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    Ref1 RNA and export factor binding protein 1 [ Drosophila melanogaster (fruit fly) ]

    Gene ID: 44029, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Ref1provided by FlyBase
    Official Full Name
    RNA and export factor binding protein 1provided by FlyBase
    Primary source
    FLYBASE:FBgn0010774
    Locus tag
    Dmel_CG1101
    See related
    AllianceGenome:FB:FBgn0010774
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Drosophila melanogaster
    Lineage
    Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila; Sophophora
    Also known as
    aly; Aly; ALY; alyref; ALYREF; BcDNA:LD24793; cg1101; CG1101; Dmel\CG1101; dmREF1; DmREF1; l(3)02267; ref1; REF1
    Summary
    Predicted to enable mRNA binding activity. Predicted to be involved in mRNA export from nucleus. Located in nuclear membrane and nucleoplasm. Part of catalytic step 2 spliceosome and precatalytic spliceosome. Is expressed in adult head; embryonic brain; larval ventral nerve cord; and organism. Used to study alcohol use disorder. Orthologous to human ALYREF (Aly/REF export factor). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
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    Genomic context

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    See Ref1 in Genome Data Viewer
    Location:
    84B2-84B2; 3-48 cM
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    Release 6.54 current Release 6 plus ISO1 MT (GCF_000001215.4) 3R NT_033777.3 (7077904..7080387, complement)
    Release 5.57 previous assembly Release 5 (GCF_000001215.2) 3R NT_033777.2 (2903626..2906109, complement)

    Chromosome 3R - NT_033777.3Genomic Context describing neighboring genes Neighboring gene uncharacterized protein Neighboring gene UFM1 specific ligase 1 Neighboring gene antisense RNA:CR45908 Neighboring gene uncharacterized protein Neighboring gene Dephospho-CoA kinase Neighboring gene tailor Neighboring gene antisense RNA:CR45907

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Drosophila Ref1/ALYREF regulates transcription and toxicity associated with ALS/FTD disease etiologies. Berson A, et al. Acta Neuropathol Commun, 2019 Apr 29. PMID 31036086, Free PMC Article
    2. SRSF1-dependent nuclear export inhibition of C9ORF72 repeat transcripts prevents neurodegeneration and associated motor deficits. Hautbergue GM, et al. Nat Commun, 2017 Jul 5. PMID 28677678, Free PMC Article
    3. RNA processing: splicing and the cytoplasmic localisation of mRNA. Palacios IM. Curr Biol, 2002 Jan 22. PMID 11818077
    4. REF, an evolutionary conserved family of hnRNP-like proteins, interacts with TAP/Mex67p and participates in mRNA nuclear export. Stutz F, et al. RNA, 2000 Apr. PMID 10786854, Free PMC Article
    5. REF1/Aly and the additional exon junction complex proteins are dispensable for nuclear mRNA export. Gatfield D, et al. J Cell Biol, 2002 Nov 25. PMID 12438415, Free PMC Article

    See all (89) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Study identified that knockdown of Ref1 is a suppressor of toxicity of TDP-43 and TDP-43 co-expressed with Ataxin-2 in a fly-based, modifier screen of 107 RNA binding proteins containing RNA recognition motifs (RRMs).
      Title: Drosophila Ref1/ALYREF regulates transcription and toxicity associated with ALS/FTD disease etiologies.
    2. Aly and a testis-specific TF(II)D complex work together to promote high transcriptional activity of spermiogenic genes specifically in primary spermatocytes.
      Title: Wake-up-call, a lin-52 paralogue, and Always early, a lin-9 homologue physically interact, but have opposing functions in regulating testis-specific gene expression.
    3. show that REF1/ALY and the additional components of the exon-exon junction complex are dispensable for export of bulk mRNA in Drosophila cells
      Title: REF1/Aly and the additional exon junction complex proteins are dispensable for nuclear mRNA export.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by FlyBase

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables mRNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in mRNA export from nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mRNA splicing, via spliceosome IC
    Inferred by Curator
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of catalytic step 2 spliceosome HDA PubMed 
    located_in nuclear membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of precatalytic spliceosome HDA PubMed 
    part_of transcription export complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    RNA and export factor binding protein 1
    Names
    Aly
    CG1101-PA
    Ref1-PA

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference assembly

    Genomic

    1. NT_033777.3 Reference assembly

      Range
      7077904..7080387 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_143711.3 → NP_651968.1  RNA and export factor binding protein 1 [Drosophila melanogaster]

      See identical proteins and their annotated locations for NP_651968.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      Q9V3E7
      Related
      FBpp0081156
      Conserved Domains (3) summary
      COG0724
      Location:108 → 187
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12680
      Location:109 → 183
      RRM_THOC4; RNA recognition motif in THO complex subunit 4 (THOC4) and similar proteins
      pfam13865
      Location:214 → 265
      FoP_duplication; C-terminal duplication domain of Friend of PRMT1
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9V3E7 Q9V3E7

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