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Aliases for ALYREF Gene

Aliases for ALYREF Gene

  • Aly/REF Export Factor 2 3 4 5
  • 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
  • THOC4 3 4
  • Tho4 3 4
  • ALY 3 4
  • BEF 3 4
  • THO Complex Subunit 4 3
  • BZIP Enhancing Factor 3
  • ALY/REF 3
  • REF 3

External Ids for ALYREF Gene

Previous HGNC Symbols for ALYREF Gene

  • THOC4

Previous GeneCards Identifiers for ALYREF Gene

  • GC17M079846
  • GC17M079849
  • GC17M079852
  • GC17M079855

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 Transport of the SLBP independent Mature mRNA and Transport of Mature Transcript to Cytoplasm. GO annotations related to this gene include nucleic acid binding and RNA 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

Regulatory Elements for ALYREF Gene

Enhancers for ALYREF Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH17F082492 1.4 FANTOM5 Ensembl ENCODE 34.5 -604.4 -604383 7.0 CREB3L1 ZFP64 DMAP1 FEZF1 YY1 SLC30A9 ZNF416 ZNF143 ZNF263 SP3 NARF ARL2BPP9 ALYREF ENSG00000262049 OGFOD3 ENSG00000262652 HGS LOC105371942 NARF-IT1 SECTM1
GH17F082367 0.2 ENCODE 32.3 -476.5 -476454 1.3 HDGF PKNOX1 ATF1 ZFP64 ARID4B DMAP1 SLC30A9 GLIS2 ZNF143 FOS ALYREF HGS NARF-IT1 ENSG00000262049 ARL2BPP9 ENSG00000262652 TEX19 LOC105371942 ACTG1 ARHGDIA
GH17F081221 0.8 ENCODE 32.2 +668.7 668665 2.5 PKNOX1 ZFP64 ARID4B SIN3A DMAP1 SLC30A9 FOS CEBPZ SP3 SP5 ALYREF HGS TEPSIN ENSG00000262049 ACTG1 SLC38A10 ARHGDIA NDUFAF8 CEP131 ENSG00000262115
GH17F081682 0.2 ENCODE 21 +207.5 207468 3.5 PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 SLC30A9 ZNF143 FOS CEBPZ ARL16 ALYREF CCDC137 PDE6G NPLOC4 TSPAN10 P4HB GCGR MCRIP1 PPP1R27
GH17F082417 0.6 ENCODE 19.1 -527.5 -527498 2.7 CREB3L1 ARID4B SIN3A ZNF48 ZNF143 ZNF207 ZMIZ1 CEBPZ SP3 YY2 HEXDC OGFOD3 ALYREF NPLOC4 LOC105371942 C17orf62 ENSG00000262049 TEX19 UTS2R NARF
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around ALYREF on UCSC Golden Path with GeneCards custom track

Genomic Location for ALYREF Gene

Chromosome:
17
Start:
81,887,835 bp from pter
End:
81,891,622 bp from pter
Size:
3,788 bases
Orientation:
Minus strand

Genomic View for ALYREF Gene

Genes around ALYREF on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ALYREF Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ALYREF Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence 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

Post-translational modifications for ALYREF Gene

  • Arg-204 is dimethylated, probably to asymmetric dimethylarginine. Arginine methylation reduces RNA binding.
  • Citrullinated by PADI4.
  • Ubiquitination at Lys 86 and Lys 164
  • Modification sites at PhosphoSitePlus

Other Protein References for ALYREF Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for ALYREF (THOC4)
  • Abcam antibodies for ALYREF

No data available for DME Specific Peptides for ALYREF Gene

Domains & Families for ALYREF Gene

Gene Families for ALYREF Gene

Protein Domains for ALYREF Gene

Suggested Antigen Peptide Sequences for ALYREF Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q86V81

UniProtKB/Swiss-Prot:

THOC4_HUMAN :
  • Contains 1 RRM (RNA recognition motif) domain.
  • Belongs to the ALYREF family.
Domain:
  • Contains 1 RRM (RNA recognition motif) domain.
Family:
  • Belongs to the ALYREF family.
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 IEA --
GO:0005515 protein binding IPI 11546874
GO:0044822 poly(A) RNA binding IDA 22658674
genes like me logo Genes that share ontologies with ALYREF: view
genes like me logo Genes that share phenotypes with ALYREF: view

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets 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 (PubMed:19324961). Localizes to regions surrounding nuclear speckles known as perispeckles in which TREX complex assembly seems to occur (PubMed:23826332). {ECO:0000269 PubMed:19324961, ECO:0000269 PubMed:23826332}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for ALYREF Gene COMPARTMENTS Subcellular localization image for ALYREF gene
Compartment Confidence
cytosol 5
extracellular 5
nucleus 5
cytoskeleton 2
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for ALYREF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000346 transcription export complex IDA 15833825
GO:0000784 colocalizes_with nuclear chromosome, telomeric region IDA 24270157
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm IDA,TAS --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with ALYREF: view

Pathways & Interactions for ALYREF Gene

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

Pathways by source for ALYREF Gene

SIGNOR curated interactions for ALYREF Gene

Is activated by:

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:0006369 termination of RNA polymerase II transcription TAS --
GO:0006405 RNA export from nucleus 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:

Inhibitory RNA Products

Flow Cytometry Products

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

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for ALYREF Gene



Protein tissue co-expression partners for ALYREF Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of ALYREF Gene:

ALYREF

SOURCE GeneReport for Unigene cluster for ALYREF Gene:

Hs.534385

mRNA Expression by UniProt/SwissProt for ALYREF Gene:

Q86V81-THOC4_HUMAN
Tissue specificity: Expressed in a wide variety of cancer types.
genes like me logo Genes that share expression patterns with ALYREF: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Protein differential expression in normal tissues for ALYREF Gene

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 35
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia ALYREF 35
  • 97 (a)
OneToOne
THOC4 34
  • 90.4 (n)
mouse
(Mus musculus)
Mammalia Alyref 35
  • 95 (a)
OneToMany
Alyref2 35
  • 88 (a)
OneToMany
Gm9476 35
  • 70 (a)
OneToMany
Gm5699 35
  • 67 (a)
OneToMany
Gm21304 35
  • 66 (a)
OneToMany
Gm5698 35
  • 66 (a)
OneToMany
Gm8764 35
  • 66 (a)
OneToMany
Gm20765 35
  • 65 (a)
OneToMany
Gm21312 35
  • 65 (a)
OneToMany
Gm6489 35
  • 65 (a)
OneToMany
Gm4340 35
  • 64 (a)
OneToMany
Gm6763 35 35
  • 64 (a)
OneToMany
Gm4781 35
  • 59 (a)
OneToMany
Gm4303 35
  • 58 (a)
OneToMany
Gm4305 35
  • 58 (a)
OneToMany
Gm4307 35
  • 58 (a)
OneToMany
Gm4301 35
  • 57 (a)
OneToMany
Gm4302 35
  • 57 (a)
OneToMany
Gm4308 35
  • 57 (a)
OneToMany
Gm4312 35
  • 57 (a)
OneToMany
cow
(Bos Taurus)
Mammalia ALYREF 34 35
  • 90.92 (n)
rat
(Rattus norvegicus)
Mammalia Alyref 34
  • 89.34 (n)
oppossum
(Monodelphis domestica)
Mammalia ALYREF 35
  • 79 (a)
OneToOne
chicken
(Gallus gallus)
Aves ALYREF 35
  • 83 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia ALYREF 35
  • 80 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.10632 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.20904 34
zebrafish
(Danio rerio)
Actinopterygii alyref 35
  • 70 (a)
OneToOne
wufb39h11 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.13971 34
fruit fly
(Drosophila melanogaster)
Insecta Ref1 35
  • 45 (a)
OneToMany
Ref2 35
  • 32 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8347 35
  • 52 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.7498 34
Species where no ortholog for ALYREF was found in the sources mined by GeneCards:
  • 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
rs111334610 -- 81,891,913(+) CCTAC(C/G)CGCCC intron-variant, upstream-variant-2KB
rs111848880 -- 81,893,481(+) CTCCT(C/T)GGCCT intron-variant, upstream-variant-2KB
rs112154648 -- 81,891,785(+) TGGTC(A/G)TTTTT intron-variant, upstream-variant-2KB, utr-variant-5-prime
rs112480169 -- 81,890,922(+) GAGAG(A/G)ATCCG intron-variant, upstream-variant-2KB
rs113130670 -- 81,893,228(+) GCTGG(A/G/T)ATTAC intron-variant, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for ALYREF Gene

Variant ID Type Subtype PubMed ID
esv21913 CNV gain+loss 19812545
esv29964 CNV loss 17803354
esv33468 CNV loss 17666407
esv33475 CNV gain+loss 17666407
esv3641407 CNV gain 21293372
nsv1070854 CNV deletion 25765185
nsv1118775 CNV deletion 24896259
nsv428351 CNV gain 18775914
nsv470620 CNV loss 18288195
nsv833569 CNV loss 17160897
nsv952392 CNV deletion 24416366

Variation tolerance for ALYREF Gene

Residual Variation Intolerance Score: 41.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.93; 19.24% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for ALYREF Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
ALYREF

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ALYREF Gene

Disorders for ALYREF Gene

Relevant External Links for ALYREF

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
ALYREF

No disorders were found for ALYREF Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ALYREF Gene

Publications for ALYREF Gene

  1. 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 22 64
  2. Recruitment of the human TREX complex to mRNA during splicing. (PMID: 15998806) Masuda S. … Reed R. (Genes Dev. 2005) 2 3 4 64
  3. 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 22 64
  4. 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 22 64
  5. Luzp4 defines a new mRNA export pathway in cancer cells. (PMID: 25662211) Viphakone N. … Wilson S.A. (Nucleic Acids Res. 2015) 3 4 64

Products for ALYREF Gene

Sources for ALYREF Gene

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