FlyBase Gene Report: Dmel\Cdk9

General Information

Symbol

Dmel\Cdk9

Species

D. melanogaster

Name

Cyclin-dependent kinase 9

Annotation Symbol

CG5179

Feature Type

protein_coding_gene

FlyBase ID

FBgn0019949

Gene Model Status

Current

Stock Availability

17 publicly available

Enzyme Name (EC)

cyclin-dependent kinase (2.7.11.22)

[RNA-polymerase]-subunit kinase (2.7.11.23)

Gene Summary

Cyclin-dependent kinase 9 (Cdk9) encodes a cyclin dependent kinase that along with the product of CycT forms the positive transcription elongation factor, which is involved in RNA polymerase II elongation control. [Date last reviewed: 2019-03-07] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
Interactive Fly

Also Known As

P-TEFb, Positive transcription elongation factor b

Key Links

Genomic Location

Cytogenetic map

58F2-58F3

Sequence location

2R:22,636,063..22,637,727 [-]

Recombination map

2-100

RefSeq locus

NT_033778 REGION:22636063..22637727

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 (17 terms)

Molecular Function (4 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

enables cyclin-dependent protein serine/threonine kinase activity

inferred from direct assay

(Peng et al., 1998)

enables RNA polymerase II CTD heptapeptide repeat kinase activity

inferred from direct assay

(Peng et al., 1998, Marshall et al., 1996)

Terms Based on Predictions or Assertions (4 terms)

CV Term

Evidence

References

enables ATP binding

inferred from electronic annotation with InterPro:IPR000719, InterPro:IPR017441

(InterPro Project Members, 2004-)

enables cyclin-dependent protein serine/threonine kinase activity

inferred from sequence or structural similarity with SGD:S000001622

(Gene Ontology Curators, 2002-)

inferred from biological aspect of ancestor with PANTHER:PTN008603371

(GO Reference Genome Project, 2011-)

enables protein kinase activity

inferred from electronic annotation with InterPro:IPR000719, InterPro:IPR008271

(InterPro Project Members, 2004-)

enables RNA polymerase II CTD heptapeptide repeat kinase activity

inferred from biological aspect of ancestor with PANTHER:PTN008603371

(GO Reference Genome Project, 2011-)

traceable author statement

(Lis et al., 2000)

Biological Process (6 terms)

Terms Based on Experimental Evidence (6 terms)

CV Term

Evidence

References

involved_in DNA-templated transcription

inferred from direct assay

(Lis et al., 2000)

involved_in positive regulation of defense response to virus by host

inferred from mutant phenotype

(Panda et al., 2014)

involved_in positive regulation of transcription by RNA polymerase II

inferred from mutant phenotype

(Panda et al., 2014)

involved_in positive regulation of transcription elongation by RNA polymerase II

inferred from direct assay

(Peng et al., 1998)

involved_in response to heat

inferred from direct assay

(Lis et al., 2000)

involved_in transcription elongation by RNA polymerase II

inferred from direct assay

(Marshall and Price, 1992)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

involved_in transcription elongation by RNA polymerase II

inferred from biological aspect of ancestor with PANTHER:PTN008603371

(GO Reference Genome Project, 2011-)

Cellular Component (7 terms)

Terms Based on Experimental Evidence (5 terms)

CV Term

Evidence

References

located_in nucleus

inferred from direct assay

(Lis et al., 2000, Marshall et al., 1996)

part_of P-TEFb complex

inferred from physical interaction with FLYBASE:Cdk9; FB:FBgn0019949

(Peng et al., 1998)

located_in polytene chromosome puff

inferred from direct assay

(Lis et al., 2000)

located_in polytene chromosome

inferred from direct assay

(Lis et al., 2000)

part_of super elongation complex

inferred from physical interaction with FLYBASE:Su(Tpl); FB:FBgn0014037

(Smith et al., 2011)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

part_of cyclin-dependent protein kinase holoenzyme complex

inferred from biological aspect of ancestor with PANTHER:PTN008603371

(GO Reference Genome Project, 2011-)

part_of cyclin/CDK positive transcription elongation factor complex

traceable author statement

(Lis et al., 2000)

is_active_in nucleus

inferred from biological aspect of ancestor with PANTHER:PTN000623091

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

CYCLIN DEPENDENT KINASES

POSITIVE TRANSCRIPTION ELONGATION FACTOR COMPLEX B

Protein Family (UniProt)

Protein Signatures (InterPro)

Catalytic Activity (EC/Rhea)

cyclin-dependent protein serine/threonine kinase activity

(1) L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H(+) (2.7.11.22)

(2) L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H(+) (2.7.11.22)

RNA polymerase II CTD heptapeptide repeat kinase activity

[DNA-directed RNA polymerase] + ATP = phospho-[DNA-directed RNA polymerase] + ADP + H(+) (2.7.11.23)

RHEA 10216:

Summaries

Gene Snapshot

Gene Group (FlyBase)

CYCLIN DEPENDENT KINASES -: Cyclin-dependent kinases (CDKs) are serine/threonine kinases whose activity depends on a regulatory cyclin subunit. (Adapted from PMID:25180339).
POSITIVE TRANSCRIPTION ELONGATION FACTOR COMPLEX B -: The positive transcription elongation factor complex b (P-TEFb) is a cyclin dependent kinase complex required for the transition from abortive elongation into productive elongation in RNA polymerase II-mediated transcription. (Adapted from FBrf0103005.)

Summary (Interactive Fly)

along with CycT forms the positive transcription elongation factor, P-TEFb, involved in RNA polymerase II elongation control

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Cdk9 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 O17432)

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 5.51

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Cdk9-RA

FBtr0071937

NM_057878

1476

404

Additional Transcript Data and Comments

Reported size (kB)

1.5 (longest cDNA)

(Zhu et al., 1997)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

Cdk9-PA

FBpp0071848

46.8

404

9.50

O17432

NP_477226

AAF46868

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)

404 (aa)

(Zhu et al., 1997)

43 (kD observed)

(Marshall and Price, 1995)

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

O17432

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Cdk9 using the Feature Mapper tool.

External Data

Crossreferences

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

Cdk9_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).

1.46

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 3

organism

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 4 -- 6

organism | ubiquitous

(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

organism | ubiquitous

(Fisher et al., 2012)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in nucleus

inferred from direct assay

(Lis et al., 2000, Marshall et al., 1996)

part_of P-TEFb complex

inferred from physical interaction with FLYBASE:Cdk9; FB:FBgn0019949

(Peng et al., 1998)

located_in polytene chromosome puff

inferred from direct assay

(Lis et al., 2000)

located_in polytene chromosome

inferred from direct assay

(Lis et al., 2000)

part_of super elongation complex

inferred from physical interaction with FLYBASE:Su(Tpl); FB:FBgn0014037

(Smith et al., 2011)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Cdk9 in JBrowse

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

View exonic expression by developmental stage for Dmel\Cdk9

View exonic expression by tissue for Dmel\Cdk9

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

FBgn0019949

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

37586/tissue=All

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

FBgn0019949

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0019949

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

FBgn0019949

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

CG5179

Flygut - An atlas of the Drosophila adult midgut

FBgn0019949

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 3 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 23 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Cdk9

Transgenic constructs containing regulatory region of Cdk9

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(2R)Exel7174

(Ryder, 2004.4.26)

Inferred from location ( 1 )

Df(2R)X58-12

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

lethal, with Scer\GAL4^insc-Mz1407

Cdk9^GD4078

lethal, with Scer\GAL4^pnr-MD237

Cdk9^GD4078

lethal - all die during embryonic stage | maternal effect, with Scer\GAL4^{VP16.mat.αTub67C}

Cdk9^HMS01391

lethal - all die during P-stage, with Scer\GAL4^Mef2.PR

Cdk9^GD4078

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

Cdk9^GD4078

viable, with Scer\GAL4^tin.CΔ4

Cdk9^GD4078

Sterility

Allele

female semi-sterile, with Scer\GAL4^{VP16.nanos.UTR}, Scer\GAL4^VP16.otu, Scer\GAL4^nanos.PG

female sterile, with Scer\GAL4^{VP16.nanos.UTR}, Scer\GAL4^VP16.otu, Scer\GAL4^nanos.PG

Cdk9^GL00230

Other Phenotypes

Allele

abnormal cell shape | blastoderm stage | maternal effect, with Scer\GAL4^{VP16.mat.αTub67C}

Cdk9^HMS01391

abnormal developmental rate | embryonic stage | maternal effect, with Scer\GAL4^{VP16.mat.αTub67C}

Cdk9^HMS01391

abnormal neuroanatomy | adult stage, with Scer\GAL4^repo

Cdk9^HMS02329

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

Cdk9^GD4078

abnormal pain response | adult stage, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

Cdk9^GD4078

decreased cell number | adult stage, with Scer\GAL4^repo

Cdk9^HMS02329

decreased cell number | blastoderm stage | maternal effect, with Scer\GAL4^{VP16.mat.αTub67C}

Cdk9^HMS01391

decreased cell number | oogenesis, with Scer\GAL4^{VP16.nanos.UTR}

Cdk9^KK101197

increased cell number | oogenesis, with Scer\GAL4^{VP16.nanos.UTR}

Cdk9^{nanos.3'UTR.UASp}

Phenotype manifest in

Allele

adult brain, with Scer\GAL4^repo

Cdk9^HMS02329

adult glial cell, with Scer\GAL4^repo

Cdk9^HMS02329

embryo | blastoderm stage | maternal effect, with Scer\GAL4^{VP16.mat.αTub67C}

Cdk9^HMS01391

embryo | gastrula stage | maternal effect, with Scer\GAL4^{VP16.mat.αTub67C}

Cdk9^HMS01391

embryo | maternal effect, with Scer\GAL4^{VP16.nanos.UTR}, Scer\GAL4^VP16.otu, Scer\GAL4^nanos.PG

Cdk9^HMS01391

female germline cell | oogenesis, with Scer\GAL4^{VP16.nanos.UTR}

Cdk9^{nanos.3'UTR.UASp}

female germline stem cell | oogenesis, with Scer\GAL4^{VP16.nanos.UTR}

Cdk9^KK101197

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

Cdk9^GD4078

germarium, with Scer\GAL4^{VP16.nanos.UTR}

germ band | maternal effect, with Scer\GAL4^{VP16.mat.αTub67C}

Cdk9^HMS01391

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

Cdk9^GD4078

mesoderm | maternal effect, with Scer\GAL4^{VP16.mat.αTub67C}

Cdk9^HMS01391

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\CDK9

14 of 14

Yes

3 of 14

3 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

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) (12)

Rnor\Cdk9

14 of 14

Yes

3 of 14

3 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

Mus musculus (laboratory mouse) (13)

Mmus\Cdk9

13 of 14

Yes

3 of 14

3 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

Xenopus tropicalis (Western clawed frog) (14)

Xtro\cdk9

11 of 13

Yes

3 of 13

3 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\cdk9

14 of 14

Yes

3 of 14

3 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

Caenorhabditis elegans (Nematode, roundworm) (13)

Cele\cdk-9

13 of 14

Yes

3 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

Yes

Cele\jnk-1

1 of 14

Cele\mapk-15

1 of 14

Anopheles gambiae (African malaria mosquito) (12)

Agam\AgaP_AGAP008541

12 of 12

Yes

3 of 12

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

Arabidopsis thaliana (thale-cress) (35)

Atha\CDKC2

6 of 13

Yes

Atha\CDKC;1

6 of 13

Yes

5 of 13

5 of 13

5 of 13

5 of 13

5 of 13

5 of 13

5 of 13

Yes

Atha\AT1G03740

4 of 13

Atha\AT1G09600

4 of 13

Atha\AT1G57700

4 of 13

Yes

Atha\AT1G74330

4 of 13

Atha\AT3G01085

4 of 13

Yes

4 of 13

4 of 13

4 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

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\SGV1

6 of 13

Yes

5 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Schizosaccharomyces pombe (Fission yeast) (6)

Spom\cdk9

9 of 12

Yes

2 of 12

1 of 12

1 of 12

1 of 12

1 of 12

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Cdk9. 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) (14)

6 of 13

4 of 13

4 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 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 ( 1 )

Allele

Disease

Interaction

References

Cdk9^UAS.ORF

exacerbates carcinoma

modeled by yki^UAS.cHa

(Nagarkar et al., 2020)

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?

CDK9; cyclin dependent kinase 9

14 of 14

603251

CDK12; cyclin dependent kinase 12

3 of 14

615514

CDK13; cyclin dependent kinase 13

3 of 14

603309

CONGENITAL HEART DEFECTS, DYSMORPHIC FACIAL FEATURES, AND INTELLECTUAL DEVELOPMENTAL DISORDER; CHDFIDD

congenital heart defects, dysmorphic facial features, and intellectual developmental disorder

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

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

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

Cdk9 - CG17601

experimental knowledge based

(Guruharsha et al., 2011)

Cdk9 - CycT

ion exchange chromatography, cosedimentation through density gradient, peptide massfingerprinting, molecular weight estimation by staining, experimental knowledge based, two hybrid, anti tag coimmunoprecipitation, western blot, pull down

(Kim et al., 2013, Guruharsha et al., 2011, Hanyu-Nakamura et al., 2008, Peng et al., 1998, Zhu et al., 1997, Marshall et al., 1996, Marshall and Price, 1995)

Cdk9 - Rchy1

anti bait coimmunoprecipitation, western blot

(Foo, 2017)

Cdk9 - Su(Tpl)

anti tag coimmunoprecipitation, peptide massfingerprinting

(Smith et al., 2011)

Cdk9 - pgc

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

(Hanyu-Nakamura et al., 2008)

Summary of Genetic Interactions

Interaction Browsers

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

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

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

E(spl)mγ-HLH

suppressible

Cdk9

(Liu et al., 2017)

suppressible

Cdk9|E(spl)mγ-HLH

(Liu et al., 2017)

suppressible

(Liu et al., 2017)

suppressible

(Liu et al., 2017)

suppressible

(Liu et al., 2017)

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

63201

DroID - A comprehensive database of gene and protein interactions.

FBgn0019949

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

37586

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

Viral life cycle - HIV-1

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

SignaLink - A signaling pathway resource with multi-layered regulatory networks.

O17432

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-100

Cytogenetic map

58F2-58F3

Sequence location

2R:22,636,063..22,637,727 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

58F2-58F3

Limits computationally determined from genome sequence between P{PZ}l(2)rG270^rG270 and P{EP}EP718^EP718

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

58F-58F

(Peng, 1997.9.29)

Experimentally Determined Recombination Data

Location

2-100

(FlyBase, 2016)

2-105.5

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (17)

Genomic Clones (16)

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

cDNA Clones (69)

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

GH21935

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.

FBgn0019949

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0019949

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Zhu et al., 1997)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Identified as a potential component of the hh signalling pathway in a genome-wide RNAi screen. dsRNA made from templates generated with primers directed affects the extent of expression of a hh signaling reporter construct in Clone 8 cells.

(Nybakken et al., 2005)

When dsRNA constructs are made and transiently transfected into S2 cells in RNAi experiments, an increase in the proportion of G1 phase cells and a decrease in the mitotic index are seen.

(Bettencourt-Dias et al., 2004)

dsRNA made from templates generated with primers directed against this gene tested in RNAi screen for effects on Kc167 and S2R⁺ cell morphology.

(Kiger et al., 2003)

RNAi screen using dsRNA made from templates generated with primers directed against this gene causes a phenotype when assayed in Kc167 and S2R⁺ cells: cells become round and detached, cell morphology is aberrant and there is an increased frequency of microtubule-based mitotic spindles, indicative of a failure in mitosis.

(Kiger et al., 2003)

Area matching Drosophila Positive transcription elongation factor b, Acc. No. AF027300. Probable intron.

(Davies, 2001.3.15)

Cdk9 encodes the small subunit of P-TEFb (positive transcription elongation factor b). Cdk9 encodes a cyclin-dependent kinase that is essentially inactive in the absence of its cyclin partner CycT.

(Peng et al., 1998)

Cdk9 is cloned and identified as the counterpart of two human protein kinases. Purified P-TEFb can functionally replace the transcriptional activity removed from HeLa extract with human PITALRE antibodies.

(Zhu et al., 1997)

Removal of the carboxy terminal domain (CTD) of the large subunit of RNA polymerase II (RpII215) abolished productive elongation. P-TEFb can phosphorylate the CTD. Both function and kinase activity of P-TEFb can be blocked by application of drugs. TfIIH cannot substitute for P-TEFb. Phosphorylation of the CTD by P-TEFb controls the transition from abortive into productive elongation mode.

(Marshall et al., 1996)

P-TEFb stimulates the level of runoff transcripts in vitro.

(Marshall and Price, 1995)

Relationship to Other Genes

Source for database merge of

Additional comments

Nomenclature History

Source for database identify of

Source for identity of: Cdk9 CG5179

(Milshina, 1999.11)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (15)

Reported As

Symbol Synonym

CDK9

(Rosendo Machado et al., 2021, Liu et al., 2017, Song et al., 2017, Kim et al., 2013, Phatnani and Greenleaf, 2006, Fisher, 2005, Galloni, 2003, Galloni and Edgar, 1999, Peng et al., 1998)

CG5179

(National Institute of Genetics Fly Stocks, 2022-, Hosono et al., 2015, Schertel et al., 2013, Ni et al., 2011.7.19, Ni et al., 2010.12.1, Keleman et al., 2009.8.5, Nybakken et al., 2005, Morrison et al., 2000)

Cdk9

(Hunt et al., 2024, Lee et al., 2024, DeBerardine et al., 2023, Evans et al., 2021, Kögler et al., 2021, Lebo et al., 2021, Ostalé et al., 2021, Li et al., 2020, Zhou et al., 2020, Hanyu-Nakamura et al., 2019, Myat et al., 2019, Liu et al., 2017, Transgenic RNAi Project members, 2017-, Yang et al., 2017, Chlamydas et al., 2016, Tsai et al., 2016, Zanet et al., 2016, Dahlberg et al., 2015, Sansone et al., 2015, Gaertner and Zeitlinger, 2014, Sopko et al., 2014, Bonke et al., 2013, Kwon et al., 2013, Lee et al., 2013, Schertel et al., 2013, Japanese National Institute of Genetics, 2012.5.21, Tokusumi et al., 2012, Guo et al., 2011, Smith et al., 2011, Chopra et al., 2009, Dworkin et al., 2009, Guo et al., 2008, Hanyu-Nakamura et al., 2008, Srinivasan et al., 2008, Basquin and Pauli, 2007, Eissenberg et al., 2007, Nybakken et al., 2005)

DmP-TEFb

(Gibbs et al., 2017)

P-TEF

(Marshall and Price, 1992)

PTefb

TEFB

(Wu et al., 2023)

cdk9

(Flora et al., 2018, Church et al., 2017, Foo, 2017, Singh et al., 2011, Mattila et al., 2008, Serras et al., 2001)

Name Synonyms

Cyclin-dependent kinase 9

Cyclin-dependent kinase9 2.7

(Kang et al., 2002)

Positive transcription elongation factor b

(Dahlberg et al., 2015, Marshall and Price, 1995)

Positive transcription elongation factor b, small subunit

p43 PITALRE

(Yamaguchi et al., 1998)

positive transcription elongation factor b

(Peng, 1997.9.29)

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 ( 49 )

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.

37586

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.

O17432

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

O17432

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.

O17432

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0019949

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

37586/tissue=All

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

FBgn0019949

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

FBgn0019949

FlyMine - An integrated database for Drosophila genomics

FBgn0019949

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

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

dme:Dmel_CG5179

MARRVEL_MODEL - MARRVEL (model organism gene)

37586

Linkouts

BioGRID - A database of protein and genetic interactions.

63201

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

FBgn0019949

DroID - A comprehensive database of gene and protein interactions.

FBgn0019949

DRSC - Results frm RNAi screens

FBgn0019949

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

Cdk9_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0019949

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0019949

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

CG5179

Flygut - An atlas of the Drosophila adult midgut

FBgn0019949

FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.

FBgn0019949

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

TC003392

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

Interactive Fly

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

Viral life cycle - HIV-1

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

37586

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

SignaLink - A signaling pathway resource with multi-layered regulatory networks.

O17432

References (140)

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

1.46

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