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

Gene ID: 44029, updated on 18-Sep-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. Orthologous to human ALYREF (Aly/REF export factor). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs
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Genomic context

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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. Studies on the role of NonA in mRNA biogenesis. Kozlova N, et al. Exp Cell Res, 2006 Aug 1. PMID 16750525

See all (87) 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

Gene LinkOut

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