adult stage, with Clk^out

abnormal circadian rhythm | adult stage, with Clk^Tag:V5.WT

Clk^out

abnormal circadian rhythm | adult stage, with Clk^{Δ657-707.Tag:V5}

Clk^out

abnormal eclosion rhythm

Clk^Jrk

abnormal feeding behavior, with Scer\GAL4^{Orco.2.642.Hsim\VP22}

Clk^DN.UAS

abnormal feeding behavior, with Scer\GAL4^to.PD

Clk^DN.UAS

abnormal locomotor rhythm

abnormal locomotor rhythm, with Clk^15A.Tag:V5

Clk^out

abnormal locomotor rhythm, with Clk^out

Clk^15A.Tag:V5

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

Clk^UAS.cZa

abnormal locomotor rhythm, with Scer\GAL4^cry.PZ

Clk^UAS.cZa

abnormal locomotor rhythm, with Scer\GAL4^P0.5.Pdf

Clk^{Δ.UAS.Tag:HA}

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

Clk^{Δ.UAS.Tag:HA}

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

Clk^{Δ.UAS.Tag:HA}

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

Clk^dsRNA.UAS

abnormal locomotor rhythm, with Scer\GAL4^to.PD

Clk^DN.UAS

abnormal locomotor rhythm (with Clk^ar)

Clk^Jrk

abnormal locomotor rhythm (with Clk^Jrk)

abnormal locomotor rhythm (with Clk^Z3-0084)

Clk^Jrk

abnormal locomotor rhythm (with Df(3L)HnD-1)

Clk^ar

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

Clk^UAS.cZa

abnormal locomotor rhythm | dominant

Clk^Jrk

abnormal locomotor rhythm | recessive

Clk^ar

abnormal locomotor rhythm | semidominant

Clk^Jrk

abnormal sleep

Clk^Jrk

abnormal sleep, with Scer\GAL4^P2.4.Pdf

Clk^{Δ.UAS.Tag:HA}

abnormal temperature response

Clk^Tag:V5.WT

abnormal temperature response, with Clk^15A.Tag:V5

Clk^out

abnormal temperature response, with Clk^out

Clk^15A.Tag:V5

abnormal visual behavior

Clk^Jrk

increased cell death | progressive

Clk^Jrk

visible, with Scer\GAL4^Bx-MS1096

Clk^KK108194

Phenotype manifest in

Allele

adult heart

Clk^ar

head

Clk^Jrk

Download All DIOPT Orthologs

Clk^Jrk

Pdf neuron

pupal Pdf neuron

Clk^SV40.Tag:V5

wing, with Scer\GAL4^Bx-MS1096

Clk^KK108194

Orthologs

Downloads

Human Orthologs (via DIOPT v8.0)

Homo sapiens (Human) (11)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Hsap\CLOCK

10 of 15

Yes

Hsap\NPAS2

10 of 15

Yes

Hsap\PASD1

4 of 15

Yes

2 of 15

1 of 15

1 of 15

1 of 15

1 of 15

Yes

Hsap\NCOA1

1 of 15

Hsap\NCOA2

1 of 15

Hsap\NCOA3

1 of 15

Model Organism Orthologs (via DIOPT v8.0)

Mus musculus (laboratory mouse) (9)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Clock

10 of 15

Yes

Mmus\Npas2

10 of 15

Yes

2 of 15

2 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

Rattus norvegicus (Norway rat) (9)

Rnor\Clock

8 of 13

Yes

Rnor\Npas2

8 of 13

Yes

2 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Xenopus tropicalis (Western clawed frog) (9)

Xtro\clock

4 of 12

Yes

Xtro\pasd1

4 of 12

Yes

Xtro\arnt2

2 of 12

Xtro\npas2

2 of 12

Yes

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

Danio rerio (Zebrafish) (11)

Drer\clocka

10 of 15

Yes

Drer\npas2

9 of 15

Yes

Drer\clockb

8 of 15

Yes

2 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

Caenorhabditis elegans (Nematode, roundworm) (2)

Cele\aha-1

1 of 15

Yes

Cele\hif-1

1 of 15

Yes

Arabidopsis thaliana (thale-cress) (0)

No records found.

Saccharomyces cerevisiae (Brewer's yeast) (0)

No records found.

Schizosaccharomyces pombe (Fission yeast) (0)

No records found.

Other Organism Orthologs (via OrthoDB)

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v8.0)

Drosophila melanogaster (Fruit fly) (5)

Gene Symbol

Score

Source

Alignment

gce

2 of 10

Met

2 of 10

tgo

2 of 10

cyc

1 of 10

tai

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 ( 0 )

Allele

Disease

Interaction

References

Disease Associations of Human Orthologs (via DIOPT v8.0 and OMIM)

Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.

Homo sapiens (Human)

Gene name

Score

OMIM

OMIM Phenotype

DO term

Complementation?

Transgene?

CLOCK; clock circadian regulator

10 of 15

601851

NPAS2; neuronal PAS domain protein 2

10 of 15

603347

PASD1; PAS domain containing repressor 1

4 of 15

300993

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

Clk - Bap111

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Kwok et al., 2015)

Clk - Bap55

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Kwok et al., 2015)

Clk - Bap60

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Kwok et al., 2015)

Clk - CkIIα

anti tag coimmunoprecipitation, western blot

(Szabó et al., 2013)

Clk - CkIIβ

anti tag coimmunoprecipitation, western blot

(Szabó et al., 2013)

Clk - Cka

anti bait coimmunoprecipitation, anti tag western blot

(Andreazza et al., 2015)

Clk - Nipped-A

anti tag coimmunoprecipitation, Identification by mass spectrometry, anti tag western blot

(Mahesh et al., 2020)

Clk - Oga

anti tag coimmunoprecipitation, anti tag western blot, western blot

(Kaasik et al., 2013)

Clk - SNF4Aγ

anti tag coimmunoprecipitation, anti tag western blot

(Cho et al., 2019)

Clk - Snr1

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Kwok et al., 2015)

Clk - Strip

anti bait coimmunoprecipitation, anti tag western blot

(Andreazza et al., 2015)

Clk - Usp8

anti tag coimmunoprecipitation, western blot, anti tag western blot

(Luo et al., 2012)

Clk - brm

anti tag coimmunoprecipitation, anti tag western blot, Identification by mass spectrometry, western blot

(Kwok et al., 2015, Kwok et al., 2015)

Clk - cyc

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

(Liu et al., 2017, Lee et al., 2016, Lee et al., 2014, Cheng et al., 2013, Kazemian et al., 2013, Maurer et al., 2009, Hung et al., 2007, Ceriani et al., 1999, Lee et al., 1999, Darlington et al., 1998)

Clk - dco

anti bait coimmunoprecipitation, western blot, anti tag coimmunoprecipitation

(Menet et al., 2010, Yu et al., 2009)

Clk - mor

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Kwok et al., 2015)

Clk - nej

anti bait coimmunoprecipitation, autoradiography

(Hung et al., 2007)

Clk - nonA

anti tag coimmunoprecipitation, western blot, tandem affinity purification, Identification by mass spectrometry

(Luo et al., 2018)

Clk - per

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

(Li et al., 2019, Agrawal et al., 2017, Fu et al., 2016, Lee et al., 2016, Lee et al., 2014, Kaasik et al., 2013, Menet et al., 2010, Sun et al., 2010, Kim et al., 2007, Lee et al., 1999)

Clk - sxc

anti tag coimmunoprecipitation, anti tag western blot

(Kaasik et al., 2013)

Clk - tim

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

(Lee et al., 2016, Menet et al., 2010, Sun et al., 2010, Lee et al., 1999)

RNA-protein

Physical Interaction

Assay

References

Clk - Atx2

anti tag coimmunoprecipitation, primer specific pcr, quantitative reverse transcription pcr

(Lee et al., 2017, Lim and Allada, 2013)

RNA-RNA

Physical Interaction

Assay

References

Clk - mir-ban

luminiscence technology, necessary binding region

(Kadener et al., 2009)

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

cyc

(Kadener et al., 2008)

suppressible

wake

(Liu et al., 2014)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

nmo

enhanceable

(Mahesh et al., 2014)

shn

suppressible