FlyBase Gene Report: Dmel\Phf5a

U2 SMALL NUCLEAR RIBONUCLEOPROTEIN PARTICLE -: The U2 small nuclear ribonucleoprotein particle (U2 snRNP) contains U2 snRNA. It is recruited to the spliceosome after U1 snRNP and forms a stable interaction with the branch site and 3' splice site in pre-mRNA. (Adapted from PMID:23829528 and PMID:21441581).
SPLICEOSOME COMPLEX A -: Nuclear pre-mRNA splicing is catalyzed by the spliceosome which assembles in a step-wise manner. Complex A, the pre-spliceosome, is composed of U1 and U2 snRNPs and proteins involved in recognition of the 5' splice site and branch point. (Adapted from PMID:24452469 and PMID:23118483).
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).

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the GBrowse view of Dmel\Phf5a or the JBrowse view of Dmel\Phf5a 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 5.50

Sequence Ontology: Class of Gene

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Phf5a-RA

FBtr0079264

NM_135194

483

111

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

Phf5a-PA

FBpp0078894

12.5

111

8.29

NP_609038

AAF52393

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

PHF5-like

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Q9VMC8

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Phf5a using the Feature Mapper tool.

External Data

Crossreferences

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

CG9548_1

Linkouts

Gene Ontology (6 terms)

Molecular Function (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

RNA binding

inferred from sequence or structural similarity with HGNC:18000

(FlyBase Curators, 2008--)

Biological Process (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

mRNA splicing, via spliceosome

inferred from sequence or structural similarity with HGNC:18000

(FlyBase Curators, 2008--)

inferred from biological aspect of ancestor with PANTHER:PTN000319347

(assigned by GO_Central )

(Gaudet et al., 2011)

inferred by curator from GO:0071011,GO:0071013

(Herold et al., 2009)

Cellular Component (4 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 (2 terms)

CV Term

Evidence

References

U12-type spliceosomal complex

inferred from biological aspect of ancestor with PANTHER:PTN000319347

(assigned by GO_Central )

(Gaudet et al., 2011)

U2 snRNP

inferred from biological aspect of ancestor with PANTHER:PTN000319347

(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 | 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

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\Phf5a 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\Phf5a

View exonic expression by tissue for Dmel\Phf5a

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

FBgn0031822

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

FBgn0031822

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG9548-RA

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

CG9548

Flygut - An atlas of the Drosophila adult midgut

FBgn0031822

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, and Transgenic Constructs

Classical and Insertion Alleles ( 0 )

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 Phf5a

Transgenic constructs containing regulatory region of Phf5a

Deletions and Duplications ( 0 )

Phenotypes

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

Lethality

Allele

lethal, with Scer\GAL4^Mef2.PR

Phf5a^GD12559

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

Phf5a^HMS00335

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

Phf5a^HMS00335

lethal - all die before end of pupal stage, with Scer\GAL4^pnr-MD237

Phf5a^GD12559

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

Phf5a^GD12559

viable, with Scer\GAL4^tin.CΔ4

Phf5a^GD12559

Sterility

Allele

female fertile, with Scer\GAL4^nos.PG

female sterile, with Scer\GAL4^VP16.otu

Phf5a^HMS00335

Other Phenotypes

Allele

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

Phf5a^GD12559

some die during pupal stage, with Scer\GAL4^pnr-MD237

Phf5a^GD12559

Phenotype manifest in

Allele

Orthologs

Downloads

Download All DIOPT Orthologs

Download All OrthoDB Orthologs

Human Orthologs (via DIOPT v7.1)

Homo sapiens (Human) (1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Hsap\PHF5A

14 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\Phf5a

13 of 15

Yes

Rattus norvegicus (Norway rat) (1)

Rnor\Phf5a

13 of 13

Yes

Xenopus tropicalis (Western clawed frog) (1)

Xtro\phf5a

12 of 12

Yes

Danio rerio (Zebrafish) (1)

Drer\phf5a

14 of 15

Yes

Caenorhabditis elegans (Nematode, roundworm) (2)

Cele\phf-5

10 of 15

Yes

Cele\Y54F10BM.1

5 of 15

Arabidopsis thaliana (thale-cress) (2)

Atha\AT1G07170

6 of 9

Yes

Atha\AT2G30000

3 of 9

Yes

Saccharomyces cerevisiae (Brewer's yeast) (1)

Scer\RDS3

14 of 15

Yes

Schizosaccharomyces pombe (Fission yeast) (1)

Spom\ini1

12 of 12

Yes

Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG09190ILT )

Organism

Common Name

Gene

AAA Syntenic Ortholog

Multiple Dmel Genes in this Orthologous Group

Drosophila melanogaster

fruit fly

Dmel\Phf5a

Drosophila suzukii

Spotted wing Drosophila

Drosophila simulans

Drosophila sechellia

Drosophila erecta

Drosophila yakuba

Drosophila ananassae

Drosophila pseudoobscura pseudoobscura

Dpse\GA21871

Drosophila persimilis

Dper\GL26100

Drosophila willistoni

Dwil\GK18690

Drosophila virilis

Dvir\GJ17895

Drosophila mojavensis

Dmoj\GI17286

Drosophila grimshawi

Dgri\GH13247

Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG09150F65 )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Lucilia cuprina

Australian sheep blowfly

Lcup\FF38_12661

Mayetiola destructor

Hessian fly

Mdes\Mdes008645

Aedes aegypti

Yellow fever mosquito

Aaeg\AAEL003695

Anopheles darlingi

American malaria mosquito

Adar\ADAC000878

Anopheles gambiae

Malaria mosquito

Agam\AGAP009905

Culex quinquefasciatus

Southern house mosquito

Cqui\CPIJ011447

Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W0KI5 )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Bombyx mori

Silkmoth

Bmor\BGIBMGA009855

Danaus plexippus

Monarch butterfly

Dple\DPOGS200866-PA

Heliconius melpomene

Postman butterfly

Hmel\HMEL012632

Apis florea

Little honeybee

Aflo\2148335635

Apis mellifera

Western honey bee

Amel\GB51735

Bombus impatiens

Common eastern bumble bee

Bimp\BIMP14616

Bombus terrestris

Buff-tailed bumblebee

Bter\15202038

Linepithema humile

Argentine ant

Lhum\LH17581

Megachile rotundata

Alfalfa leafcutting bee

Mrot\MROTU:0008a1

Nasonia vitripennis

Parasitic wasp

Nvit\Nasvi2EG012590

Tribolium castaneum

Red flour beetle

Tcas\TC008542

Pediculus humanus

Human body louse

Phum\PHUM300840

Rhodnius prolixus

Kissing bug

Rpro\RPRC004273

Cimex lectularius

Bed bug

Clec\CLEC001399

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI009324

Zootermopsis nevadensis

Nevada dampwood termite

Znev\Znev_01796

Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0J0D )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strigamia maritima

European centipede

Smar\SMAR009814

Ixodes scapularis

Black-legged tick

Isca\ISCW018236

Tetranychus urticae

Two-spotted spider mite

Turt\tetur01g06330

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_56587

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_219863

Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0W8V )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strongylocentrotus purpuratus

Purple sea urchin

Spur\Sp-Sf3b14b

Gallus gallus

Domestic chicken

Ggal\PHF5A

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?

PHF5A; PHD finger protein 5A

14 of 15

617846

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

Phf5a - Sf3b5

anti tag coimmunoprecipitation, peptide massfingerprinting

(Stegeman et al., 2016)

Phf5a - snf

anti tag coimmunoprecipitation, peptide massfingerprinting

(Stegeman et al., 2016)

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.

FBgn0031822

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

33909

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

CG9548

Pathways

Gene Group - Pathway Membership (FlyBase)

External Data

Linkouts

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

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

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-20

Cytogenetic map

26D9-26D9

Sequence location

2L:6,490,155..6,490,843 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

26D9-26D9

Limits computationally determined from genome sequence between P{EP}Sec61α^EP2180 and P{lacW}Ate1^k10809

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

2-20

(FlyBase, 2016)

2-20.8

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (5)

Bloomington

32344

y¹ sc^* v¹ sev²¹; P{TRiP.HMS00335}attP2

FlyORF

F002916

M{UAS-Phf5a.ORF.3xHA.GW}ZH-86Fb

VDRC

v106102

P{KK108965}VIE-260B

v35454

w¹¹¹⁸; P{GD12559}v35454

v35453

w¹¹¹⁸; P{GD12559}v35453/TM3

Genomic Clones (14)

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

cDNA Clones (15)

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

RH02789

Other clones

FI02869

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.

FBgn0031822

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0031822

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

33909

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Other Information

Relationship to Other Genes

Source for database identify of

Source for identity of: Phf5a CG9548

(Stegeman et al., 2016)

Source for database merge of

Source for merge of: CG9548 BcDNA:RH02789

(FlyBase, 1996-)

Additional comments

Source for merge of CG9548 BcDNA:RH02789 was a shared cDNA ( date:030728 ).

(FlyBase, 1996-)

Other Comments

Origin and Etymology

Discoverer

Etymology

Identification

External Crossreferences and Linkouts ( 28 )

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.

33909

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

Q9VMC8

Other crossreferences

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0031822

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

FBgn0031822

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

CG9548_1

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

CG9548

Flygut - An atlas of the Drosophila adult midgut

FBgn0031822

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

33909

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

PHF5-like

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

Dmel_CG9548

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

Spliceosome

modMine - A data warehouse for the modENCODE project

FBgn0031822

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.

FBgn0031822

DRSC - Results frm RNAi screens

FBgn0031822

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

FBgn0031822

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG9548-RA

FlyMine - An integrated database for Drosophila genomics

FBgn0031822

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

33909

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

Spliceosome

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

CG9548

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

BcDNA:RH02789

CG9548

(Çiçek et al., 2016, Saha et al., 2016, Stegeman et al., 2016, Hosono et al., 2015, Ugrankar et al., 2015, Czech et al., 2013, Ni et al., 2010.12.1, Herold et al., 2009, Keleman et al., 2009.8.5, Zhou et al., 2008, Mack et al., 2006)

PHF5A

(Stegeman et al., 2016)

Phf5a

Name Synonyms

PHD finger protein 5a

Secondary FlyBase IDs

FBgn0062970

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

References (32)

Report Sections

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