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ALYREF
Available structures PDB Ortholog search: PDBe RCSB List of PDB id codes 3ULH
Identifiers
Aliases	ALYREF, ALY, ALY/REF, BEF, REF, THOC4, Aly/REF export factor
External IDs	OMIM: 604171; MGI: 1341044; HomoloGene: 134554; GeneCards: ALYREF; OMA:ALYREF - orthologs
Gene location (Human) Chr. Chromosome 17 (human) Band 17q25.3 Start 81,887,835 bp End 81,891,586 bp
Gene location (Mouse) Chr. Chromosome 11 (mouse) Band 11|11 E2 Start 120,482,947 bp End 120,489,191 bp
RNA expression pattern Bgee Human Mouse (ortholog) Top expressed in ganglionic eminence ventricular zone stromal cell of endometrium left testis mucosa of transverse colon right testis monocyte granulocyte appendix skin of abdomen Top expressed in maxillary prominence mandibular prominence ventricular zone somite epiblast abdominal wall renal corpuscle yolk sac gastrula thymus More reference expression data BioGPS n/a
Gene ontology Molecular function protein binding nucleic acid binding RNA binding Cellular component cytoplasm cytosol nuclear speck catalytic step 2 spliceosome membrane transcription export complex exon-exon junction complex spliceosomal complex extracellular exosome nucleus nucleoplasm Biological process regulation of DNA recombination mRNA splicing, via spliceosome termination of RNA polymerase II transcription mRNA transport mRNA processing viral mRNA export from host cell nucleus mRNA export from nucleus positive regulation of DNA-templated transcription, elongation osteoblast differentiation replication fork processing viral process mRNA 3'-end processing RNA splicing RNA export from nucleus transport Sources:Amigo / QuickGO
Orthologs Species Human Mouse Entrez 10189 21681 Ensembl ENSG00000183684 ENSMUSG00000025134 UniProt Q86V81 O08583 RefSeq (mRNA) NM_005782 NM_011568 RefSeq (protein) NP_005773 NP_035698 Location (UCSC) Chr 17: 81.89 – 81.89 Mb Chr 11: 120.48 – 120.49 Mb PubMed search
Wikidata
View/Edit Human View/Edit Mouse

Aly/REF export factor, also known as THO complex subunit 4 is a protein that in humans is encoded by the ALYREF gene.

The ALYREF gene encodes Aly/REF export factor (ALY; THO complex subunit 4, Tho4; RNA and export factor binding protein 1, Refbp1), a ubiquitously expressed nuclear protein that functions as a molecular chaperone and export adapter involved in nuclear export of spliced and unspliced mRNA. The TRanscription-EXport (TREX) complex, a key player in mRNA export, includes the THO subcomplex, the RNA helicase UAP56, and the RNA-binding protein ALY. In yeast, TREX is recruited co-transcriptionally; in human cells it is recruited during a late step of splicing. The human TREX complex is recruited to a region near the 5' end of mRNA by interaction of ALY and THO with the nuclear cap-binding complex. As a chaperone, ALY promotes dimerization of transcription factors containing basic leucine zipper (bZIP) domains., thereby promoting transcriptional activation. ALY has key roles in 3'-end processing of polyadenylated mRNAs and in nuclear export of both polyadenylated and non-polyadenylated mRNAs. After mRNA binds to ALY, it is apparently transferred to the NXF1-NXT1 heterodimer for export (TAP/NFX1 pathway). The full-length ALY protein (Refbp1-I, 255 amino acids encoded by six exons) has a conserved RNA recognition motif (RRM; amino acids 105-182) flanked by alanine/arginine/glycine-rich sequences; an N-terminal region (amino acids 16-37) is sufficient for RNA binding and interaction with the NXF1-NXT1 heterodimer.

References

1. ^ GRCh38: Ensembl release 89: ENSG00000183684 – Ensembl, May 2017
2. ^ GRCm38: Ensembl release 89: ENSMUSG00000025134 – Ensembl, May 2017
3. "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
4. "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
5. Muravenko OV, Gizatullin RZ, Al-Amin AN, Protopopov AI, Kashuba VI, Zelenin AV, Zabarovsky ER (Jan 2001). "Human ALY/BEF gene Map position 17q25.3". Chromosome Res. 8 (6): 562. doi:10.1023/A:1009236126053. PMID 11032328. S2CID 6859937.
6. "Entrez Gene: ALYREF Aly/REF export factor".
7. "Entrez Gene: THOC4 THO complex 4".
8. Shi M, Zhang H, Wu X, He Z, Wang L, Yin S, Tian B, Li G, Cheng H (Sep 2017). "ALYREF mainly binds to the 5' and the 3' regions of the mRNA in vivo". Nucleic Acids Res. 45 (16): 9640–9653. doi:10.1093/nar/gkx597. PMC 5766156. PMID 28934468.
9. Shi M, Zhang H, Wu X, He Z, Wang L, Yin S, Tian B, Li G, Cheng H (Mar 2019). "ALYREF links 3'-end processing to nuclear export of non-polyadenylated mRNAs". EMBO J. 38 (9): e99910. doi:10.15252/embj.201899910. PMC 6484419. PMID 30858280.
10. "Ensembl: Gene ALYREF ENSG00000183684 (human)".
11. "UniProtKB Q86V81 (THOC4_HUMAN)".

Further reading

• Bruhn L, Munnerlyn A, Grosschedl R (1997). "ALY, a context-dependent coactivator of LEF-1 and AML-1, is required for TCRalpha enhancer function". Genes Dev. 11 (5): 640–53. doi:10.1101/gad.11.5.640. PMID 9119228.
• Neubauer G, King A, Rappsilber J, et al. (1998). "Mass spectrometry and EST-database searching allows characterization of the multi-protein spliceosome complex". Nat. Genet. 20 (1): 46–50. doi:10.1038/1700. PMID 9731529. S2CID 585778.
• Wichmann I, Garcia-Lozano JR, Respaldiza N, et al. (1999). "Autoantibodies to transcriptional regulation proteins DEK and ALY in a patient with systemic lupus erythematosus". Hum. Immunol. 60 (1): 57–62. doi:10.1016/S0198-8859(98)00085-8. PMID 9952027.
• Virbasius CM, Wagner S, Green MR (1999). "A human nuclear-localized chaperone that regulates dimerization, DNA binding, and transcriptional activity of bZIP proteins". Mol. Cell. 4 (2): 219–28. doi:10.1016/S1097-2765(00)80369-X. PMID 10488337.
• Le Hir H, Izaurralde E, Maquat LE, Moore MJ (2001). "The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions". EMBO J. 19 (24): 6860–9. doi:10.1093/emboj/19.24.6860. PMC 305905. PMID 11118221.
• Kim VN, Kataoka N, Dreyfuss G (2001). "Role of the nonsense-mediated decay factor hUpf3 in the splicing-dependent exon-exon junction complex". Science. 293 (5536): 1832–6. Bibcode:2001Sci...293.1832K. doi:10.1126/science.1062829. PMID 11546873. S2CID 12018200.
• Luo ML, Zhou Z, Magni K, et al. (2001). "Pre-mRNA splicing and mRNA export linked by direct interactions between UAP56 and Aly". Nature. 413 (6856): 644–7. Bibcode:2001Natur.413..644L. doi:10.1038/35098106. PMID 11675789. S2CID 4395388.
• Kataoka N, Diem MD, Kim VN, et al. (2002). "Magoh, a human homolog of Drosophila mago nashi protein, is a component of the splicing-dependent exon-exon junction complex". EMBO J. 20 (22): 6424–33. doi:10.1093/emboj/20.22.6424. PMC 125744. PMID 11707413.
• Strässer K, Masuda S, Mason P, et al. (2002). "TREX is a conserved complex coupling transcription with messenger RNA export". Nature. 417 (6886): 304–8. Bibcode:2002Natur.417..304S. doi:10.1038/nature746. PMID 11979277. S2CID 1112194.
• Jurica MS, Licklider LJ, Gygi SR, et al. (2002). "Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis". RNA. 8 (4): 426–39. doi:10.1017/S1355838202021088. PMC 1370266. PMID 11991638.
• Rappsilber J, Ryder U, Lamond AI, Mann M (2002). "Large-scale proteomic analysis of the human spliceosome". Genome Res. 12 (8): 1231–45. doi:10.1101/gr.473902. PMC 186633. PMID 12176931.
• Chen IH, Sciabica KS, Sandri-Goldin RM (2002). "ICP27 interacts with the RNA export factor Aly/REF to direct herpes simplex virus type 1 intronless mRNAs to the TAP export pathway". J. Virol. 76 (24): 12877–89. doi:10.1128/JVI.76.24.12877-12889.2002. PMC 136725. PMID 12438613.
• Strausberg RL, Feingold EA, Grouse LH, et al. (2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16899–903. Bibcode:2002PNAS...9916899M. doi:10.1073/pnas.242603899. PMC 139241. PMID 12477932.
• McCracken S, Longman D, Johnstone IL, et al. (2004). "An evolutionarily conserved role for SRm160 in 3'-end processing that functions independently of exon junction complex formation". J. Biol. Chem. 278 (45): 44153–60. doi:10.1074/jbc.M306856200. PMID 12944400.
• Pryor A, Tung L, Yang Z, et al. (2004). "Growth-regulated expression and G0-specific turnover of the mRNA that encodes URH49, a mammalian DExH/D box protein that is highly related to the mRNA export protein UAP56". Nucleic Acids Res. 32 (6): 1857–65. doi:10.1093/nar/gkh347. PMC 390356. PMID 15047853.
• Gerhard DS, Wagner L, Feingold EA, et al. (2004). "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)". Genome Res. 14 (10B): 2121–7. doi:10.1101/gr.2596504. PMC 528928. PMID 15489334.
• Ong SE, Mittler G, Mann M (2005). "Identifying and quantifying in vivo methylation sites by heavy methyl SILAC". Nat. Methods. 1 (2): 119–26. doi:10.1038/nmeth715. PMID 15782174. S2CID 6654604.
• Masuda S, Das R, Cheng H, et al. (2005). "Recruitment of the human TREX complex to mRNA during splicing". Genes Dev. 19 (13): 1512–7. doi:10.1101/gad.1302205. PMC 1172058. PMID 15998806.
• Mertz JA, Kobayashi R, Dudley JP (2007). "ALY is a common coactivator of RUNX1 and c-Myb on the type B leukemogenic virus enhancer". J. Virol. 81 (7): 3503–13. doi:10.1128/JVI.02253-06. PMC 1866045. PMID 17229714.
• Quaresma AJ, Sievert R, Nickerson JA (2013). "Regulation of mRNA export by the PI3 kinase/AKT signal transduction pathway". Mol. Biol. Cell. 24 (8): 1208–21. doi:10.1091/mbc.E12-06-0450. PMC 3623641. PMID 23427269.

External links

• ALYREF human gene location in the UCSC Genome Browser.
• ALYREF human gene details in the UCSC Genome Browser.
• Overview of all the structural information available in the PDB for UniProt: Q86V81 (THO complex subunit 4) at the PDBe-KB.

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