FB2020_06, released Dec 22, 2020

Gene: Dmel\Phf5a

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General Information
Symbol
Dmel\Phf5a
Species
D. melanogaster
Name
PHD finger protein 5a
Annotation Symbol
CG9548
Feature Type
protein_coding_gene
FlyBase ID
FBgn0031822
Gene Model Status
Current
Stock Availability
5 publicly available
Gene Snapshot
Contributions welcome
Other Summaries
Key Links
Genomic Location
Cytogenetic map
26D9-26D9
Sequence location
2L:6,490,155..6,490,843 [-]
Recombination map

2-20

RefSeq locus
NT_033779 REGION:6490155..6490843
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (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
enables 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
involved_in mRNA splicing, via spliceosome
inferred from biological aspect of ancestor with PANTHER:PTN000319347
(assigned by GO_Central )
(Gaudet et al., 2011)
inferred from sequence or structural similarity with HGNC:18000
(FlyBase Curators, 2008--)
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
part_of catalytic step 2 spliceosome
inferred from high throughput direct assay
(Herold et al., 2009)
part_of precatalytic spliceosome
inferred from high throughput direct assay
(Herold et al., 2009)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
part_of precatalytic spliceosome
inferred from biological aspect of ancestor with PANTHER:PTN000319347
(assigned by GO_Central )
(Gaudet et al., 2011)
part_of U12-type spliceosomal complex
inferred from biological aspect of ancestor with PANTHER:PTN000319347
(assigned by GO_Central )
(Gaudet et al., 2011)
part_of U2 snRNP
inferred from biological aspect of ancestor with PANTHER:PTN000319347
(assigned by GO_Central )
(Gaudet et al., 2011)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the PHF5 family. (Q9VMC8)
Protein Signatures (InterPro)
Summaries
Gene Group (FlyBase)
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
1
Number of Unique Polypeptides
1

Please see 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
Linkouts
Sequences Consistent with the Gene Model
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.
Linkouts
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
part_of catalytic step 2 spliceosome
inferred from high throughput direct assay
(Herold et al., 2009)
part_of 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
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
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
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
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Hsap\PHF5A
14 of 15
Yes
Yes
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Mmus\Phf5a
13 of 15
Yes
Yes
Rattus norvegicus (Norway rat) (1)
Rnor\Phf5a
13 of 13
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
Xtro\phf5a
13 of 12
Yes
Yes
Danio rerio (Zebrafish) (1)
Drer\phf5a
14 of 15
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (2)
Cele\phf-5
9 of 15
Yes
Yes
Cele\ppm-1.D
6 of 15
No
No
Arabidopsis thaliana (thale-cress) (2)
Atha\AT1G07170
7 of 9
Yes
Yes
Atha\AT2G30000
4 of 9
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\RDS3
13 of 15
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\ini1
11 of 12
Yes
Yes
Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG09190ILT )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00001399
Drosophila simulans
Dsim\GD22570
Drosophila sechellia
Dsec\GM17932
Drosophila erecta
Dere\GG23616
Drosophila yakuba
Dyak\GE18435
Drosophila ananassae
Dana\GF15704
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 v8.0)
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
    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?
    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
        Show neighbor-neighbor interactions:
        Select Layout:
        Legend:
        Protein
        RNA
        Selected Interactor(s)
        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)
        RNA-protein
        Physical Interaction
        Assay
        References
        Phf5a - rin
        anti tag coimmunoprecipitation, quantitative reverse transcription pcr
        (Laver et al., 2020)
        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.
        InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
        MIST (protein-protein) - An integrated Molecular Interaction Database
        Pathways
        Signaling Pathways (FlyBase)
        Metabolic Pathways
        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)
        2L
        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}Sec61αEP2180 and P{lacW}Ate1k10809
        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)
        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 sequenced
        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.

        cDNA Clones, End Sequenced (ESTs)
        BDGP DGC clones
          Other clones
          RNAi and Array Information
          Linkouts
          DRSC - Results frm RNAi screens
          GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
          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 ( 27 )
          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.
          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
          Other crossreferences
          BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
          Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
          Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
          Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
          Flygut - An atlas of the Drosophila adult midgut
          GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
          InterPro - A database of protein families, domains and functional sites
          KEGG Genes - Molecular building blocks of life in the genomic space.
          modMine - A data warehouse for the modENCODE project
          Linkouts
          DroID - A comprehensive database of gene and protein interactions.
          DRSC - Results frm RNAi screens
          FLIGHT - Cell culture data for RNAi and other high-throughput technologies
          FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
          FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
          FlyMine - An integrated database for Drosophila genomics
          InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
          KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
          MIST (protein-protein) - An integrated Molecular Interaction Database
          Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
          Synonyms and Secondary IDs (5)
          Datasets (0)
          Study focus (0)
          Experimental Role
          Project
          Project Type
          Title
          References (34)