FB2025_01 , released February 20, 2025
Gene: Dmel\pal
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General Information
Symbol
Dmel\pal
Species
D. melanogaster
Name
paternal loss
Annotation Symbol
CG31882
Feature Type
protein_coding_gene
FlyBase ID
FBgn0289678
Gene Model Status
Current
Stock Availability
10 publicly available
Gene Summary
paternal loss (pal) encodes a male-germline specific protein which localizes to spermatid nuclei during the histone-to-protamine transition. pal protein is required for the eviction of H3 and H4 histones after the removal of H2A and H2B during spermiogenesis. [Date last reviewed: 2024-01-11] (FlyBase Gene Snapshot)
All Summaries
Key Links
Genomic Location
Cytogenetic map
30C1-30C1
Sequence location
Recombination map
2-36
RefSeq locus
NT_033779 REGION:9624452..9625285
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 (3 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
enables H3-H4 histone complex chaperone activity
inferred from genetic interaction with FLYBASE:Hira; FB:FBgn0022786
(Dubruille et al., 2023)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
involved_in sperm DNA condensation
inferred from mutant phenotype
(Dubruille et al., 2023)
Terms Based on Predictions or Assertions (0 terms)
Cellular Component (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
is_active_in nucleus
inferred from mutant phenotype
(Dubruille et al., 2023)
Terms Based on Predictions or Assertions (0 terms)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
    -
    Summaries
    Gene Snapshot
    paternal loss (pal) encodes a male-germline specific protein which localizes to spermatid nuclei during the histone-to-protamine transition. pal protein is required for the eviction of H3 and H4 histones after the removal of H2A and H2B during spermiogenesis. [Date last reviewed: 2024-01-11]
    Phenotypic Description (Red Book; Lindsley and Zimm 1992)
    pal: paternal loss
    Behaves as a recessive meiotic mutant in males; causes the loss of paternally-derived chromosomes among the progeny of homozygous males. Different chromosomes are lost at different rates. Loss may occur in the zygote and affect the whole body or during early mitotic divisions giving rise to mosaicism. The site responsible for the sensitivity of the X chromosome to pal has been located at or near the X centromere. pal+ function seems to be necessary during meiosis for normal transmission of paternal chromosomes in the early divisions of the fertilized egg.
    Gene Model and Products
    Number of Transcripts
    1
    Number of Unique Polypeptides
    1

    Please see the JBrowse view of Dmel\pal 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 Q8IPE5)

    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 5.47

    Transcript Data
    Annotated Transcripts
    Name
    FlyBase ID
    RefSeq ID
    Length (nt)
    Assoc. CDS (aa)
    pal-RA
    FBtr0079853
    NM_164865
    834
    121
    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
    pal-PA
    FBpp0079449
    14.0
    121
    10.97
    Q8IPE5
    NP_723477
    AAN10702
    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
    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\pal using the Feature Mapper tool.

    External Data
    Crossreferences
    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).

    5.06

    Transcript Expression
    Additional Descriptive Data
    Marker for
     
    Subcellular Localization
    CV Term
    Polypeptide Expression
    Additional Descriptive Data
    Marker for
     
    Subcellular Localization
    CV Term
    Evidence
    References
    is_active_in nucleus
    inferred from mutant phenotype
    (Dubruille et al., 2023)
    Expression Deduced from Reporters
    High-Throughput Expression Data
    Associated Tools

    JBrowse - Visual display of RNA-Seq signals

    View Dmel\pal 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
    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
    Images
    FlyBase Wiki
    Image Based Resources
    Alleles, Insertions, Transgenic Constructs, and Aberrations
    Classical and Insertion Alleles ( 6 )
    For All Classical and Insertion Alleles Show
     
    Other relevant insertions
    Transgenic Constructs ( 7 )
    For All Alleles Carried on Transgenic Constructs Show
    Transgenic constructs containing/affecting coding region of pal
    Transgenic constructs containing regulatory region of pal
    Aberrations (Deficiencies and Duplications) ( 5 )
    Variants
    Variant Molecular Consequences
    Alleles Representing Disease-Implicated Variants
    Phenotypes
    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) (0)
    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) (0)
    Mus musculus (laboratory mouse) (0)
    Xenopus tropicalis (Western clawed frog) (0)
    Danio rerio (Zebrafish) (0)
    Caenorhabditis elegans (Nematode, roundworm) (0)
    Anopheles gambiae (African malaria mosquito) (0)
    Arabidopsis thaliana (thale-cress) (0)
    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:pal. Refer to their site for version information.
    Paralogs
    Downloads
    Download All DIOPT Paralogs
    Paralogs (via DIOPT v9.1)
    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?
      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:
      Show/hide secondary interactors 
      (data from AllianceMine provided by esyN)
      Select Layout:
      Legend:
      Protein
      RNA
      Selected Interactor(s)
      Other Interaction Browsers
      View in FlyBase Interactions Browser   View in MIST tool (external link)
      Please see the Physical Interaction reports below for full details
      protein-protein
      Physical Interaction
      Assay
      References
      pal - HIP-R
      experimental knowledge based
      (Guruharsha et al., 2011)
      Summary of Genetic Interactions
      esyN Network Diagram
      Show/hide secondary interactors 
      (data from AllianceMine provided by esyN)
      esyN Network Key:
      Suppression
      Enhancement
      Other Interaction Browsers
      View in FlyBase Interactions Browser   View in MIST tool (external link)
      Please look at the allele data for full details of the genetic interactions
      Starting gene(s)
      Interaction type
      Interacting gene(s)
      Reference
      pal
      suppressible
      aurB
      (Dubruille et al., 2023)
      Starting gene(s)
      Interaction type
      Interacting gene(s)
      Reference
      Hira
      suppressible
      pal
      (Dubruille et al., 2023)
      External Data
      Linkouts
      Pathways
      Signaling Pathways (FlyBase)
      Metabolic Pathways
      FlyBase
      External Links
      External Data
      Linkouts
      Class of Gene
      Genomic Location and Detailed Mapping Data
      Chromosome (arm)
      2L
      Recombination map
      2-36
      Cytogenetic map
      30C1-30C1
      Sequence location
      FlyBase Computed Cytological Location
      Cytogenetic map
      Evidence for location
      30C1-30C1
      Limits computationally determined from genome sequence between P{EP}EP361&P{EP}peloEP2160 and P{lacW}zf30Ck02506&P{EP}undEP424
      Experimentally Determined Cytological Location
      Cytogenetic map
      Notes
      References
      Experimentally Determined Recombination Data
      Location

      2-36

      (FlyBase, 2016)

      2-31.3

      (Comeron et al., 2012)

      2-

      (Wakimoto et al., 2004)

      2-35.7

      Left of (cM)
      Right of (cM)
      Notes
      Stocks and Reagents
      Stocks (10)
      Genomic Clones (23)
      cDNA Clones (8)
       

      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
          Antibody Information
          Laboratory Generated Antibodies
           
          Commercially Available Antibodies
           
          Cell Line Information
          Publicly Available Cell Lines
           
            Other Stable Cell Lines
             
              Other Comments

              New annotation (CG31882) in release 3 of the genome annotation.

              (FlyBase Genome Annotators, 2002-2003)

              Phenotypic analysis of pal suggests a specific structural role of heterochromatic regions during early cleavage.

              (Omel'yanchuk, 1996)

              The site responsible for the sensitivity of the X chromosome to pal has been located at or near the X centromere.

              (Lindsley and Zimm, 1992)

              pal+ function seems to be necessary during meiosis for normal transmission of paternal chromosomes in the early divisions of the fertilized egg.

              (Lindsley and Zimm, 1992)

              Homozygous pal males produce progeny that lose paternally derived chromosomes during the early zygotic divisions.

              (Tomkiel et al., 1991)
              Relationship to Other Genes
              Source for database merge of

              Source for merge of: CG31882 NEST:bs35a07

              (Rana, 2004.7.8)

              Source for merge of: pal CG31882

              (Dubruille et al., 2023)
              Additional comments
              Nomenclature History
              Source for database identify of
              Nomenclature comments
              Etymology
              Synonyms and Secondary IDs (7)
              Reported As
              Symbol Synonym
              CG31882
              (Dubruille et al., 2023, National Institute of Genetics Fly Stocks, 2022-, Kondo et al., 2017, Chen et al., 2012, Chen et al., 2010, Zhang et al., 2010, Keleman et al., 2009.8.5)
              NEST:bs35a07
              bs35a07.y1
              (Andrews et al., 2000)
              mei-W5
              pal
              (Dubruille et al., 2023, Haigh and Lloyd, 2007, Lindsley and Zimm, 1992)
              Name Synonyms
              paternal loss
              (Lindsley and Zimm, 1992)
              paternal loss inducer
              Secondary FlyBase IDs
              • FBgn0003033
              • FBgn0051882
              • FBgn0045094
              Datasets (0)
              Study focus (0)
              Experimental Role
              Project
              Project Type
              Title
              Study result (0)
              Result
              Result Type
              Title
              External Crossreferences and Linkouts ( 13 )
              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.
              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
              KEGG Genes - Molecular building blocks of life in the genomic space.
              MARRVEL_MODEL - MARRVEL (model organism gene)
              References (48)