ALYREF [The Human Chemical-Genetic Interaction Map Project]

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======= ALYREF =======


== Gene Information ==
  * **<color #00a2e8>Official Symbol</color>**: ALYREF
  * **<color #00a2e8>Official Name</color>**: Aly/REF export factor
  * **<color #00a2e8>Aliases and Previous Symbols</color>**: N/A
  * **<color #00a2e8>Entrez ID</color>**: [[https://www.ncbi.nlm.nih.gov/gene/?term=10189|10189]]
  * **<color #00a2e8>UniProt</color>**: [[https://www.uniprot.org/uniprot/Q86V81|Q86V81]]
  * **<color #00a2e8>Interactions</color>**: [[https://thebiogrid.org/search.php?search=ALYREF&organism=9606|BioGRID]]
  * **<color #00a2e8>PubMed articles</color>**: [[https://www.ncbi.nlm.nih.gov/pubmed/?term=gene%20ALYREF|Open PubMed]]
  * **<color #00a2e8>OMIM</color>**: [[https://omim.org/entry/604171|Open OMIM]]

== Function Summary ==
  * **<color #00a2e8>Entrez Summary</color>**: N/A
  * **<color #00a2e8>UniProt Summary</color>**:  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 Kaposi's 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. {ECO:0000269|PubMed:25662211}.

<button type='primary' size='sm' modal='Pfam_Domains'>Pfam Domains</button>
<button type='primary' size='sm' modal='GO_terms'>GO Terms</button>


<modal id='Pfam_Domains' size='lg' title='Pfam Domains'>
|RRM 1|
</modal>

<modal id='GO_terms' size='lg' title='GO Terms'>
|viral mRNA export from host cell nucleus|
|translocation of molecules into host|
|translocation of molecules into other organism involved in symbiotic interaction|
|transcription export complex|
|exon-exon junction complex|
|replication fork processing|
|positive regulation of DNA-templated transcription, elongation|
|DNA-dependent DNA replication maintenance of fidelity|
|regulation of DNA-templated transcription, elongation|
|multi-organism localization|
|multi-organism transport|
|mRNA 3-end processing|
|catalytic step 2 spliceosome|
|regulation of DNA recombination|
|mRNA-containing ribonucleoprotein complex export from nucleus|
|mRNA export from nucleus|
|nuclear chromosome, telomeric region|
|DNA-dependent DNA replication|
|ribonucleoprotein complex export from nucleus|
|ribonucleoprotein complex localization|
|osteoblast differentiation|
|RNA export from nucleus|
|RNA 3-end processing|
|protein export from nucleus|
|mRNA transport|
|interaction with host|
|nuclear export|
|RNA transport|
|nucleic acid transport|
|establishment of RNA localization|
|DNA replication|
|RNA localization|
|nucleobase-containing compound transport|
|protein-containing complex localization|
|ossification|
|nucleocytoplasmic transport|
|nuclear transport|
|mRNA splicing, via spliceosome|
|RNA splicing, via transesterification reactions with bulged adenosine as nucleophile|
|RNA splicing, via transesterification reactions|
|regulation of DNA metabolic process|
|RNA splicing|
|nuclear speck|
|mRNA processing|
|mRNA metabolic process|
|viral process|
|DNA metabolic process|
|symbiotic process|
|interspecies interaction between organisms|
|RNA processing|
|intracellular protein transport|
|RNA binding|
|protein transport|
|intracellular transport|
|peptide transport|
|positive regulation of transcription, DNA-templated|
|amide transport|
|cellular protein localization|
|cellular macromolecule localization|
|establishment of protein localization|
|positive regulation of nucleic acid-templated transcription|
|positive regulation of RNA biosynthetic process|
|RNA metabolic process|
|cellular macromolecule biosynthetic process|
|positive regulation of RNA metabolic process|
|macromolecule biosynthetic process|
|establishment of localization in cell|
|nitrogen compound transport|
|positive regulation of nucleobase-containing compound metabolic process|
|positive regulation of macromolecule biosynthetic process|
|positive regulation of cellular biosynthetic process|
|positive regulation of gene expression|
|membrane|
|gene expression|
|positive regulation of biosynthetic process|
</modal>
\\

 === CRISPR Data ===
<button type='primary' size='small' modal='Compound_Hit'>Compound Hit</button>
<button type='default' size='small' modal='Most_Correlated_Genes'>Most Correlated Genes in Chemogenomics</button>
<button type='primary' size='small' modal='Essential_Avana'>Tissues where Essential in the Avana Dataset (DepMap 20Q1)</button>

<modal id='Compound_Hit' size='lg' title='Compound Hit'>
^Screen^Score^
|[[:results:exp529|Thimerosal 0.85μM R08 exp529]]|-1.85|
|[[:results:exp135|MS023 7μM R03 exp135]]|-1.7|
|[[:results:exp199|Etoposide 0.3μM R05 exp199]]|1.71|
|[[:results:exp530|Thioridazine 5μM R08 exp530]]|1.82|
|[[:results:exp455|Benzoate 10000μM R08 exp455]]|1.84|
|[[:results:exp345|Cidofovir 10μM R07 exp345]]|2.22|
</modal>

<modal id='Most_Correlated_Genes' size='lg' title='Most Correlated Genes in Chemogenomics'>
No correlation found to any other genes in chemogenomics.
</modal>

<modal id='Essential_Avana' size='lg' title='Tissues where Essential in the Avana Dataset (DepMap 20Q1)'>
Global Fraction of Cell Lines Where Essential: 53/726
^Tissue^Fraction Of Cell Lines Where Essential^
|1290807.0|0/1|
|909776.0|0/1|
|bile duct|1/28|
|blood|1/28|
|bone|3/25|
|breast|1/33|
|central nervous system|4/56|
|cervix|1/4|
|colorectal|1/17|
|esophagus|0/13|
|fibroblast|0/1|
|gastric|2/15|
|kidney|0/21|
|liver|2/20|
|lung|4/75|
|lymphocyte|0/14|
|ovary|3/26|
|pancreas|1/24|
|peripheral nervous system|1/16|
|plasma cell|2/15|
|prostate|0/1|
|skin|0/24|
|soft tissue|1/7|
|thyroid|1/2|
|upper aerodigestive|1/22|
|urinary tract|6/29|
|uterus|0/5|
</modal>

== Essentiality in NALM6  ==
    * **<color #00a2e8>Essentiality Rank</color>**: 563
    * **<color #00a2e8>Expression level (log2 read counts)</color>**: 7.04 
<button type='primary' size='small' modal='Dist_expr'>Expression Distribution</button>
<modal id='Dist_expr' size='lg' title='ALYREF Expression in NALM6 Cells: 7.04'>
{{:chemogenomics:nalm6 dist.png?nolink |}}
</modal>