FlyBase Gene Report: Dmel\Cpsf6

Predictions / Assertions

Summaries

Protein Function (UniProtKB)

May play a role in pre-mRNA 3'-processing.

(UniProt, Q9VSH4)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the GBrowse view of Dmel\Cpsf6 or the JBrowse view of Dmel\Cpsf6 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 5.56

Sequence Ontology: Class of Gene

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Cpsf6-RA

FBtr0076710

NM_139949

2862

652

Cpsf6-RB

FBtr0304628

NM_001259736

2721

605

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

Cpsf6-PA

FBpp0076433

71.1

652

10.13

NP_648206

AAF50445

Cpsf6-PB

FBpp0293170

66.1

605

9.86

NP_001246665

AFH04336

Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

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

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\Cpsf6 using the Feature Mapper tool.

External Data

Crossreferences

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

CG7185_1

Linkouts

Gene Ontology (5 terms)

Molecular Function (1 term)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

inferred from direct assay

(Tang et al., 2018)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

positive regulation of autophagy

inferred from sequence or structural similarity

(Lasko, 2000)

Biological Process (3 terms)

Terms Based on Experimental Evidence (3 terms)

CV Term

Evidence

References

inferred from genetic interaction with FLYBASE:gig; FB:FBgn0005198, FLYBASE:Tsc1; FB:FBgn0026317

(Tang et al., 2018)

inferred from genetic interaction with FLYBASE:Cdk8; FB:FBgn0015618

(Tang et al., 2018)

inferred from genetic interaction with FLYBASE:Doa; FB:FBgn0265998

(Tang et al., 2018)

regulation of alternative mRNA splicing, via spliceosome

inferred from high throughput mutant phenotype

(Park et al., 2004)

regulation of RNA splicing

inferred from mutant phenotype

(Tang et al., 2018)

Terms Based on Predictions or Assertions (0 terms)

Cellular Component (1 term)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

nucleus

inferred from direct assay

(Tang et al., 2018)

inferred from high throughput direct assay

(Sarov et al., 2016)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

nucleus

inferred by curator from GO:0000381

(Park et al., 2004)

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

organism

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 4 -- 6

(Fisher et al., 2012)

embryonic stage 7 -- 8

organism | faint | ubiquitous

(Fisher et al., 2012)

(Fisher et al., 2012)

embryonic stage 9 -- 10

organism | faint | ubiquitous

(Fisher et al., 2012)

anterior midgut primordium

(Fisher et al., 2012)

embryonic stage 11 -- 12

(Fisher et al., 2012)

central brain primordium

(Fisher et al., 2012)

organism | faint | ubiquitous

(Fisher et al., 2012)

posterior midgut primordium

(Fisher et al., 2012)

(Fisher et al., 2012)

ventral nerve cord primordium

(Fisher et al., 2012)

embryonic stage 13 -- 16

embryonic brain

(Fisher et al., 2012)

embryonic/larval nervous system

(Fisher et al., 2012)

gonad

(Fisher et al., 2012)

ventral nerve cord

(Fisher et al., 2012)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

adult head

• membrane

(Aradska et al., 2015)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

nucleus

inferred from direct assay

(Tang et al., 2018)

inferred from high throughput direct assay

(Sarov et al., 2016)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Cpsf6 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\Cpsf6

View exonic expression by tissue for Dmel\Cpsf6

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

FBgn0035872

FLIGHT - Cell culture data for RNAi and other high-throughput technologies

FBgn0035872

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG7185-RA

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

CG7185

Flygut - An atlas of the Drosophila adult midgut

FBgn0035872

Images

FlyExpress - Embryonic expression images (BDGP data)

Show all FlyExpress processed images for Dmel\Cpsf6

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

FlyBase Wiki

Image Based Resources

Alleles, Insertions, and Transgenic Constructs

Classical and Insertion Alleles ( 5 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 7 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Cpsf6

Transgenic constructs containing regulatory region of Cpsf6

Deletions and Duplications ( 1 )

Disrupted in

Df(3L)Exel6112

(Ryder, 2004.4.26)

Phenotypes

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

Lethality

Allele

lethal, with Scer\GAL4^nub-AC-62

Cpsf6^HMS00113

lethal | female limited, with Scer\GAL4^dome-PG14

Cpsf6^HMS00113

viable

Cpsf6^CC00645

Sterility

Allele

female sterile, with Scer\GAL4^VP16.otu

Cpsf6^HMS00113

Other Phenotypes

Allele

starvation stress response defective | larval stage | somatic clone

Cpsf6⁰⁹¹

starvation stress response defective | larval stage | somatic clone, with Scer\GAL4^Act.PU

Phenotype manifest in

Allele

autophagosome | larval stage | somatic clone | conditional

Cpsf6⁰⁹¹

autophagosome | larval stage | somatic clone | conditional, with Scer\GAL4^Act.PU

embryonic/larval fat body | larval stage | somatic clone | conditional

Cpsf6⁰⁹¹

embryonic/larval fat body | larval stage | somatic clone | conditional, with Scer\GAL4^Act.PU

lipid droplet | larval stage | somatic clone | conditional, with Scer\GAL4^Act.PU

Cpsf6^HMS00113

Orthologs

Downloads

Download All DIOPT Orthologs

Download All OrthoDB Orthologs

Human Orthologs (via DIOPT v7.1)

Homo sapiens (Human) (2)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Hsap\CPSF6

13 of 15

Yes

Hsap\CPSF7

10 of 15

Yes

Model Organism Orthologs (via DIOPT v7.1)

Mus musculus (laboratory mouse) (2)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Cpsf6

13 of 15

Yes

Mmus\Cpsf7

9 of 15

Yes

Rattus norvegicus (Norway rat) (2)

Rnor\Cpsf6

12 of 13

Yes

Rnor\Cpsf7

9 of 13

Yes

Xenopus tropicalis (Western clawed frog) (2)

Xtro\cpsf6

6 of 12

Yes

Xtro\cpsf7

6 of 12

Yes

Danio rerio (Zebrafish) (1)

Drer\cpsf6

12 of 15

Yes

Caenorhabditis elegans (Nematode, roundworm) (1)

Cele\cfim-2

11 of 15

Yes

Arabidopsis thaliana (thale-cress) (2)

Atha\AT5G55670

5 of 9

Yes

Atha\AT1G13190

3 of 9

Yes

Saccharomyces cerevisiae (Brewer's yeast) (0)

No records found.

Schizosaccharomyces pombe (Fission yeast) (1)

Spom\SPBC660.15

1 of 12

Yes

Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG09190F0H )

Organism

Common Name

Gene

AAA Syntenic Ortholog

Multiple Dmel Genes in this Orthologous Group

Drosophila melanogaster

fruit fly

Dmel\Cpsf6

Drosophila suzukii

Spotted wing Drosophila

Drosophila simulans

Drosophila sechellia

Drosophila erecta

Drosophila yakuba

Drosophila ananassae

Drosophila pseudoobscura pseudoobscura

Dpse\GA20165

Drosophila persimilis

Dper\GL22549

Drosophila willistoni

Dwil\GK16997

Drosophila virilis

Dvir\GJ13124

Drosophila mojavensis

Dmoj\GI12981

Drosophila grimshawi

Dgri\GH15377

Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG09150BQT )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Musca domestica

House fly

Mdoa\17015450

Glossina morsitans

Tsetse fly

Gmor\GMOY001549

Lucilia cuprina

Australian sheep blowfly

Lcup\FF38_07773

Mayetiola destructor

Hessian fly

Mdes\Mdes003649

Aedes aegypti

Yellow fever mosquito

Aaeg\AAEL017164

Anopheles darlingi

American malaria mosquito

Adar\ADAC010301

Anopheles gambiae

Malaria mosquito

Agam\AGAP005062

Culex quinquefasciatus

Southern house mosquito

Cqui\CPIJ004892

Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W0J9P )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Bombyx mori

Silkmoth

Bmor\BGIBMGA009409

Danaus plexippus

Monarch butterfly

Dple\DPOGS205980-PA

Heliconius melpomene

Postman butterfly

Hmel\HMEL017652

Apis florea

Little honeybee

Aflo\3054552292

Apis mellifera

Western honey bee

Amel\GB46014

Bombus impatiens

Common eastern bumble bee

Bimp\BIMP24737

Bombus terrestris

Buff-tailed bumblebee

Bter\15214449

Linepithema humile

Argentine ant

Lhum\LH18807

Megachile rotundata

Alfalfa leafcutting bee

Mrot\MROTU:001342

Nasonia vitripennis

Parasitic wasp

Nvit\Nasvi2EG012132

Dendroctonus ponderosae

Mountain pine beetle

Dpod\YQE_03898

Dendroctonus ponderosae

Mountain pine beetle

Dpod\YQE_01379

Tribolium castaneum

Red flour beetle

Tcas\GLEAN_08014

Pediculus humanus

Human body louse

Phum\PHUM544500

Rhodnius prolixus

Kissing bug

Rpro\RPRC009232

Rhodnius prolixus

Kissing bug

Rpro\RPRC012139

Cimex lectularius

Bed bug

Clec\CLEC004008

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI007967

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI068574

Zootermopsis nevadensis

Nevada dampwood termite

Znev\Znev_03273

Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0JE4 )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Ixodes scapularis

Black-legged tick

Isca\ISCW006578

Stegodyphus mimosarum

African social velvet spider

Smim\KFM79694.1

Tetranychus urticae

Two-spotted spider mite

Turt\tetur06g01000

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_224649

Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0CVC )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strongylocentrotus purpuratus

Purple sea urchin

Spur\Sp-Cpsf6L

Gallus gallus

Domestic chicken

Ggal\CPSF6

Gallus gallus

Domestic chicken

Ggal\ENSGALG00000013298

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v7.1)

Drosophila melanogaster (Fruit fly) (0)

No records found.

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

Comments on Models/Modifiers Based on Experimental Evidence ( 0 )

Disease Associations of Human Orthologs (via DIOPT v7.1 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?

CPSF6; cleavage and polyadenylation specific factor 6

13 of 15

604979

CPSF7; cleavage and polyadenylation specific factor 7

10 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

Cpsf6 - AGO1

(Guruharsha et al., 2011)

Cpsf6 - Bap60

(Guruharsha et al., 2011)

Cpsf6 - CG10077

(Guruharsha et al., 2011)

Cpsf6 - CG17002

(Guruharsha et al., 2011)

Cpsf6 - CG2017

(Guruharsha et al., 2011)

Cpsf6 - CG2199

(Guruharsha et al., 2011)

Cpsf6 - CG3008

(Guruharsha et al., 2011)

Cpsf6 - CG34159

(Guruharsha et al., 2011)

Cpsf6 - CG7542

enzymatic study, autoradiography, experimental knowledge based, anti tag coimmunoprecipitation, anti tag western blot

(Guruharsha et al., 2011)

Cpsf6 - Cdk8

(Tang et al., 2018, Guruharsha et al., 2011)

Cpsf6 - Cpsf5

anti bait coimmunoprecipitation, western blot, peptide massfingerprinting

(Guruharsha et al., 2011)

Cpsf6 - CstF64

(Sabath et al., 2013)

Cpsf6 - Doa

anti tag coimmunoprecipitation, anti tag western blot, enzymatic study, autoradiography

(Tang et al., 2018)

Cpsf6 - Larp4B

(Guruharsha et al., 2011)

Cpsf6 - MED10

(Guruharsha et al., 2011)

Cpsf6 - MED11

(Guruharsha et al., 2011)

Cpsf6 - MED14

(Guruharsha et al., 2011)

Cpsf6 - MED15

(Guruharsha et al., 2011)

Cpsf6 - MED16

(Guruharsha et al., 2011)

Cpsf6 - MED17

(Guruharsha et al., 2011)

Cpsf6 - MED18

(Guruharsha et al., 2011)

Cpsf6 - MED20

(Guruharsha et al., 2011)

Cpsf6 - MED23

(Guruharsha et al., 2011)

Cpsf6 - MED24

(Guruharsha et al., 2011)

Cpsf6 - MED25

(Guruharsha et al., 2011)

Cpsf6 - MED27

(Guruharsha et al., 2011)

Cpsf6 - MED30

(Guruharsha et al., 2011)

Cpsf6 - MED4

(Guruharsha et al., 2011)

Cpsf6 - MED6

(Guruharsha et al., 2011)

Cpsf6 - MED7

(Guruharsha et al., 2011)

Cpsf6 - MED8

(Guruharsha et al., 2011)

Cpsf6 - Pa1

(Guruharsha et al., 2011)

Cpsf6 - Psi

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Guruharsha et al., 2011)

Cpsf6 - Pten

(Vinayagam et al., 2016)

Cpsf6 - Ptip

anti tag coimmunoprecipitation, peptide massfingerprinting

(Guruharsha et al., 2011)

Cpsf6 - RasGAP1

(Friedman et al., 2011)

Cpsf6 - S6kII

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

Cpsf6 - Sec23

(Guruharsha et al., 2011)

Cpsf6 - Sec24AB

experimental knowledge based, anti bait coimmunoprecipitation, western blot

(Guruharsha et al., 2011)

Cpsf6 - Snr1

(Yu et al., 2018, Guruharsha et al., 2011)

Cpsf6 - Usp10

(Guruharsha et al., 2011)

Cpsf6 - ZAP3

(Guruharsha et al., 2011)

Cpsf6 - boca

anti bait coimmunoprecipitation, western blot, experimental knowledge based, Identification by mass spectrometry

(Guruharsha et al., 2011)

Cpsf6 - brm

(Yu et al., 2018, Guruharsha et al., 2011)

Cpsf6 - dsh

(Guruharsha et al., 2011)

Cpsf6 - ebi

(Guruharsha et al., 2011)

Cpsf6 - enc

(Guruharsha et al., 2011)

Cpsf6 - ix

proximity-dependent biotin identification, Identification by mass spectrometry

(Guruharsha et al., 2011)

Cpsf6 - kel

(Mannix et al., 2019)

Cpsf6 - mor

(Guruharsha et al., 2011)

Cpsf6 - osa

(Guruharsha et al., 2011)

Cpsf6 - skd

anti tag coimmunoprecipitation, peptide massfingerprinting, anti tag western blot

(Guruharsha et al., 2011)

Cpsf6 - yki

(Kwon et al., 2013, Kwon et al., 2013)

RNA-protein

Physical Interaction

Assay

References

Cpsf6 - Atg1

anti tag coimmunoprecipitation, quantitative reverse transcription pcr

(Tang et al., 2018)

Cpsf6 - Atg8a

anti tag coimmunoprecipitation, quantitative reverse transcription pcr

(Tang et al., 2018)

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

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Atg1

suppressible

(Tang et al., 2018)

Cdk8

suppressible

(Tang et al., 2018)

Doa

suppressible

(Tang et al., 2018)

Tsc1|gig

suppressible