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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

ALYREF Gene

protein-coding   GIFtS: 54
GCID: GC17M079852

Aly/REF Export Factor

(Previous name: THO complex 4)
(Previous symbol: THOC4)
Microbiology & Infectious Diseases Congress
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Aly/REF Export Factor1 2 3     BZIP-Enhancing Factor BEF2 3
THOC41 2 3 5     ALY/REF2
ALY2 3 5     REF2
BEF2 3 5     BZIP Enhancing Factor2
THO Complex 41 2     THO Complex Subunit 42
Ally Of AML-1 And LEF-12 3     tho42
Transcriptional Coactivator Aly/REF2 3     Tho43

External Ids:    HGNC: 190711   Entrez Gene: 101892   Ensembl: ENSG000001836847   OMIM: 6041715   UniProtKB: Q86V813   

Export aliases for ALYREF gene to outside databases

Previous GC identifers: GC17M079846 GC17M079849


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

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. Diseases associated with ALYREF include kaposi's sarcoma, and conjunctivitis, and among its related super-pathways are mRNA Processing and Post-Elongation Processing of Intron-Containing pre-mRNA. GO annotations related to this gene include RNA binding and nucleotide binding.

UniProtKB/Swiss-Prot: THOC4_HUMAN, Q86V81
Function: Component of the THO subcomplex of the TREX complex. The TREX complex specifically associates with
spliced mRNA and not with unspliced pre-mRNA. It 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. The recruitment
occurs via an interaction between ALYREF/THOC4 and the cap-binding protein NCBP1. DDX39B functions as a bridge
between ALYREF/THOC4 and the THO complex. ALYREF/THOC4 in conjunction with THOC5 functions in NXF1-NXT1 mediated
nuclear export of HSP70 mRNA
Function: Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction
on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear
and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during
subsequent mRNA metabolism. Acts as chaperone and promotes the dimerization of transcription factors containing
basic leucine zipper (bZIP) domains and thereby promotes transcriptional activation. Plays a role in mRNA
processing and export. May function as scaffold that mediates interactions between proteins and/or RNA. Is part
of the exon junction complex that remains associated with spliced mRNA and plays an important role in mRNA export
and nonsense-mediated RNA decay

Gene Wiki entry for ALYREF (THOC4) Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000017.10  NT_010663.15  NC_018928.2  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for ALYREF
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for ALYREF

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat ALYREF


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 17q25.3   Ensembl cytogenetic band:  17q25.3   HGNC cytogenetic band: 17q25.3

ALYREF Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ALYREF gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17M079852:  view genomic region     (about GC identifiers)

Start:
79,845,711 bp from pter      End:
79,849,462 bp from pter
Size:
3,752 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: THOC4_HUMAN, Q86V81 (See protein sequence)
Recommended Name: THO complex subunit 4  
Size: 257 amino acids; 26888 Da
Subunit: Homomultimer. Component of the THO complex, which is composed of THOC1, THOC2, THOC5, THOC6 and THOC7.
Together with THOC3, ALYREF/THOC4 and DDX39B, THO forms the transcription/export (TREX) complex. Interacts (via
C-terminus) with DDX39B. Interacts with NCBP1 and THOC5. Binds LEF1 and RUNX1 (By similarity). Is part of several
complexes involved in mRNA processing and export. Associates with the spliceosome. Binds NXF1 and RBM8A directly
and is part of the exon junction complex (EJC) containing NCBP1, NCBP2, RBM8A, RNPS1, SRRM1, NXF1, UPF2, UPF3B,
ALYREF/THOC4 and/or REFBP2 (By similarity). Found in a mRNA splicing-dependent exon junction complex (EJC) with
ACIN1, CASC3, DEK, EIF4A3, MAGOH, PNN, RBM8A, RNPS1, SAP18, SRRM1 and ALYREF/THOC4. Found in a mRNP complex with
UPF3A and UPF3B. Interacts with BAT1, EIF4A3, RBM8A, RNPS1 and SRRM1. Identified in the spliceosome C complex.
Interacts with human Kaposi's 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
Subcellular location: 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
Miscellaneous: Antibodies against ALYREF/THOC4 are found in sera of patients with systemic lupus erythematosus
(SLE)
1 PDB 3D structure from and Proteopedia for ALYREF:
3ULH (3D)    
Secondary accessions: O43672

Explore the universe of human proteins at neXtProt for ALYREF: NX_Q86V81

Explore proteomics data for ALYREF at MOPED 

Post-translational modifications:

  • UniProtKB: Arg-50 and Arg-204 are dimethylated, probably to asymmetric dimethylarginine
  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q86V81

  • ALYREF Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    ALYREF Protein Expression
    REFSEQ proteins: NP_005773.3  
    ENSEMBL proteins: 
     ENSP00000421592   ENSP00000331817  
    Reactome Protein details: Q86V81
    Human Recombinant Protein Products for ALYREF: 
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    OriGene Protein Over-expression Lysate for ALYREF
    OriGene Custom MassSpec 
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    Novus Biologicals ALYREF Protein
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp. 

    Gene Ontology (GO): 5/8 cellular component terms (GO ID links to tree view) (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000346transcription export complex IDA15833825
    GO:0005634nucleus IDA--
    GO:0005654nucleoplasm TAS--
    GO:0005730NOT nucleolus IDA--
    GO:0005829cytosol TAS--

    ALYREF for ontologies           About GeneDecksing



    ALYREF Antibody Products: 
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    Novus Biologicals ALYREF Antibodies
    Abcam antibodies for ALYREF
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    LSBio Antibodies in human, mouse, rat for ALYREF 

    Assay Products for ALYREF: 
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    GenScript Custom Assay Services for ALYREF
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    Browse ELISAs at Cloud-Clone Corp. 
    Browse CLIAs at Cloud-Clone Corp.


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    RBM: RNA binding motif (RRM) containing
    THOC: THO complex subunits

    3 InterPro protein domains:
     IPR000504 RRM_dom
     IPR012677 Nucleotide-bd_a/b_plait
     IPR025715 FoP_duplication

    Graphical View of Domain Structure for InterPro Entry Q86V81

    ProtoNet protein and cluster: Q86V81

    1 Blocks protein domain: IPB000504 RNA-binding region RNP-1 (RNA recognition motif)

    UniProtKB/Swiss-Prot: THOC4_HUMAN, Q86V81
    Similarity: Belongs to the ALYREF family
    Similarity: Contains 1 RRM (RNA recognition motif) domain


    ALYREF for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: THOC4_HUMAN, Q86V81
    Function: Component of the THO subcomplex of the TREX complex. The TREX complex specifically associates with
    spliced mRNA and not with unspliced pre-mRNA. It 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. The recruitment
    occurs via an interaction between ALYREF/THOC4 and the cap-binding protein NCBP1. DDX39B functions as a bridge
    between ALYREF/THOC4 and the THO complex. ALYREF/THOC4 in conjunction with THOC5 functions in NXF1-NXT1 mediated
    nuclear export of HSP70 mRNA
    Function: Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction
    on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear
    and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during
    subsequent mRNA metabolism. Acts as chaperone and promotes the dimerization of transcription factors containing
    basic leucine zipper (bZIP) domains and thereby promotes transcriptional activation. Plays a role in mRNA
    processing and export. May function as scaffold that mediates interactions between proteins and/or RNA. Is part
    of the exon junction complex that remains associated with spliced mRNA and plays an important role in mRNA export
    and nonsense-mediated RNA decay

         Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000166nucleotide binding IEA--
    GO:0003676nucleic acid binding ----
    GO:0003723RNA binding IEA--
    GO:0005515protein binding IPI15047853
         
    ALYREF for ontologies           About GeneDecksing


    Phenotypes:
         2 GenomeRNAi human phenotypes for ALYREF:
     Decreased TP53 protein express  Decreased homologous recombina 

    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for ALYREF 
       inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for ALYREF

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for ALYREF 
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for ALYREF 

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    Inhib. RNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ALYREF


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for ALYREF About   (see all 11)                                                                                              See pathways by source

    SuperPathContained pathways About
    1mRNA Splicing - Major Pathway
    Processing of Capped Intron-Containing Pre-mRNA0.85
    mRNA Splicing0.82
    mRNA Processing0.85
    Spliceosome0.31
    mRNA Splicing - Major Pathway0.82
    2RNA Polymerase II Transcription Termination
    RNA Polymerase II Transcription Termination0.79
    Post-Elongation Processing of the Transcript0.79
    Post-Elongation Processing of Intron-Containing pre-mRNA0.79
    mRNA 3'-end processing0.79
    Cleavage of Growing Transcript in the Termination Region 0.79
    3Transport of Mature mRNA Derived from an Intronless Transcript
    Transport of Mature mRNAs Derived from Intronless Transcripts0.89
    Transport of Mature mRNA Derived from an Intronless Transcript0.89
    4Transport of Mature Transcript to Cytoplasm
    Transport of Mature Transcript to Cytoplasm0.85
    Transport of Mature mRNA derived from an Intron-Containing Transcript0.85
    5Transport of the SLBP independent Mature mRNA
    Transport of the SLBP Dependant Mature mRNA0.83
    Transport of the SLBP independent Mature mRNA0.83

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 Cell Signaling Technology (CST) Pathway for ALYREF
        Translational Control

    5/18        Reactome Pathways for ALYREF (see all 18)
        Transport of Mature mRNA derived from an Intron-Containing Transcript
    Transport of Mature Transcript to Cytoplasm
    mRNA Splicing
    Transport of Mature mRNA Derived from an Intronless Transcript
    RNA Polymerase II Transcription


    4         Kegg Pathways  (Kegg details for ALYREF):
        RNA transport
    mRNA surveillance pathway
    Spliceosome
    Herpes simplex infection


    ALYREF for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for ALYREF

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/224 Interacting proteins for ALYREF (Q86V812, 3 ENSP000003318174) via UniProtKB, MINT, STRING, and/or I2D (see all 224)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    NXF1Q9UBU92, 3, ENSP000002941724MINT-7234858 I2D: score=1 STRING: ENSP00000294172
    ENSG00000225073Q138383, ENSP000004003264I2D: score=3 STRING: ENSP00000400326
    DDX39BQ138383, ENSP000003794754I2D: score=3 STRING: ENSP00000379475
    ENSG00000215425Q138383I2D: score=3 
    ENSG00000225859Q138383I2D: score=3 
    About this table

    Gene Ontology (GO): 5/9 biological process terms (GO ID links to tree view) (see all 9):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000398mRNA splicing, via spliceosome TAS--
    GO:0006366transcription from RNA polymerase II promoter TAS--
    GO:0006369termination of RNA polymerase II transcription TAS--
    GO:0006406mRNA export from nucleus TAS--
    GO:0008380RNA splicing TAS--

    ALYREF for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for ALYREF (THOC4)

    Search CenterWatch for drugs/clinical trials and news about ALYREF / THOC4

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for ALYREF gene: 
    NM_005782.3  

    Unigene Cluster for ALYREF:

    Aly/REF export factor
    Hs.534385  [show with all ESTs]
    Unigene Representative Sequence: BU943861
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000505490 ENST00000504015 ENST00000512673 ENST00000511412 ENST00000331204(uc002kbu.2)

    Congresses - knowledge worth sharing:  
    European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 10 - 13 May 2014

    miRNA
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    Additional mRNA sequence: 

    AF047002.1 AF086513.1 BC052302.1 

    8 DOTS entries:

    DT.95304701  DT.113574  DT.100738694  DT.86849160  DT.92056696  DT.95158694  DT.100826159  DT.95158693 

    24/123 AceView cDNA sequences (see all 123):

    BM766572 BU957767 AI088790 BM785773 AI343405 BM782350 AI824093 BM782652 
    AI934760 AI299722 AW082296 AI206071 AI085289 BF446070 AI452979 BM854462 
    AI423863 BQ919512 AF086513 BF512771 AI285920 AI378380 BU624466 BU538782 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for ALYREF    About this scheme

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


    ECgene alternative splicing isoforms for ALYREF

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    ALYREF expression in normal human tissues (normalized intensities)      ALYREF embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TAAAGGTTTT
    ALYREF Expression
    About this image


    ALYREF expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/35 selected tissues (see all 35) fully expand
     
     Epithelium
             vagina ; squamous epithelial cells   
     
     Uterus
             uterus, post-menopause ; glandular cells   
     
     Testis (Reproductive System)    fully expand to see all 4 entries
             Leydig Cells Testis Interstitium
             seminal vesicle ; glandular cells   
     
     Colon (Gastrointestinal Tract)    fully expand to see all 4 entries
             colon ; peripheral nerve/ganglion   
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex

    See ALYREF Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for ALYREF

    SOURCE GeneReport for Unigene cluster: Hs.534385
        SABiosciences Custom PCR Arrays for ALYREF
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ALYREF

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of eukaryotes.

    Orthologs for ALYREF gene from 8/19 species (see all 19)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Alyref1 , 5 Aly/REF export factor1, 5 88.5(n)1
    96.86(a)1
      11 (84.31 cM)5
    216811  NM_011568.11  NP_035698.11 
     1205921215 
    chicken
    (Gallus gallus)
    Aves THOC41 THO complex 4 78.13(n)
    88.93(a)
      769169  XM_001232392.2  XP_001232393.2 
    lizard
    (Anolis carolinensis)
    Reptilia ALYREF6
    Uncharacterized protein
    75(a)
    1 ↔ 1
    2(118563537-118566808)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.209042 Xenopus laevis transcribed sequence with moderate similarity more 75.82(n)    CA972927.1 
    zebrafish
    (Danio rerio)
    Actinopterygii wufb39h112 Transcribed sequence with weak similarity to protein more 79.24(n)    CK148094.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Aly1 Aly 56.28(n)
    51.82(a)
      44029  NM_143711.2  NP_651968.1 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT5G025301 THO complex subunit 4 52.36(n)
    55.42(a)
      831923  NM_120331.4  NP_195873.2 
    rice
    (Oryza sativa)
    Liliopsida AK068868.12   -- 71.78(n)    AK068868.1 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for ALYREF gene

    ALYREF for paralogs           About GeneDecksing


    2 Pseudogenes.org Pseudogenes for ALYREF
    PGOHUM00000233434 PGOHUM00000262546


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/77 SNPs in ALYREF are shown (see all 77)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 17 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1823148441,2
    --79845320(+) AGAAGA/GAAAGG 1 -- ds50010--------
    rs1866844911,2
    --79845366(+) TGGACA/GGCACA 1 -- ds50010--------
    rs1925760051,2
    --79845606(+) TGGGGA/CTGCTC 1 -- ds50010--------
    rs1858258361,2
    --79845818(+) AAAACA/CGGTCT 1 -- ut310--------
    rs1498528471,2
    C--79845941(+) CCACCA/GCCCCC 1 -- ut310--------
    rs1886893221,2
    C--79845947(+) CCCCCC/GAACCA 1 -- ut310--------
    rs1932024601,2
    C--79845954(+) ACCAGG/AGAGCA 1 -- ut311Minor allele frequency- A:0.01EU 425
    rs1458909261,2
    C--79845968(+) GGAGAC/TGCCTG 1 -- ut311Minor allele frequency- T:0.00EU 775
    rs3772016581,2
    C--79846035(+) CAGAGA/GAGAAA 1 -- int10--------
    rs2017887221,2
    C--79846043(+) AAAGAG/AGCTTG 1 -- int11Minor allele frequency- A:0.00EU 1067

    HapMap Linkage Disequilibrium report for ALYREF (79845711 - 79849462 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for ALYREF: --
    SABiosciences Cancer Mutation PCR Assays
    SeqTarget long-range PCR primers for resequencing ALYREF
    DNA2.0 Custom Variant and Variant Library Synthesis for ALYREF

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 604171    OMIM disorders: --

    8 diseases for ALYREF:    About MalaCards
    kaposi's sarcoma    conjunctivitis    herpes simplex    systemic lupus erythematosus
    lupus erythematosus    sarcoma    hepatocellular carcinoma    breast cancer


    ALYREF for disorders           About GeneDecksing


    Export disorders for ALYREF gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for ALYREF gene, integrated from 9 sources (see all 95):
    (articles sorted by number of sources associating them with ALYREF)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Autoantibodies to transcriptional regulation proteins DEK and ALY in a patient with systemic lupus erythematosus. (PubMed id 9952027)1, 2, 9 Wichmann I.... Nunez-Roldan A. (1999)
    2. A human nuclear-localized chaperone that regulates dimerization, DNA binding, and transcriptional activity of bZIP proteins. (PubMed id 10488337)1, 2, 9 Virbasius C.-M.... Green M.R. (1999)
    3. Recruitment of the complete hTREX complex is required for Kaposi's sarcoma-associated herpesvirus intronless mRNA nuclear export and virus replication. (PubMed id 18974867)1, 2, 9 Boyne J.R.... Whitehouse A. (2008)
    4. Adaptor Aly and co-adaptor Thoc5 function in the Tap-p15-mediated nuclear export of HSP70 mRNA. (PubMed id 19165146)1, 2 Katahira J.... Yoneda Y. (2009)
    5. Human mRNA export machinery recruited to the 5' end of mRNA. (PubMed id 17190602)1, 2 Cheng H.... Reed R. (2006)
    6. Linking transcriptional elongation and messenger RNA export to metastatic breast cancers. (PubMed id 15833825)1, 2 Guo S.... Shiekhattar R. (2005)
    7. Biochemical analysis of the EJC reveals two new factors and a stable tetrameric protein core. (PubMed id 16314458)1, 2 Tange T.O.... Moore M.J. (2005)
    8. Recruitment of the human TREX complex to mRNA during splicing. (PubMed id 15998806)1, 2 Masuda S.... Reed R. (2005)
    9. Identifying and quantifying in vivo methylation sites by heavy methyl SILAC. (PubMed id 15782174)1, 2 Ong S.E.... Mann M. (2004)
    10. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 10189 HGNC: 19071 AceView: THOC4 Ensembl:ENSG00000183684 euGenes: HUgn10189
    ECgene: ALYREF Kegg: 10189 H-InvDB: ALYREF

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for ALYREF Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for ALYREF gene:
    Search GeneIP for patents involving ALYREF

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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    About This Section

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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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