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    ALYREF Aly/REF export factor [ Homo sapiens ]

    Gene ID: 10189, updated on 11-May-2012
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    Summary

    Official Symbol
    ALYREFprovided by HGNC
    Official Full Name
    Aly/REF export factorprovided by HGNC
    Primary source
    HGNC:19071
    See related
    Ensembl:ENSG00000183684; HPRD:09168; MIM:604171; Vega:OTTHUMG00000160470
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ALY; BEF; REF; THOC4; ALY/REF
    Summary
    The protein encoded by this gene is a heat stable, nuclear protein and functions as a molecular chaperone. It is thought to regulate dimerization, DNA binding, and transcriptional activity of basic region-leucine zipper (bZIP) proteins. [provided by RefSeq, Jul 2008]
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    Genomic context

    Location :
    17q25.3
    Sequence :
    Chromosome: 17; NC_000017.10 (79845711..79849462, complement)
    See ALYREF in Epigenomics, MapViewer

    Chromosome 17 - NC_000017.10Genomic Context describing neighboring genes Neighboring gene prolyl 4-hydroxylase, beta polypeptide Neighboring gene Rho GDP dissociation inhibitor (GDI) alpha Neighboring gene anaphase promoting complex subunit 11 Neighboring gene phosphate cytidylyltransferase 2, ethanolamine Neighboring gene neuropeptide B

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    Genomic regions, transcripts, and products

    Go to nucleotideGraphics FASTA GenBank

    Go to reference sequence details
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    Bibliography

    Related articles in PubMed

    1. Integrative analysis of the ubiquitin proteome isolated using Tandem Ubiquitin Binding Entities (TUBEs). Lopitz-Otsoa F, et al. J Proteomics, 2012 Jun 6. PMID 22178446.
    2. A cohesin-RAD21 interactome. Panigrahi AK, et al. Biochem J, 2012 Mar 15. PMID 22145905.
    3. Interactome study suggests multiple cellular functions of hepatoma-derived growth factor (HDGF). Zhao J, et al. J Proteomics, 2011 Dec 21. PMID 21907836.
    4. Systematic and quantitative assessment of the ubiquitin-modified proteome. Kim W, et al. Mol Cell, 2011 Oct 21. PMID 21906983.
    5. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. Wagner SA, et al. Mol Cell Proteomics, 2011 Oct. PMID 21890473.

    See all (49) citations in PubMed

    See citations in PubMed for homologs of this gene provided by HomoloGene

    GeneRIFs: Gene References Into Functions What's a GeneRIF?

    1. When the TREX components UAP56 or Aly are knocked down, spliced mRNA, as well as total polyA+ RNA, accumulates in nuclear speckle domains.
      Title: A role for TREX components in the release of spliced mRNA from nuclear speckle domains.
    2. A differential connection between tumorogenesis and the expression levels of human THO and ALY.
      Title: Differential expression of THOC1 and ALY mRNP biogenesis/export factors in human cancers.
    3. Results describe the subcellular localization of ICP27 and its colocalization with cellular RNA export factors Aly/REF and TAP/NXF1.
      Title: ICP27 phosphorylation site mutants display altered functional interactions with cellular export factors Aly/REF and TAP/NXF1 but are able to bind herpes simplex virus 1 RNA.
    4. These results indicate that ICP27 RGG box methylation regulates interaction ALY and SRPK1 proteins.
      Title: Arginine methylation of the ICP27 RGG box regulates the functional interactions of ICP27 with SRPK1 and Aly/REF during herpes simplex virus 1 infection.
    5. The authors demonstrate that ORF57 recruits several members of hTREX, namely Aly, UAP56 and hTHO-complex proteins, onto the viral mRNAs to assemble an export-competent ribonucleoprotein particle.
      Title: Uncoupling of hTREX demonstrates that UAP56 and hTHO-complex recruitment onto herpesvirus saimiri intronless transcripts is required for replication.
    6. TAP/NXF1, but not Aly/REF, is required for RNA export during HSV-1 infection.
      Title: The cellular RNA export receptor TAP/NXF1 is required for ICP27-mediated export of herpes simplex virus 1 RNA, but the TREX complex adaptor protein Aly/REF appears to be dispensable.
    7. Adaptor Aly functions in the Tap-p15-mediated nuclear export of HSP70 mRNA.
      Title: Adaptor Aly and co-adaptor Thoc5 function in the Tap-p15-mediated nuclear export of HSP70 mRNA.
    8. Aly is a physiological target of nuclear PI3K signaling, which regulates its subnuclear residency, cell proliferation, and mRNA export activities through nuclear Akt phosphorylation and phosphoinositide association.
      Title: Akt phosphorylation and nuclear phosphoinositide association mediate mRNA export and cell proliferation activities by ALY.
    9. Increased TAP binding correlates with increased SF2/ASF binding, but not increased REF/Aly or Y14 binding.
      Title: Efficiency of the pioneer round of translation affects the cellular site of nonsense-mediated mRNA decay.
    10. suggest a central role for ALY in T-cell enhancer function and oncogene activation
      Title: ALY is a common coactivator of RUNX1 and c-Myb on the type B leukemogenic virus enhancer.
    Submit: New GeneRIF Correction See all (11)
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    Phenotypes

    Review eQTL and phenotype association data in this region using PheGenI

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    Interactions

    Products Interactant Other Gene Complex Source Pubs Description
    NP_005773.1 NP_005795.2 DDX39A    BIND  PubMed URH49 interacts with Aly. 
    NP_005773.1 NP_004631.1 DDX39B    BIND  PubMed UAP56 interacts with Aly. 
    Q86V81 Q86V81 ALYREF    HPRD  PubMed  
    Q86V81 Q13838 DDX39B    HPRD  PubMed  
    Q86V81 Q9UJU2 LEF1    HPRD  PubMed  
    Q86V81 P61326 MAGOH    HPRD  PubMed  
    Q86V81 Q9H1J1 UPF3A    HPRD  PubMed  
    BioGRID:115486 BioGRID:115486 ALYREF    BioGRID  PubMed Reconstituted Complex 
    BioGRID:115486 BioGRID:115507 DDX39A    BioGRID  PubMed Affinity Capture-Western; Reconstituted Complex 
    BioGRID:115486 BioGRID:113649 DDX39B    BioGRID  PubMed Reconstituted Complex 
    BioGRID:115486 BioGRID:124082 DOT1L    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:115486 BioGRID:199505 Erh    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:115486 BioGRID:109268 H2AFX    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:115486 BioGRID:109318 HDGF    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:115486 BioGRID:200937 Kif1c    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:115486 BioGRID:119354 LEF1    BioGRID  PubMed Reconstituted Complex 
    BioGRID:115486 BioGRID:121122 MEPCE    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:115486 BioGRID:119622 PCF11    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:115486 BioGRID:111822 RAD21    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:115486 BioGRID:115265 RBM8A    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:115486 BioGRID:116708 RRP1B    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:115486 BioGRID:107308 RUNX2    BioGRID  PubMed Reconstituted Complex 
    BioGRID:115486 BioGRID:215383 Rrp1b    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:115486 BioGRID:113164 UBC    BioGRID  PubMed Affinity Capture-MS; Affinity Capture-Western 
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    General gene information

    Markers

    Genotypes

    Homology

    Pathways from BioSystems

    • Cleavage of Growing Transcript in the Termination Region, organism-specific biosystem (from REACTOME)
      Cleavage of Growing Transcript in the Termination Region, organism-specific biosystemThis section includes the cleavage of both polyadenylated and non-polyadenylated transcripts. In the former case polyadenylation has to precede transcript cleavage, while in the latter case there is ...
    • Exon junction complex (EJC), organism-specific biosystem (from KEGG)
      Exon junction complex (EJC), organism-specific biosystemStructural complex; Genetic information processing; RNA processing
    • Gene Expression, organism-specific biosystem (from REACTOME)
      Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
    • Herpes simplex infection, organism-specific biosystem (from KEGG)
      Herpes simplex infection, organism-specific biosystemHerpes simplex virus (HSV) infections are very common worldwide, with the prevalence of HSV-1 reaching up to 80%-90%. Primary infection with HSV takes place in the mucosa, followed by the establishme...
    • Herpes simplex infection, conserved biosystem (from KEGG)
      Herpes simplex infection, conserved biosystemHerpes simplex virus (HSV) infections are very common worldwide, with the prevalence of HSV-1 reaching up to 80%-90%. Primary infection with HSV takes place in the mucosa, followed by the establishme...
    • Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystem (from REACTOME)
      Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
    • RNA Polymerase II Transcription, organism-specific biosystem (from REACTOME)
      RNA Polymerase II Transcription, organism-specific biosystem
      RNA Polymerase II Transcription
    • RNA Polymerase II Transcription Termination, organism-specific biosystem (from REACTOME)
      RNA Polymerase II Transcription Termination, organism-specific biosystemThe detailed annotation of this section will be completed in the next release.
    • RNA transport, organism-specific biosystem (from KEGG)
      RNA transport, organism-specific biosystemRNA transport from the nucleus to the cytoplasm is fundamental for gene expression. The different RNA species that are produced in the nucleus are exported through the nuclear pore complexes (NPCs) ...
    • RNA transport, conserved biosystem (from KEGG)
      RNA transport, conserved biosystemRNA transport from the nucleus to the cytoplasm is fundamental for gene expression. The different RNA species that are produced in the nucleus are exported through the nuclear pore complexes (NPCs) ...
    • Spliceosome, organism-specific biosystem (from KEGG)
      Spliceosome, organism-specific biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
    • Spliceosome, conserved biosystem (from KEGG)
      Spliceosome, conserved biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
    • TREX complex, organism-specific biosystem (from KEGG)
      TREX complex, organism-specific biosystemStructural complex; Genetic information processing; RNA processing
    • Transport of Mature Transcript to Cytoplasm, organism-specific biosystem (from REACTOME)
      Transport of Mature Transcript to Cytoplasm, organism-specific biosystemTransport of mRNA through the Nuclear Pore Complex (NPC) is a dynamic process involving distinct machinery and receptor subsets. The separation of the two compartments and the regulation of this tran...
    • Transport of Mature mRNA Derived from an Intronless Transcript, organism-specific biosystem (from REACTOME)
      Transport of Mature mRNA Derived from an Intronless Transcript, organism-specific biosystemTransport of mRNA from the nucleus to the cytoplasm, where it is translated into protein, is highly selective and closely coupled to correct RNA processing.
    • Transport of Mature mRNA derived from an Intron-Containing Transcript, organism-specific biosystem (from REACTOME)
      Transport of Mature mRNA derived from an Intron-Containing Transcript, organism-specific biosystemTransport of mRNA from the nucleus to the cytoplasm, where it is translated into protein, is highly selective and closely coupled to correct RNA processing. This coupling is achieved by the nuclear p...
    • Transport of Mature mRNAs Derived from Intronless Transcripts, organism-specific biosystem (from REACTOME)
      Transport of Mature mRNAs Derived from Intronless Transcripts, organism-specific biosystemTransport of mature mRNAs derived from intronless transcripts require some of the same protein complexes as mRNAs derived from intron containing complexes, including TAP and Aly/Ref. However a number...
    • Transport of the SLBP Dependant Mature mRNA, organism-specific biosystem (from REACTOME)
      Transport of the SLBP Dependant Mature mRNA, organism-specific biosystemTransport of U7 snRNP and stem-loop binding protein (SLBP) processed mRNA.
    • Transport of the SLBP independent Mature mRNA, organism-specific biosystem (from REACTOME)
      Transport of the SLBP independent Mature mRNA, organism-specific biosystemTransport of the SLBP independent Mature mRNA through the nuclear pore.
    • mRNA 3'-end processing, organism-specific biosystem (from REACTOME)
      mRNA 3'-end processing, organism-specific biosystemThe 3' ends of eukaryotic mRNAs are generated by posttranscriptional processing of an extended primary transcript. For almost all RNAs, 3'-end processing consists of two steps: (i) the mRNA is first ...
    • mRNA Splicing, organism-specific biosystem (from REACTOME)
      mRNA Splicing, organism-specific biosystemThe process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing...
    • mRNA Splicing - Major Pathway, organism-specific biosystem (from REACTOME)
      mRNA Splicing - Major Pathway, organism-specific biosystemThe splicing of pre-mRNA occurs within a large, very dynamic complex, designated the 'spliceosome'. The 50-60S spliceosomes are estimated to be 40-60 nm in diameter, and have molecular weights in the...
    • mRNA surveillance pathway, organism-specific biosystem (from KEGG)
      mRNA surveillance pathway, organism-specific biosystemThe mRNA surveillance pathway is a quality control mechanism that detects and degrades abnormal mRNAs. These pathways include nonsense-mediated mRNA decay (NMD), nonstop mRNA decay (NSD), and no-go ...
    • mRNA surveillance pathway, conserved biosystem (from KEGG)
      mRNA surveillance pathway, conserved biosystemThe mRNA surveillance pathway is a quality control mechanism that detects and degrades abnormal mRNAs. These pathways include nonsense-mediated mRNA decay (NMD), nonstop mRNA decay (NSD), and no-go ...

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    nucleotide binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    RNA splicing TAS
    Traceable Author Statement
    more info
    		  
    gene expression TAS
    Traceable Author Statement
    more info
    		  
    interspecies interaction between organisms IEA
    Inferred from Electronic Annotation
    more info
    		  
    intronless viral mRNA export from host nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    mRNA 3'-end processing TAS
    Traceable Author Statement
    more info
    		  
    mRNA export from nucleus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    mRNA export from nucleus TAS
    Traceable Author Statement
    more info
    		  
    nuclear mRNA splicing, via spliceosome IC
    Inferred by Curator
    more info
    		 PubMed 
    nuclear mRNA splicing, via spliceosome TAS
    Traceable Author Statement
    more info
    		  
    termination of RNA polymerase II transcription TAS
    Traceable Author Statement
    more info
    		  
    transcription from RNA polymerase II promoter TAS
    Traceable Author Statement
    more info
    		  
    transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    catalytic step 2 spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    cytosol TAS
    Traceable Author Statement
    more info
    		  
    nuclear speck IEA
    Inferred from Electronic Annotation
    more info
    		  
    NOT nucleolus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    transcription export complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
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    General protein information

    Preferred Names
    THO complex subunit 4
    Names
    THO complex subunit 4
    tho4
    THO complex 4
    bZIP enhancing factor
    ally of AML-1 and LEF-1
    bZIP-enhancing factor BEF
    transcriptional coactivator Aly/REF
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    NCBI Reference Sequences (RefSeq)

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_005782.3 → NP_005773.3  THO complex subunit 4

      Status: REVIEWED

      Source sequence(s)
      BC052302, BU624466
      Consensus CDS
      CCDS32768.2
      UniProtKB/TrEMBL
      E9PB61
      UniProtKB/Swiss-Prot
      Q86V81
      Related
      ENSP00000421592, OTTHUMP00000218275, ENST00000505490, OTTHUMT00000360729
      Conserved Domains (1) summary
      cd00590
      Location:114 – 187
      Blast Score: 199
      RRM; RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA ...

    RefSeqs of Annotated Genomes: Build 37.3

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

    Reference GRCh37.p5 Primary Assembly

    Genomic

    1. NC_000017.10 Reference GRCh37.p5 Primary Assembly

      Range
      79845711..79849462, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate HuRef

    Genomic

    1. AC_000149.1 Alternate HuRef

      Range
      75247636..75271256, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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    Related Sequences

    Nucleotide Protein
    Heading Accession and Version
    genomic AC137723.5 (59833..63575) None
    genomic AC145207.2 (95393..99135) None
    genomic CH471099.1 EAW89699.1
    mRNA AF047002.1 AAD09608.1
    mRNA AF086513.1 None
    mRNA BC052302.1 AAH52302.1
    mRNA BU624466.1 None
    other-genetic EU831428.1 ACE87115.1
    other-genetic EU831521.1 ACE86440.1
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86V81.3 GenPept UniProtKB/Swiss-Prot:Q86V81
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    Additional Links

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
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