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    ALYREF Aly/REF export factor [ Homo sapiens (human) ]

    Gene ID: 10189, updated on 10-Dec-2024

    Summary

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    Official Symbol
    ALYREFprovided by HGNC
    Official Full Name
    Aly/REF export factorprovided by HGNC
    Primary source
    HGNC:HGNC:19071
    See related
    Ensembl:ENSG00000183684 MIM:604171; AllianceGenome:HGNC:19071
    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]
    Expression
    Ubiquitous expression in bone marrow (RPKM 44.1), testis (RPKM 33.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ALYREF in Genome Data Viewer
    Location:
    17q25.3
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (81887835..81891587, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (82754997..82758749, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (79845711..79849463, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene prolyl 4-hydroxylase subunit beta Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79813353-79813852 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9153 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9154 Neighboring gene uncharacterized LOC124904086 Neighboring gene Sharpr-MPRA regulatory region 9355 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12979 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79823980-79824608 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79825239-79825867 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79825868-79826497 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79826498-79827126 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9158 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12981 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9159 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12982 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12983 Neighboring gene Rho GDP dissociation inhibitor alpha Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:79846281-79847480 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9161 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:79850899-79851114 Neighboring gene anaphase promoting complex subunit 11 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9162 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9163 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9164 Neighboring gene phosphate cytidylyltransferase 2, ethanolamine Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9165 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9166 Neighboring gene neuropeptide B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9167 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79875237-79876133 Neighboring gene sirtuin 7

    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. Human ALY/BEF gene Map position 17q25.3. Muravenko OV, et al. Chromosome Res, 2000. PMID 11032328
    2. ALY is a common coactivator of RUNX1 and c-Myb on the type B leukemogenic virus enhancer. Mertz JA, et al. J Virol, 2007 Apr. PMID 17229714, Free PMC Article
    3. The interaction of the cellular export adaptor protein Aly/REF with ICP27 contributes to the efficiency of herpes simplex virus 1 mRNA export. Tian X, et al. J Virol, 2013 Jul. PMID 23637401, Free PMC Article
    4. ALY as a potential contributor to metastasis in human oral squamous cell carcinoma. Saito Y, et al. J Cancer Res Clin Oncol, 2013 Apr. PMID 23242234
    5. ICP27 interacts with the RNA export factor Aly/REF to direct herpes simplex virus type 1 intronless mRNAs to the TAP export pathway. Chen IH, et al. J Virol, 2002 Dec. PMID 12438613, Free PMC Article

    See all (277) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. HnRNPA2B1 ISGylation Regulates m6A-Tagged mRNA Selective Export via ALYREF/NXF1 Complex to Foster Breast Cancer Development.
      Title: HnRNPA2B1 ISGylation Regulates m6A-Tagged mRNA Selective Export via ALYREF/NXF1 Complex to Foster Breast Cancer Development.
    2. ALYREF promotes the metastasis of nasopharyngeal carcinoma by increasing the stability of NOTCH1 mRNA.
      Title: ALYREF promotes the metastasis of nasopharyngeal carcinoma by increasing the stability of NOTCH1 mRNA.
    3. Pan-cancer analysis of RNA 5-methylcytosine reader (ALYREF).
      Title: Pan-cancer analysis of RNA 5-methylcytosine reader (ALYREF).
    4. ALYREF (Aly/REF export factor): A potential biomarker for predicting cancer occurrence and therapeutic efficacy.
      Title: ALYREF (Aly/REF export factor): A potential biomarker for predicting cancer occurrence and therapeutic efficacy.
    5. m[5]C-dependent cross-regulation between nuclear reader ALYREF and writer NSUN2 promotes urothelial bladder cancer malignancy through facilitating RABL6/TK1 mRNAs splicing and stabilization.
      Title: m(5)C-dependent cross-regulation between nuclear reader ALYREF and writer NSUN2 promotes urothelial bladder cancer malignancy through facilitating RABL6/TK1 mRNAs splicing and stabilization.
    6. ALYREF, a novel factor involved in breast carcinogenesis, acts through transcriptional and post-transcriptional mechanisms selectively regulating the short NEAT1 isoform.
      Title: ALYREF, a novel factor involved in breast carcinogenesis, acts through transcriptional and post-transcriptional mechanisms selectively regulating the short NEAT1 isoform.
    7. The role of the HIF-1alpha/ALYREF/PKM2 axis in glycolysis and tumorigenesis of bladder cancer.
      Title: The role of the HIF-1α/ALYREF/PKM2 axis in glycolysis and tumorigenesis of bladder cancer.
    8. An ALYREF-MYCN coactivator complex drives neuroblastoma tumorigenesis through effects on USP3 and MYCN stability.
      Title: An ALYREF-MYCN coactivator complex drives neuroblastoma tumorigenesis through effects on USP3 and MYCN stability.
    9. We demonstrate that eIF4A3 stimulates Alyref deposition not only on spliced RNAs close to exon junction complex sites but also on single-exon transcripts
      Title: Co-transcriptional Loading of RNA Export Factors Shapes the Human Transcriptome.
    10. In both ORF57 and ICP27 the interaction sites for ALYREF and UIF partially overlap, suggestive of mutually exclusive binding. The data provide a map of the binding sites responsible for promoting herpes virus mRNA export, enabling future studies to accurately probe these interactions and reveal the functional consequences for UIF and ALYREF redundancy
      Title: Overlapping motifs on the herpes viral proteins ICP27 and ORF57 mediate interactions with the mRNA export adaptors ALYREF and UIF.
    Submit: New GeneRIF Correction See all GeneRIFs (33)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify Aly/REF export factor (ALYREF; THO complex subunit 4, THOC4), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify Aly/REF export factor (ALYREF; THO complex subunit 4, THOC4), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Nef nef Tandem affinity purification and mass spectrometry analysis identify Aly/REF export factor (ALYREF; THO complex subunit 4, THOC4), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify Aly/REF export factor (ALYREF; THO complex subunit 4, THOC4), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Rev rev HIV-1 Rev specifically inhibits the association of ALY/REF and UAP56 with spliced RRE-containing RNA PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables C5-methylcytidine-containing RNA reader activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA binding HDA PubMed 
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in RNA export from nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in RNA splicing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA export from nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mRNA export from nucleus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in osteoblast differentiation HDA PubMed 
    Component Evidence Code Pubs
    part_of catalytic step 2 spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    colocalizes_with chromosome, telomeric region IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    part_of exon-exon junction complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extracellular exosome HDA PubMed 
    located_in membrane HDA PubMed 
    located_in nuclear speck IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    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 transcription export complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    THO complex subunit 4
    Names
    THO complex 4
    ally of AML-1 and LEF-1
    bZIP enhancing factor
    bZIP-enhancing factor BEF
    tho4
    transcriptional coactivator Aly/REF

    NCBI Reference Sequences (RefSeq)

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    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_005782.4 → NP_005773.3  THO complex subunit 4

      Status: REVIEWED

      Source sequence(s)
      BC052302, BU624466
      Consensus CDS
      CCDS32768.2
      UniProtKB/Swiss-Prot
      O43672, Q86V81
      UniProtKB/TrEMBL
      E9PB61
      Related
      ENSP00000421592.2, ENST00000505490.3
      Conserved Domains (3) summary
      COG0724
      Location:114 → 210
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12680
      Location:114 → 187
      RRM_THOC4; RNA recognition motif in THO complex subunit 4 (THOC4) and similar proteins
      pfam07078
      Location:4 → 23
      FYTT; Forty-two-three protein

    RNA

    1. NR_158770.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC145207

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      81887835..81891587 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      82754997..82758749 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86V81.3 GenPept UniProtKB/Swiss-Prot:Q86V81

    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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