FB2020_02, released Apr 14, 2020

Gene: Dmel\phol

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General Information
Symbol
Dmel\phol
Species
D. melanogaster
Name
pleiohomeotic like
Annotation Symbol
CG3445
Feature Type
protein_coding_gene
FlyBase ID
FBgn0035997
Gene Model Status
Current
Stock Availability
10 publicly available
Gene Snapshot
pleiohomeotic like (phol) encodes a zinc-finger protein that is 80% identical in the zinc-finger region to the product of pho. The product of phol plays a role in Polycomb group protein recruitment to Polycomb response elements, but it has additional roles, most likely as a transcriptional activator. [Date last reviewed: 2019-03-14]
Other Summaries
Also Known As

Pho-like

Key Links
Genomic Location
Cytogenetic map
67B7-67B8
Sequence location
3L:9,452,803..9,456,281 [-]
Recombination map

3-29

RefSeq locus
NT_037436 REGION:9452803..9456281
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 Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Molecular Function (GO)
[Detailed GO annotations]
Experimental Evidence
sequence-specific DNA binding
Predictions / Assertions
DNA binding; RNA polymerase II cis-regulatory region sequence-specific DNA binding; sequence-specific DNA binding
Summaries
Gene Group (FlyBase)
POLYCOMB GROUP RECRUITERS/DNA-BINDING PROTEINS -
The Polycomb group (PcG) proteins are epigenetic regulators, best characterized for the repression of Hox gene expression. In Drosophila, PcG proteins repress their target genes by binding to specific DNA elements called Polycomb Response Elements (PREs). PcG DNA binding proteins contribute to the recruitment of Polycomb complexes to PREs. (Adapted from FBrf0228921).
PHO REPRESSIVE COMPLEX -
In Drosophila, the Pho repressive complex (PhoRC) can bind Polycomb Response Elements (PREs) and recruit Polycomb repressive complexes. (Adapted from FBrf0190547 and FBrf0220020).
C2H2 ZINC FINGER TRANSCRIPTION FACTORS -
Zinc finger C2H2 transcription factors are sequence-specific DNA binding proteins that regulate transcription. They possess DNA-binding domains that are formed from repeated Cys2His2 zinc finger motifs. (Adapted from PMID:1835093, FBrf0220103 and FBrf0155739).
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

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

Gene model reviewed during 5.56

Sequence Ontology: Class of Gene
gene_with_edited_transcript
(Graveley et al., 2011)
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
phol-RA
FBtr0076475
NM_140060
3139
669
phol-RB
FBtr0345600
NM_001300076
3384
669
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
phol-PA
FBpp0076203
73.2
669
4.64
NP_648317
AAF50265
phol-PB
FBpp0311669
73.2
669
4.64
NP_001287005
AHN58030
Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

669 aa isoforms: phol-PA, phol-PB
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\phol using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Gene Ontology (8 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
sequence-specific DNA binding
inferred from direct assay
(Brown et al., 2003)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
DNA binding
traceable author statement
(Levine et al., 2004)
inferred from biological aspect of ancestor with PANTHER:PTN000360827
(assigned by GO_Central )
(Gaudet et al., 2011)
RNA polymerase II cis-regulatory region sequence-specific DNA binding
inferred from biological aspect of ancestor with PANTHER:PTN000360827
(assigned by GO_Central )
(Gaudet et al., 2011)
sequence-specific DNA binding
inferred from biological aspect of ancestor with PANTHER:PTN000360827
(assigned by GO_Central )
(Gaudet et al., 2011)
Biological Process (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
gene silencing
inferred from genetic interaction with FLYBASE:pho; FB:FBgn0002521
(Brown et al., 2003)
Terms Based on Predictions or Assertions (0 terms)
Cellular Component (4 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
nucleus
inferred from direct assay
(Klymenko et al., 2006)
Terms Based on Predictions or Assertions (4 terms)
CV Term
Evidence
References
nuclear chromatin
inferred from biological aspect of ancestor with PANTHER:PTN000360827
(assigned by GO_Central )
(Gaudet et al., 2011)
nucleus
inferred from biological aspect of ancestor with PANTHER:PTN000360827
(assigned by GO_Central )
(Gaudet et al., 2011)
PcG protein complex
inferred from biological aspect of ancestor with PANTHER:PTN000360827
(assigned by GO_Central )
(Gaudet et al., 2011)
transcription factor complex
inferred from biological aspect of ancestor with PANTHER:PTN000360827
(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
nucleus
inferred from direct assay
(Klymenko et al., 2006)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\phol 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 ( 5 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 6 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of phol
Transgenic constructs containing regulatory region of phol
Deletions and Duplications ( 0 )
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (3)
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\YY1
7 of 15
Yes
No
 
Hsap\YY2
7 of 15
Yes
No
Hsap\ZFP42
4 of 15
No
No
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (5)
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\Yy1
7 of 15
Yes
No
Mmus\Yy2
4 of 15
No
No
Mmus\Zfp42
4 of 15
No
Yes
Mmus\Gm12845
1 of 15
No
Yes
Mmus\Zfp143
1 of 15
No
Yes
Rattus norvegicus (Norway rat) (4)
Rnor\Yy1
6 of 13
Yes
No
Rnor\Yy2
3 of 13
No
No
Rnor\Zfp42l
2 of 13
No
Yes
Rnor\Zfp42
1 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (1)
Xtro\yy1
4 of 12
Yes
No
Danio rerio (Zebrafish) (2)
Drer\yy1a
7 of 15
Yes
No
Drer\yy1b
7 of 15
Yes
No
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\ztf-17
2 of 15
Yes
Yes
Arabidopsis thaliana (thale-cress) (1)
Atha\YY1
3 of 9
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (2)
Scer\NRG1
1 of 15
Yes
Yes
Scer\NRG2
1 of 15
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (0)
No records found.
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG091908FC )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00003856
Drosophila simulans
Dsim\GD12921
Drosophila sechellia
Dsec\GM24870
Drosophila erecta
Dere\GG14036
Drosophila yakuba
Dyak\GE21239
Drosophila ananassae
Dana\GF24664
Drosophila pseudoobscura pseudoobscura
Dpse\GA17456
Drosophila persimilis
Dper\GL17968
Drosophila willistoni
Dwil\GK20506
Drosophila virilis
Dvir\GJ13188
Drosophila mojavensis
Dmoj\GI13359
Drosophila grimshawi
Dgri\GH16213
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091504VN )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17018872
Glossina morsitans
Tsetse fly
Gmor\GMOY011086
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_07101
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W02BX )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bmor\BGIBMGA011179
Danaus plexippus
Monarch butterfly
Dple\DPOGS200468-PA
Heliconius melpomene
Postman butterfly
Hmel\HMEL010415
Apis florea
Little honeybee
Aflo\2355231940
Apis mellifera
Western honey bee
Amel\GB49343
Bombus impatiens
Common eastern bumble bee
Bimp\BIMP22139
Bombus terrestris
Buff-tailed bumblebee
Bter\15213295
Linepithema humile
Argentine ant
Lhum\LH14355
Megachile rotundata
Alfalfa leafcutting bee
Mrot\MROTU:001aef
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG000131
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_09404
Tribolium castaneum
Red flour beetle
Tcas\pho
Pediculus humanus
Human body louse
Phum\PHUM284920
Rhodnius prolixus
Kissing bug
Rpro\RPRC009167
Cimex lectularius
Bed bug
Clec\CLEC004566
Cimex lectularius
Bed bug
Clec\CLEC004565
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI007734
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_08817
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X029J )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Smar\SMAR005684
Ixodes scapularis
Black-legged tick
Isca\ISCW010258
Stegodyphus mimosarum
African social velvet spider
Smim\KFM82896.1
Stegodyphus mimosarum
African social velvet spider
Smim\KFM73407.1
Stegodyphus mimosarum
African social velvet spider
Smim\KFM73406.1
Tetranychus urticae
Two-spotted spider mite
Turt\tetur09g00130
Tetranychus urticae
Two-spotted spider mite
Turt\tetur09g00290
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_59123
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G03FM )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Yyi
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000018982
Gallus gallus
Domestic chicken
Ggal\YY1
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (1)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
pho
6 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?
    YY1; YY1 transcription factor
    7 of 15
    600013
       
      YY2; YY2 transcription factor
      7 of 15
      300570
          ZFP42; ZFP42 zinc finger protein
          4 of 15
          614572
              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
              phol - Ank2
              two hybrid
              (Hu et al., 2017.6.13)
              phol - CG11906
              two hybrid array
              (Shokri et al., 2019)
              phol - CG14407
              two hybrid
              (Hu et al., 2017.6.13)
              phol - CG2712
              two hybrid array
              (Shokri et al., 2019)
              phol - CG31955
              two hybrid array
              (Shokri et al., 2019)
              phol - CG3726
              two hybrid array
              (Shokri et al., 2019)
              phol - CG4730
              two hybrid array
              (Shokri et al., 2019)
              phol - CG9650
              two hybrid array
              (Shokri et al., 2019)
              phol - Cenp-C
              two hybrid array
              (Shokri et al., 2019)
              phol - Fkbp12
              anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based
              (Rhee et al., 2014)
              phol - MBD-R2
              two hybrid array
              (Shokri et al., 2019)
              phol - Sfmbt
              anti bait coimmunoprecipitation, western blot, anti tag coimmunoprecipitation, molecular weight estimation by staining
              (Klymenko et al., 2006)
              phol - Sgf11
              anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based
              (Rhee et al., 2014)
              phol - esc
              pull down, autoradiography
              (Wang et al., 2004)
              phol - gcm
              two hybrid
              (Jacques et al., 2009)
              phol - h
              two hybrid array
              (Shokri et al., 2019)
              phol - kn
              two hybrid array
              (Shokri et al., 2019)
              phol - sens-2
              two hybrid array
              (Shokri et al., 2019)
              phol - sr
              two hybrid array
              (Shokri et al., 2019)
              phol - sv
              two hybrid array
              (Shokri et al., 2019)
              phol - unpg
              two hybrid array
              (Shokri et al., 2019)
              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
              BioGRID - A database of protein and genetic interactions.
              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
              Genomic Location and Detailed Mapping Data
              Chromosome (arm)
              3L
              Recombination map

              3-29

              Cytogenetic map
              67B7-67B8
              Sequence location
              3L:9,452,803..9,456,281 [-]
              FlyBase Computed Cytological Location
              Cytogenetic map
              Evidence for location
              67B7-67B8
              Limits computationally determined from genome sequence between P{EP}Hsp26EP3336&P{EP}Hsp26EP3315 and P{PZ}fry02240
              Experimentally Determined Cytological Location
              Cytogenetic map
              Notes
              References
              Experimentally Determined Recombination Data
              Location

              3-29

              (FlyBase, 2016)

              3-23.0

              (Comeron et al., 2012)
              Left of (cM)
              Right of (cM)
              Notes
              Stocks and Reagents
              Stocks (10)
              Genomic Clones (12)
               

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

              cDNA Clones (33)
               

              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.

                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: phol CG3445

                (Kassis, 2003.2.10)
                Source for database merge of
                Additional comments
                Other Comments

                DNA-protein interactions: genome-wide binding profile assayed for phol protein in Kc167 cells; see Chromatin_types_NKI collection report. Individual protein-binding experiments listed under "Samples" at GEO_GSE22069 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22069).

                (Filion et al., 2010)

                pho and phol act redundantly to repress homeotic genes.

                (Brown et al., 2003)
                Origin and Etymology
                Discoverer
                Etymology
                Identification
                External Crossreferences and Linkouts ( 35 )
                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/TrEMBL - Automatically annotated and unreviewed 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
                SignaLink - A signaling pathway resource with multi-layered regulatory networks.
                Linkouts
                BioGRID - A database of protein and genetic interactions.
                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.
                MIST (protein-protein) - An integrated Molecular Interaction Database
                Synonyms and Secondary IDs (12)
                Datasets (1)
                Study focus (1)
                Experimental Role
                Project
                Project Type
                Title
                • transgene_used
                FBGSE22069
                Protein profiling reveals five principal chromatin types in Drosophila cells.
                References (78)