FlyBase Gene Report: Dmel\Cypl

SPLICEOSOME COMPLEX B -: Nuclear pre-mRNA splicing is catalyzed by the spliceosome which assembles in a step-wise manner. After the assembly of complex A on pre-mRNA, the U4-U6 and U5 snRNPs are recruited as a preassembled tri-snRNP to form complex B. U5 snRNP binds exons at the 5' site. (Adapted from PMID:24452469 and PMID:23118483).
SPLICEOSOME COMPLEX C -: Nuclear pre-mRNA splicing is catalyzed by the spliceosome which assembles in a step-wise manner. Complex B undergoes a number of structural rearrangements and U4 and U1 snRNPs dissociate to generate complex C, the catalytic spliceosome. (Adapted from PMID:24452469 and PMID:23118483).
SPLICEOSOME COMPLEX P -: Nuclear pre-mRNA splicing is catalyzed by the spliceosome which assembles in a step-wise manner. Complex P, the post-spliceosomal complex, is formed after the catalytic removal of the intron by complex C. Complex P contains the lariat intron and spliced exons. (Adapted from PMID:24452469 and PMID:23118483).
CYCLOPHILINS -: Cyclophilins are a class of evolutionary conserved peptidyl prolyl cis/trans isomerases. In vertebrates, they form binary complexes with their ligand, cyclosporine A, and are involved in key biochemical processes including protein folding, receptor signalling, protein trafficking, and transcription. Cyclophilins are characterized by the presence of a 'Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain' (IPR002130). (Adapted from PMID:25986569.)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the GBrowse view of Dmel\Cypl or the JBrowse view of Dmel\Cypl 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

Gene model reviewed during 5.45

Sequence Ontology: Class of Gene

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Cypl-RA

FBtr0072564

NM_079150

718

176

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

Cypl-PA

FBpp0072463

19.5

176

7.16

NP_523874

AAF47391

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)

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

Q9W0Q2

Mapped Features

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

External Data

Crossreferences

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

Cypl_1

Linkouts

Gene Ontology (7 terms)

Molecular Function (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

peptidyl-prolyl cis-trans isomerase activity

inferred from biological aspect of ancestor with PANTHER:PTN000116297

(assigned by GO_Central )

(Gaudet et al., 2011)

Biological Process (3 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

mRNA splicing, via spliceosome

inferred by curator from GO:0071011,GO:0071013

(Herold et al., 2009)

protein folding

inferred from electronic annotation with InterPro:IPR002130, InterPro:IPR020892, InterPro:IPR024936

(assigned by InterPro )

(FlyBase Curators et al., 2004-)

protein peptidyl-prolyl isomerization

inferred from biological aspect of ancestor with PANTHER:PTN000116297

(assigned by GO_Central )

(Gaudet et al., 2011)

Cellular Component (3 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

catalytic step 2 spliceosome

inferred from high throughput direct assay

(Herold et al., 2009)

precatalytic spliceosome

inferred from high throughput direct assay

(Herold et al., 2009)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

nucleus

inferred from biological aspect of ancestor with PANTHER:PTN000116951

(assigned by GO_Central )

(Gaudet et al., 2011)

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

organism

(Fisher et al., 2012)

embryonic stage 7 -- 8

organism | faint | ubiquitous

(Fisher et al., 2012)

embryonic stage 9 -- 10

organism | faint | ubiquitous

(Fisher et al., 2012)

embryonic stage 11 -- 12

organism | faint | ubiquitous

(Fisher et al., 2012)

embryonic stage 13 -- 16

organism | faint | 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

catalytic step 2 spliceosome

inferred from high throughput direct assay

(Herold et al., 2009)

precatalytic spliceosome

inferred from high throughput direct assay

(Herold et al., 2009)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Cypl 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\Cypl

View exonic expression by tissue for Dmel\Cypl

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

FBgn0035141

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

FBgn0035141

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG13892-RA

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

CG13892

Flygut - An atlas of the Drosophila adult midgut

FBgn0035141

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, and Transgenic Constructs

Classical and Insertion Alleles ( 1 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 4 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Cypl

Transgenic constructs containing regulatory region of Cypl

Deletions and Duplications ( 1 )

Partially disrupted in

Df(3L)hipk³

(Lee et al., 2009)

Phenotypes

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

Lethality

Allele

lethal, with Scer\GAL4^Act5C.PU

Cypl^KK107406

viable, with Scer\GAL4^Mef2.PR

Cypl^GD8156

viable, with Scer\GAL4^pnr-MD237

Cypl^GD8156

viable, with Scer\GAL4^tin.CΔ4

Cypl^GD8156

Phenotype manifest in

Allele

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\PPIL1

14 of 15

Yes

Hsap\SNX14

1 of 15

Yes

Model Organism Orthologs (via DIOPT v7.1)

Mus musculus (laboratory mouse) (1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Ppil1

13 of 15

Yes

Rattus norvegicus (Norway rat) (1)

Rnor\Ppil1

10 of 13

Yes

Xenopus tropicalis (Western clawed frog) (1)

Xtro\ppil1

8 of 12

Yes

Danio rerio (Zebrafish) (1)

Drer\ppil1

14 of 15

Yes

Caenorhabditis elegans (Nematode, roundworm) (2)

Cele\cyn-12

14 of 15

Yes

Cele\snx-14

1 of 15

Yes

Arabidopsis thaliana (thale-cress) (1)

Atha\AT2G36130

9 of 9

Yes

Saccharomyces cerevisiae (Brewer's yeast) (3)

Scer\CPR2

1 of 15

Yes

Scer\CPR3

1 of 15

Yes

Scer\CPR5

1 of 15

Yes

Schizosaccharomyces pombe (Fission yeast) (1)

Spom\cyp1

11 of 12

Yes

Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG09190GVM )

Organism

Common Name

Gene

AAA Syntenic Ortholog

Multiple Dmel Genes in this Orthologous Group

Drosophila melanogaster

fruit fly

Dmel\Cypl

Drosophila suzukii

Spotted wing Drosophila

Drosophila simulans

Drosophila sechellia

Drosophila erecta

Drosophila yakuba

Drosophila ananassae

Drosophila pseudoobscura pseudoobscura

Dpse\GA12606

Drosophila persimilis

Dper\GL22598

Drosophila willistoni

Dwil\GK20536

Drosophila virilis

Dvir\GJ23427

Drosophila mojavensis

Dmoj\GI22699

Drosophila grimshawi

Dgri\GH21768

Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG09150DES )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Musca domestica

House fly

Mdoa\17007816

Lucilia cuprina

Australian sheep blowfly

Lcup\FF38_05596

Mayetiola destructor

Hessian fly

Mdes\Mdes015222

Aedes aegypti

Yellow fever mosquito

Aaeg\AAEL007061

Anopheles darlingi

American malaria mosquito

Adar\ADAC008605

Anopheles gambiae

Malaria mosquito

Agam\AGAP012376

Culex quinquefasciatus

Southern house mosquito

Cqui\CPIJ014089

Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W0G8M )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Bombyx mori

Silkmoth

Bmor\BGIBMGA002151

Danaus plexippus

Monarch butterfly

Dple\DPOGS201358-PA

Heliconius melpomene

Postman butterfly

Hmel\HMEL014707

Apis florea

Little honeybee

Aflo\4998569172

Apis mellifera

Western honey bee

Amel\LOC727378

Apis mellifera

Western honey bee

Amel\GB41018

Bombus impatiens

Common eastern bumble bee

Bimp\BIMP24322

Bombus terrestris

Buff-tailed bumblebee

Bter\15207572

Linepithema humile

Argentine ant

Lhum\LH15158

Megachile rotundata

Alfalfa leafcutting bee

Mrot\MROTU:001897

Nasonia vitripennis

Parasitic wasp

Nvit\Nasvi2EG007087

Dendroctonus ponderosae

Mountain pine beetle

Dpod\YQE_09828

Tribolium castaneum

Red flour beetle

Tcas\TC003442

Pediculus humanus

Human body louse

Phum\PHUM463210

Cimex lectularius

Bed bug

Clec\CLEC002035

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI003448

Zootermopsis nevadensis

Nevada dampwood termite

Znev\Znev_07349

Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0FWY )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Ixodes scapularis

Black-legged tick

Isca\ISCW011728

Stegodyphus mimosarum

African social velvet spider

Smim\KFM74887.1

Tetranychus urticae

Two-spotted spider mite

Turt\tetur02g02450

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_61631

Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0NXS )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strongylocentrotus purpuratus

Purple sea urchin

Spur\SPU_011362gn

Strongylocentrotus purpuratus

Purple sea urchin

Spur\Sp-Pdpi(cyclophilin)L6

Strongylocentrotus purpuratus

Purple sea urchin

Spur\Sp-Snx14_1

Strongylocentrotus purpuratus

Purple sea urchin

Spur\SPU_027168gn

Strongylocentrotus purpuratus

Purple sea urchin

Spur\Sp-Snx14

Ciona intestinalis

Vase tunicate

Cint\ENSCING00000011780

Ciona intestinalis

Vase tunicate

Cint\LOC100180391

Gallus gallus

Domestic chicken

Ggal\ENSGALG00000028189

Gallus gallus

Domestic chicken

Ggal\ENSGALG00000015831

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v7.1)

Drosophila melanogaster (Fruit fly) (8)

Gene Symbol

Score

Source

Alignment

2 of 10

2 of 10

2 of 10

2 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 ( 0 )

Allele

Disease

Interaction

References

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?

PPIL1; peptidylprolyl isomerase like 1

14 of 15

601301

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

Cypl - CG4335

two hybrid

(Hu et al., 2017.6.13)

Summary of Genetic Interactions

esyN Network Diagram

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0035141

InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.

38069

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

Cypl

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.

Spliceosome

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

mRNA Splicing - Major Pathway

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-0.5

Cytogenetic map

61C3-61C3

Sequence location

3L:542,122..542,931 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

61C3-61C3

Limits computationally determined from genome sequence between P{EP}EP3104^EP3104 and P{PZ}l(3)05967⁰⁵⁹⁶⁷

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-0.5

(FlyBase, 2016)

3-0.2

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (2)

VDRC

v104316

P{KK107406}VIE-260B

v44823

w¹¹¹⁸; P{GD8156}v44823/TM3

Genomic Clones (18)

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

cDNA Clones (10)

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 sequences

BDGP DGC clones

Other clones

Drosophila Genomics Resource Center cDNA clones

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

FBgn0035141

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0035141

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

38069

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Other Information

Relationship to Other Genes

Source for database identify of

Source for identity of: Cypl CG13892

(Nakayama, 2001.3.7)

Source for database merge of

Additional comments

Other Comments

Cypl is required for the regulation of ovulation upon mating.

(Nakayama and Aigaki, 2001)

Mutants are homozygous viable and showed no obvious defects in morphology and behavior. However, mutant females mated with wild-type males showed a reduced ovulation rate and laid fewer eggs than control females.

(Nakayama and Aigaki, 2001)

Origin and Etymology

Discoverer

Etymology

Identification

External Crossreferences and Linkouts ( 32 )

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.

38069

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

Q9W0Q2

Other crossreferences

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0035141

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

FBgn0035141

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

Cypl_1

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

CG13892

Flygut - An atlas of the Drosophila adult midgut

FBgn0035141

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

38069

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

TC003442

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

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

Dmel_CG13892

modMine - A data warehouse for the modENCODE project

FBgn0035141

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

mRNA Splicing - Major Pathway

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0035141

DRSC - Results frm RNAi screens

FBgn0035141

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

FBgn0035141

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG13892-RA

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0035141

FlyMine - An integrated database for Drosophila genomics

FBgn0035141

InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.

38069

KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.

Spliceosome

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

Cypl

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

mRNA Splicing - Major Pathway

Synonyms and Secondary IDs (5)

Reported As

Symbol Synonym

CG13892

(Hosono et al., 2015, Guilgur et al., 2014, Herold et al., 2009, Keleman et al., 2009.8.5, Molnar et al., 2006)

Cypl

(Hu et al., 2017.6.13, Bischof and FlyORF project members, 2014.6.20, Butchar et al., 2012, Japanese National Institute of Genetics, 2012.5.21, Friedman et al., 2011, Herold et al., 2009, Molnar et al., 2006)

cycl

(Lee et al., 2009)

cypl

(Guilgur et al., 2014)

Name Synonyms

Cyclophilin-like

(Lee et al., 2009, Nakayama and Aigaki, 2001)

Secondary FlyBase IDs

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

References (32)

Report Sections

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