FB2025_05 , released December 11, 2025
Gene: Dmel\Pbp49
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General Information
Symbol
Dmel\Pbp49
Species
D. melanogaster
Name
PSEA-binding protein 49kD
Annotation Symbol
CG42515
Feature Type
protein_coding_gene
FlyBase ID
FBgn0260398
Gene Model Status
Current
Stock Availability
8 publicly available
Gene Summary
PSEA-binding protein 49kD (Pbp49) encodes a protein that functions as one of three subunits of the small nuclear RNA (snRNA) activating protein complex, which binds as a complex to a proximal sequence element A (PSEA) to activate transcription of snRNA genes. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)
All Summaries
Also Known As

DmSNAP50, DmPBP

Key Links
Genomic Location
Cytogenetic map
44B3-44B3
Sequence location
Recombination map
2-58
RefSeq locus
NT_033778 REGION:8129354..8131323
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
Gene Ontology (GO) Annotations (12 terms)
Molecular Function (7 terms)
Terms Based on Experimental Evidence (7 terms)
CV Term
Evidence
References
enables bent DNA binding
inferred from direct assay
(Hardin et al., 2000)
contributes_to core promoter sequence-specific DNA binding
inferred from direct assay
(Barakat and Stumph, 2008)
enables DNA binding
inferred from direct assay
(Li et al., 2004, Su et al., 1997)
enables protein binding
inferred from physical interaction with FLYBASE:Pbp95; FB:FBgn0037540
(Hung et al., 2009)
contributes_to RNA polymerase II cis-regulatory region sequence-specific DNA binding
inferred from direct assay
(Lai et al., 2008)
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding
inferred from direct assay
(Kim et al., 2010, Hung et al., 2009)
enables RNA polymerase III type 3 promoter sequence-specific DNA binding
inferred from direct assay
(Kim et al., 2010)
enables sequence-specific DNA binding
inferred from direct assay
(Wang and Stumph, 1998)
Terms Based on Predictions or Assertions (4 terms)
CV Term
Evidence
References
enables bent DNA binding
inferred from biological aspect of ancestor with PANTHER:PTN000334776
(GO Reference Genome Project, 2011-)
contributes_to core promoter sequence-specific DNA binding
inferred from biological aspect of ancestor with PANTHER:PTN000334776
(GO Reference Genome Project, 2011-)
contributes_to RNA polymerase II cis-regulatory region sequence-specific DNA binding
inferred from biological aspect of ancestor with PANTHER:PTN000334776
(GO Reference Genome Project, 2011-)
enables RNA polymerase III type 3 promoter sequence-specific DNA binding
inferred from biological aspect of ancestor with PANTHER:PTN000334776
(GO Reference Genome Project, 2011-)
Biological Process (4 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
involved_in protein-DNA complex assembly
inferred from direct assay
(Li et al., 2004, Wang and Stumph, 1998)
involved_in snRNA transcription by RNA polymerase III
inferred from direct assay
(Wang and Stumph, 1998, Su et al., 1997)
involved_in snRNA transcription by RNA polymerase II
inferred from direct assay
(Barakat and Stumph, 2008, Wang and Stumph, 1998, Su et al., 1997)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
involved_in snRNA transcription by RNA polymerase III
inferred from biological aspect of ancestor with PANTHER:PTN000334776
(GO Reference Genome Project, 2011-)
involved_in snRNA transcription by RNA polymerase II
inferred from biological aspect of ancestor with PANTHER:PTN000334776
(GO Reference Genome Project, 2011-)
inferred by curator from GO:0000978,GO:0019185
(Kim et al., 2010, Hung et al., 2009)
involved_in transcription by RNA polymerase III
inferred by curator from GO:0001006,GO:0019185
(Kim et al., 2010)
Cellular Component (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
part_of snRNA-activating protein complex
inferred from direct assay
(Kim et al., 2010, Lai et al., 2008)
inferred from physical interaction with FLYBASE:Pbp95; FB:FBgn0037540
(Hung et al., 2009)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
part_of snRNA-activating protein complex
inferred from biological aspect of ancestor with PANTHER:PTN000334776
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Snapshot
PSEA-binding protein 49kD (Pbp49) encodes a protein that functions as one of three subunits of the small nuclear RNA (snRNA) activating protein complex, which binds as a complex to a proximal sequence element A (PSEA) to activate transcription of snRNA genes. [Date last reviewed: 2019-03-14]
Gene Model and Products
Number of Transcripts
3
Number of Unique Polypeptides
2

Please see the JBrowse view of Dmel\Pbp49 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
Structure
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry Q7JUY8)

If you don't see a structure in the viewer, refresh your browser.
Model Confidence:
  • Very high (pLDDT > 90)
  • Confident (90 > pLDDT > 70)
  • Low (70 > pLDDT > 50)
  • Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures
Crossreferences
Comments on Gene Model

Gene model reviewed during 5.49

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Pbp49-RA
FBtr0300658
NM_136513
1970
377
Pbp49-RB
FBtr0300659
NM_165588
1887
377
Pbp49-RD
FBtr0339298
NM_001144144
1913
358
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
UniProt
RefSeq ID
GenBank
Pbp49-PA
FBpp0289882
43.1
377
6.37
Q7JUY8
NP_610357
AAF59128
Pbp49-PB
FBpp0289883
43.1
377
6.37
Q7JUY8
NP_724647
AAM68851
Pbp49-PD
FBpp0308407
40.9
358
5.92
A0A0C4DHH3
NP_001137616
ACL83070
Polypeptides with Identical Sequences

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

377 aa isoforms: Pbp49-PA, Pbp49-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\Pbp49 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
Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

-0.08

Transcript Expression
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
part_of snRNA-activating protein complex
inferred from direct assay
(Kim et al., 2010, Lai et al., 2008)
inferred from physical interaction with FLYBASE:Pbp95; FB:FBgn0037540
(Hung et al., 2009)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Pbp49 in JBrowse
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
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 1 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 5 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Pbp49
Transgenic constructs containing regulatory region of Pbp49
Aberrations (Deficiencies and Duplications) ( 3 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
viable, with Dcr-2UAS.cDa, Scer\GAL4elav.PLu
viable, with Scer\GAL4Mef2.PR
viable, with Scer\GAL4tin.CΔ4
Other Phenotypes
Allele
abnormal pain response | adult stage, with Dcr-2UAS.cDa, Scer\GAL4elav.PLu
Phenotype manifest in
Allele
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (7)
Hsap\SNAPC3
10 of 14
Yes
Yes
Hsap\EHF
1 of 14
No
No
Hsap\ELF5
1 of 14
No
No
Hsap\ETV7
1 of 14
No
No
1  
Hsap\FLI1
1 of 14
No
No
1  
Hsap\GABPA
1 of 14
No
No
Hsap\SPDEF
1 of 14
No
No
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (6)
Rnor\Snapc3
10 of 14
Yes
Yes
Rnor\Ehf
1 of 14
No
No
Rnor\Elf5
1 of 14
No
No
Rnor\Fli1
1 of 14
No
No
Rnor\Gabpa
1 of 14
No
No
Rnor\Spdef
1 of 14
No
No
Mus musculus (laboratory mouse) (6)
Mmus\Snapc3
10 of 14
Yes
Yes
Mmus\Ehf
1 of 14
No
No
Mmus\Elf5
1 of 14
No
No
Mmus\Fli1
1 of 14
No
No
Mmus\Gabpa
1 of 14
No
No
Mmus\Spdef
1 of 14
No
No
Xenopus tropicalis (Western clawed frog) (5)
Xtro\snapc3
7 of 13
Yes
Yes
Xtro\ehf
1 of 13
No
Yes
Xtro\elf5
1 of 13
No
Yes
Xtro\fli1
1 of 13
No
No
Xtro\gabpa
1 of 13
No
No
Danio rerio (Zebrafish) (5)
Drer\snapc3
9 of 14
Yes
Yes
Drer\fli1
1 of 14
No
No
Drer\fli1rs
1 of 14
No
No
Drer\gabpa
1 of 14
No
No
Drer\spdef
1 of 14
No
No
Caenorhabditis elegans (Nematode, roundworm) (5)
Cele\snpc-3.4
10 of 14
Yes
Yes
Cele\snpc-3.1
9 of 14
No
Yes
Cele\snpc-3.2
9 of 14
No
Yes
Cele\snpc-3.3
2 of 14
No
Yes
Cele\Y48G1BL.8
1 of 14
No
Yes
Anopheles gambiae (African malaria mosquito) (3)
Agam\AgaP_AGAP003852
10 of 12
Yes
Yes
Agam\AgaP_AGAP004337
1 of 12
No
No
Agam\AgaP_AGAP009494
1 of 12
No
No
Arabidopsis thaliana (thale-cress) (1)
Atha\SRD2
9 of 13
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (0)
Schizosaccharomyces pombe (Fission yeast) (0)
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Pbp49. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Gene Symbol
Score
Source
Compara
Domainoid
eggNOG
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Drosophila melanogaster (Fruit fly) (2)
Ets21C
1 of 13
Ets97D
1 of 13
Human Disease Associations
FlyBase Human Disease Model Reports
    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 v9.1 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?
    SNAPC3; small nuclear RNA activating complex polypeptide 3
    10 of 14
    602348
        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
        Summary of Genetic Interactions
        Interaction Browsers
        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.
        MIST (protein-protein) - An integrated Molecular Interaction Database
        Pathways
        Signaling Pathways (FlyBase)
        Metabolic Pathways
        FlyBase
        External Links
        External Data
        Linkouts
        Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
        Class of Gene
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        2R
        Recombination map
        2-58
        Cytogenetic map
        44B3-44B3
        Sequence location
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        44B3-44B3
        Limits computationally determined from genome sequence between P{lacW}Vps28k16503 and P{EP}kermitEP493
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        Experimentally Determined Recombination Data
        Location

        2-58

        (FlyBase, 2016)

        2-57.4

        (Comeron et al., 2012)
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (8)
        Genomic Clones (14)
         

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

        cDNA Clones (87)
         

        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 JBrowse 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
          Antibody Information
          Laboratory Generated Antibodies
           

          polyclonal

          (Barakat and Stumph, 2008, Li et al., 2004)
          Commercially Available Antibodies
           
          Cell Line Information
          Publicly Available Cell Lines
           
            Other Stable Cell Lines
             

            • New stable cell line derived from S2-unspecified : S2 cells were stably transfected with inducible Tag:FLAG-tagged full-length as well as N-terminally and C-terminally truncated Pbp95 constructs. Each was co-transfected with complementary full length Pbp45 and Pbp49 constructs.

              (Hung et al., 2009)
            Other Comments

            The Pbp49 product cross-links to positions in the 3' half of the PSEA element found in the promoters of snRNA genes. However, there are significant differences in the cross-linking pattern when PSEAs from a U1 or U6 gene are compared.

            (Wang and Stumph, 1998)
            Relationship to Other Genes
            Source for database merge of
            Additional comments

            Source for split of: CG11508

            (FlyBase Genome Annotators, 2008)

            Annotation CG11508 split into Pbp49 (CG42515) and CG42516 in release 5.14 of the genome annotation.

            (FlyBase Genome Annotators, 2008)

            One or more of the processed transcripts for this gene contain(s) two non-overlapping open reading frames (ORFs). The non-overlapping ORFs are represented by Pbp49 (CG42515) and CG42516.

            (FlyBase Genome Annotators, 2008)

            Source for split of: Pbp375 into Pbp95, Pbp49 and Pbp45. The PSEA-binding activity was originally asssigned as one gene product (Pbp375) but has now been shown to be due to a complex of three subunits, Pbp95, Pbp49 and Pbp45.

            (Wang and Stumph, 1998)
            Nomenclature History
            Source for database identify of

            Source for identity of: Pbp49 CG11508

            (Li et al., 2004)
            Nomenclature comments
            Etymology
            Synonyms and Secondary IDs (15)
            Reported As
            Symbol Synonym
            CG11508
            (Keleman et al., 2009.8.5, Hayden and Bosco, 2008, Zhang et al., 2007, Li et al., 2004)
            CG42515
            (National Institute of Genetics Fly Stocks, 2022-, Hosono et al., 2015, Perkins et al., 2009, FlyBase Genome Annotators, 2008)
            DMPBP49
            (Li et al., 2004)
            DmPBP
            (Hardin et al., 2000, Wang and Stumph, 1998, Su et al., 1997)
            DmPBP49
            (Hayden and Bosco, 2008)
            DmSNAP50
            (Hung and Stumph, 2011, Kim et al., 2010, Hung et al., 2009, Barakat and Stumph, 2008, Hayden and Bosco, 2008, Lai et al., 2008, Lai et al., 2005, Li et al., 2004)
            DmSNAPc
            (Kim et al., 2010)
            Dromel_CG11508_FBtr0088817_mORF
            (Hayden and Bosco, 2008)
            Pbp49
            (Malik et al., 2024, Zhan et al., 2013)
            Name Synonyms
            CG11508
            Drosophila melanogaster PSE-binding protein 49-kDa subunit
            (Wang and Stumph, 1998)
            PSEA-binding protein
            (Hardin et al., 2000)
            PSEA-binding protein 49kD
            PSEA-binding protein of 49 kDa
            (Zhan et al., 2013)
            Proximal Sequence Element-Binding Protein 49
            (Hayden and Bosco, 2008)
            snRNA activator protein 50
            (Hayden and Bosco, 2008)
            Secondary FlyBase IDs
            • FBgn0033267
            • FBgn0022383
            • FBgn0260389
            Datasets (0)
            Study focus (0)
            Experimental Role
            Project
            Project Type
            Title
            Study result (0)
            Result
            Result Type
            Title
            External Crossreferences and Linkouts ( 36 )
            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/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.
            UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
            Other crossreferences
            AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.
            BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
            DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
            EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
            FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
            InterPro - A database of protein families, domains and functional sites
            KEGG Genes - Molecular building blocks of life in the genomic space.
            MARRVEL_MODEL - MARRVEL (model organism gene)
            Linkouts
            BioGRID - A database of protein and genetic interactions.
            Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
            DroID - A comprehensive database of gene and protein interactions.
            DRSC - Results frm RNAi screens
            Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
            FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
            Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
            iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
            MIST (protein-protein) - An integrated Molecular Interaction Database
            Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
            References (40)