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Aliases for ALYREF Gene

Aliases for ALYREF Gene

  • Aly/REF Export Factor 2 3 4
  • THOC4 3 4 6
  • ALY 3 4 6
  • BEF 3 4 6
  • Transcriptional Coactivator Aly/REF 3 4
  • BZIP-Enhancing Factor BEF 3 4
  • Ally Of AML-1 And LEF-1 3 4
  • THO Complex 4 2 3
  • Tho4 3 4
  • THO Complex Subunit 4 3
  • BZIP Enhancing Factor 3
  • ALY/REF 3
  • REF 3

External Ids for ALYREF Gene

Previous Symbols for ALYREF Gene

  • THOC4

Summaries for ALYREF Gene

Entrez Gene Summary for ALYREF Gene

  • 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]

GeneCards Summary for ALYREF Gene

ALYREF (Aly/REF Export Factor) is a Protein Coding gene. Among its related pathways are Translational Control and Gene Expression. GO annotations related to this gene include RNA binding and nucleotide binding.

UniProtKB/Swiss-Prot for ALYREF Gene

  • Export adapter involved in nuclear export of spliced and unspliced mRNA. Binds mRNA which is thought to be transferred to the NXF1-NXT1 heterodimer for export (TAP/NFX1 pathway). Component of the TREX complex which is thought to couple mRNA transcription, processing and nuclear export, and specifically associates with spliced mRNA and not with unspliced pre-mRNA. TREX is recruited to spliced mRNAs by a transcription-independent mechanism, binds to mRNA upstream of the exon-junction complex (EJC) and is recruited in a splicing- and cap-dependent manner to a region near the 5 end of the mRNA where it functions in mRNA export to the cytoplasm. TREX recruitment occurs via an interaction between ALYREF/THOC4 and the cap-binding protein NCBP1. The TREX complex is essential for the export of Kaposis sarcoma-associated herpesvirus (KSHV) intronless mRNAs and infectious virus production; ALYREF/THOC4 mediates the recruitment of the TREX complex to the intronless viral mRNA. Required for TREX complex assembly and for linking DDX39B to the cap-binding complex (CBC). In conjunction with THOC5 functions in NXF1-NXT1 mediated nuclear export of HSP70 mRNA; both proteins enhance the RNA binding activity of NXF1 and are required for NXF1 localization to the nuclear rim. Involved in the nuclear export of intronless mRNA; proposed to be recruited to intronless mRNA by ATP-bound DDX39B. Involved in transcription elongation and genome stability

  • Acts as chaperone and promotes the dimerization of transcription factors containing basic leucine zipper (bZIP) domains and thereby promotes transcriptional activation

Gene Wiki entry for ALYREF Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ALYREF Gene

Genomics for ALYREF Gene

Genomic Location for ALYREF Gene

Start:
81,887,835 bp from pter
End:
81,891,586 bp from pter
Size:
3,752 bases
Orientation:
Minus strand

Genomic View for ALYREF Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for ALYREF Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ALYREF Gene

No data available for Regulatory Elements for ALYREF Gene

Proteins for ALYREF Gene

  • Protein details for ALYREF Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q86V81-THOC4_HUMAN
    Recommended name:
    THO complex subunit 4
    Protein Accession:
    Q86V81
    Secondary Accessions:
    • O43672

    Protein attributes for ALYREF Gene

    Size:
    257 amino acids
    Molecular mass:
    26888 Da
    Quaternary structure:
    • Homomultimer. Is part of several complexes involved in mRNA processing and export. Component of the transcription/export (TREX) complex at least composed of ALYREF/THOC4, DDX39B, SARNP/CIP29, CHTOP and the THO subcomplex; TREX seems to have a dynamic structure involving ATP-dependent remodeling; in the complex interacts (via C-terminus) directly with DDX39B and interacts directly with THOC1 and THOC2. Found in mRNA splicing-dependent exon junction complexes (EJC). Identified in the spliceosome C complex. Found in a mRNP complex with UPF3A and UPF3B. Interacts with RBM8A, NCBP1, THOC5, LEF1, RUNX1, EIF4A3, RNPS1, SRRM1, IWS1 and EXOSC1. Interacts with NXF1; the interaction is direct. Interacts with human Kaposis sarcoma-associated herpesvirus (HHV-8) ORF57 protein; this interaction allows efficient export of HHV-8 early and late intronless transcripts. Interacts with HHV-1 ICP27 protein; this interaction recruits ALYREF to viral replication compartments and probably directs viral mRNA to the TAP/NFX1 pathway.
    Miscellaneous:
    • Antibodies against ALYREF/THOC4 are found in sera of patients with systemic lupus erythematosus (SLE)

    Three dimensional structures from OCA and Proteopedia for ALYREF Gene

neXtProt entry for ALYREF Gene

Proteomics data for ALYREF Gene at MOPED

Post-translational modifications for ALYREF Gene

  • Arg-204 is dimethylated, probably to asymmetric dimethylarginine. Arginine methylation reduces RNA binding.
  • Citrullinated by PADI4.
  • Modification sites at PhosphoSitePlus
  • Ubiquitination at Lys4, Lys14, Lys81, Lys86, Lys164, and Lys235

Other Protein References for ALYREF Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for ALYREF Gene

Domains for ALYREF Gene

Gene Families for ALYREF Gene

HGNC:
  • RBM :RNA binding motif (RRM) containing
  • THOC :THO complex subunits

Protein Domains for ALYREF Gene

UniProtKB/Swiss-Prot:

THOC4_HUMAN
Domain:
  • Contains 1 RRM (RNA recognition motif) domain.:
    • Q86V81
Family:
  • Belongs to the ALYREF family.:
    • Q86V81
genes like me logo Genes that share domains with ALYREF: view

Function for ALYREF Gene

Molecular function for ALYREF Gene

UniProtKB/Swiss-Prot Function: Export adapter involved in nuclear export of spliced and unspliced mRNA. Binds mRNA which is thought to be transferred to the NXF1-NXT1 heterodimer for export (TAP/NFX1 pathway). Component of the TREX complex which is thought to couple mRNA transcription, processing and nuclear export, and specifically associates with spliced mRNA and not with unspliced pre-mRNA. TREX is recruited to spliced mRNAs by a transcription-independent mechanism, binds to mRNA upstream of the exon-junction complex (EJC) and is recruited in a splicing- and cap-dependent manner to a region near the 5 end of the mRNA where it functions in mRNA export to the cytoplasm. TREX recruitment occurs via an interaction between ALYREF/THOC4 and the cap-binding protein NCBP1. The TREX complex is essential for the export of Kaposis sarcoma-associated herpesvirus (KSHV) intronless mRNAs and infectious virus production; ALYREF/THOC4 mediates the recruitment of the TREX complex to the intronless viral mRNA. Required for TREX complex assembly and for linking DDX39B to the cap-binding complex (CBC). In conjunction with THOC5 functions in NXF1-NXT1 mediated nuclear export of HSP70 mRNA; both proteins enhance the RNA binding activity of NXF1 and are required for NXF1 localization to the nuclear rim. Involved in the nuclear export of intronless mRNA; proposed to be recruited to intronless mRNA by ATP-bound DDX39B. Involved in transcription elongation and genome stability
UniProtKB/Swiss-Prot Function: Acts as chaperone and promotes the dimerization of transcription factors containing basic leucine zipper (bZIP) domains and thereby promotes transcriptional activation

Gene Ontology (GO) - Molecular Function for ALYREF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0003676 nucleic acid binding --
GO:0003697 single-stranded DNA binding --
GO:0003723 RNA binding --
GO:0005515 protein binding IPI 11546874
genes like me logo Genes that share ontologies with ALYREF: view
genes like me logo Genes that share phenotypes with ALYREF: view

miRNA for ALYREF Gene

miRTarBase miRNAs that target ALYREF

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting and HOMER Transcription for ALYREF Gene

Localization for ALYREF Gene

Subcellular locations from UniProtKB/Swiss-Prot for ALYREF Gene

Nucleus. Nucleus speckle. Cytoplasm. Note=Colocalizes with the core EJC, ALYREF/THOC4, NXF1 and DDX39B in the nucleus and nuclear speckles. Travels to the cytoplasm as part of the exon junction complex (EJC) bound to mRNA. Localizes to regions surrounding nuclear speckles known as perispeckles in which TREX complex assembly seems to occur.

Gene Ontology (GO) - Cellular Components for ALYREF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000346 transcription export complex IDA 15833825
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm TAS --
GO:0005829 cytosol TAS --
GO:0016020 membrane IDA 16210410
genes like me logo Genes that share ontologies with ALYREF: view

Pathways for ALYREF Gene

genes like me logo Genes that share pathways with ALYREF: view

Gene Ontology (GO) - Biological Process for ALYREF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000018 regulation of DNA recombination IMP 22144908
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0001649 osteoblast differentiation IDA 16210410
GO:0006366 transcription from RNA polymerase II promoter TAS --
GO:0006369 termination of RNA polymerase II transcription TAS --
genes like me logo Genes that share ontologies with ALYREF: view

Transcripts for ALYREF Gene

mRNA/cDNA for ALYREF Gene

Unigene Clusters for ALYREF Gene

Aly/REF export factor:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for ALYREF Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b
SP1: -
SP2:
SP3: - -

Relevant External Links for ALYREF Gene

GeneLoc Exon Structure for
ALYREF
ECgene alternative splicing isoforms for
ALYREF

Expression for ALYREF Gene

mRNA expression in normal human tissues for ALYREF Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for ALYREF Gene

SOURCE GeneReport for Unigene cluster for ALYREF Gene Hs.534385

genes like me logo Genes that share expressions with ALYREF: view

Orthologs for ALYREF Gene

This gene was present in the common ancestor of animals.

Orthologs for ALYREF Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia ALYREF 37
  • 98 (a)
OneToOne
cow
(Bos Taurus)
Mammalia ALYREF 36
  • 90.92 (n)
  • 98.05 (a)
ALYREF 37
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia ALYREF 37
  • 97 (a)
OneToOne
THOC4 36
  • 90.4 (n)
  • 97.28 (a)
mouse
(Mus musculus)
Mammalia Alyref 16
Alyref 37
  • 95 (a)
OneToMany
Alyref2 37
  • 88 (a)
OneToMany
Gm20765 37
  • 65 (a)
OneToMany
Gm21304 37
  • 66 (a)
OneToMany
Gm21312 37
  • 65 (a)
OneToMany
Gm4301 37
  • 57 (a)
OneToMany
Gm4302 37
  • 57 (a)
OneToMany
Gm4303 37
  • 58 (a)
OneToMany
Gm4305 37
  • 58 (a)
OneToMany
Gm4307 37
  • 58 (a)
OneToMany
Gm4308 37
  • 57 (a)
OneToMany
Gm4312 37
  • 57 (a)
OneToMany
Gm4340 37
  • 64 (a)
OneToMany
Gm4781 37
  • 59 (a)
OneToMany
Gm5698 37
  • 66 (a)
OneToMany
Gm5699 37
  • 67 (a)
OneToMany
Gm6489 37
  • 65 (a)
OneToMany
Gm6763 37
  • 64 (a)
OneToMany
Gm6763 37
  • 66 (a)
OneToMany
Gm8764 37
  • 66 (a)
OneToMany
Gm9476 37
  • 70 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia ALYREF 37
  • 79 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Alyref 36
  • 89.34 (n)
  • 98.26 (a)
chicken
(Gallus gallus)
Aves ALYREF 37
  • 83 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia ALYREF 37
  • 80 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.20904 36
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.10632 36
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.13971 36
zebrafish
(Danio rerio)
Actinopterygii alyref 37
  • 70 (a)
OneToOne
wufb39h11 36
fruit fly
(Drosophila melanogaster)
Insecta Ref1 37
  • 45 (a)
OneToMany
Ref2 37
  • 32 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.7498 36
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8347 37
  • 52 (a)
OneToOne
Species with no ortholog for ALYREF:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for ALYREF Gene

ENSEMBL:
Gene Tree for ALYREF (if available)
TreeFam:
Gene Tree for ALYREF (if available)

Paralogs for ALYREF Gene

Pseudogenes.org Pseudogenes for ALYREF Gene

genes like me logo Genes that share paralogs with ALYREF: view

No data available for Paralogs for ALYREF Gene

Variants for ALYREF Gene

Sequence variations from dbSNP and Humsavar for ALYREF Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type MAF
rs34992198 -- 81,887,836(+) CAGTT(-/C)CCAGT utr-variant-3-prime
rs75583866 -- 81,888,340(+) CCTCC(A/G)CGGGT reference, synonymous-codon, downstream-variant-500B
rs115610695 -- 81,888,484(+) ACCCT(C/T)GGCCA intron-variant, downstream-variant-500B
rs138567865 -- 81,888,542(+) CTGTG(C/T)GTCAA missense, reference, downstream-variant-500B
rs145890926 -- 81,888,092(+) GGAGA(C/T)GCCTG utr-variant-3-prime

Relevant External Links for ALYREF Gene

HapMap Linkage Disequilibrium report
ALYREF

No data available for Structural Variations from Database of Genomic Variants (DGV) for ALYREF Gene

Disorders for ALYREF Gene

No disorders were found for ALYREF Gene.

No data available for UniProtKB/Swiss-Prot for ALYREF Gene

Publications for ALYREF Gene

  1. Autoantibodies to transcriptional regulation proteins DEK and ALY in a patient with systemic lupus erythematosus. (PMID: 9952027) Wichmann I. … Nunez-Roldan A. (Hum. Immunol. 1999) 3 4 23
  2. A human nuclear-localized chaperone that regulates dimerization, DNA binding, and transcriptional activity of bZIP proteins. (PMID: 10488337) Virbasius C.-M. … Green M.R. (Mol. Cell 1999) 3 4 23
  3. Recruitment of the complete hTREX complex is required for Kaposi's sarcoma-associated herpesvirus intronless mRNA nuclear export and virus replication. (PMID: 18974867) Boyne J.R. … Whitehouse A. (PLoS Pathog. 2008) 3 4 23
  4. Recruitment of the human TREX complex to mRNA during splicing. (PMID: 15998806) Masuda S. … Reed R. (Genes Dev. 2005) 2 3 4
  5. Aly and THO are required for assembly of the human TREX complex and association of TREX components with the spliced mRNA. (PMID: 23222130) Chi B. … Cheng H. (Nucleic Acids Res. 2013) 3 4

Products for ALYREF Gene

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat
  • QIAGEN qRT-PCR Assays for microRNAs that regulate ALYREF
    • QuantiTect SYBR Green Assays in human,mouse,rat
    • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
    • QuantiFast Probe-based Assays in human,mouse,rat
    • Predesigned siRNA for gene silencing in human,mouse,rat for ALYREF
    • Block miRNA regulation of ALYREF using miScript Target Protectors

    Sources for ALYREF Gene

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