ALYREF Aly/REF export factor [Homo sapiens (human)] - Gene

Summary

Official Symbol: ALYREFprovided by HGNC
Official Full Name: Aly/REF export factorprovided by HGNC
Primary source: HGNC:HGNC:19071
See related: Ensembl:ENSG00000183684 MIM:604171; AllianceGenome:HGNC:19071
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: ALY; BEF; REF; THOC4; ALY/REF
Summary: 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]
Expression: Ubiquitous expression in bone marrow (RPKM 44.1), testis (RPKM 33.0) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17q25.3

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (81887835..81891587, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (82754997..82758749, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (79845711..79849463, complement)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pan-cancer analysis of RNA 5-methylcytosine reader (ALYREF).
Title: Pan-cancer analysis of RNA 5-methylcytosine reader (ALYREF).
ALYREF (Aly/REF export factor): A potential biomarker for predicting cancer occurrence and therapeutic efficacy.
Title: ALYREF (Aly/REF export factor): A potential biomarker for predicting cancer occurrence and therapeutic efficacy.
m[5]C-dependent cross-regulation between nuclear reader ALYREF and writer NSUN2 promotes urothelial bladder cancer malignancy through facilitating RABL6/TK1 mRNAs splicing and stabilization.
Title: m(5)C-dependent cross-regulation between nuclear reader ALYREF and writer NSUN2 promotes urothelial bladder cancer malignancy through facilitating RABL6/TK1 mRNAs splicing and stabilization.
ALYREF, a novel factor involved in breast carcinogenesis, acts through transcriptional and post-transcriptional mechanisms selectively regulating the short NEAT1 isoform.
Title: ALYREF, a novel factor involved in breast carcinogenesis, acts through transcriptional and post-transcriptional mechanisms selectively regulating the short NEAT1 isoform.
The role of the HIF-1alpha/ALYREF/PKM2 axis in glycolysis and tumorigenesis of bladder cancer.
Title: The role of the HIF-1α/ALYREF/PKM2 axis in glycolysis and tumorigenesis of bladder cancer.
An ALYREF-MYCN coactivator complex drives neuroblastoma tumorigenesis through effects on USP3 and MYCN stability.
Title: An ALYREF-MYCN coactivator complex drives neuroblastoma tumorigenesis through effects on USP3 and MYCN stability.
We demonstrate that eIF4A3 stimulates Alyref deposition not only on spliced RNAs close to exon junction complex sites but also on single-exon transcripts
Title: Co-transcriptional Loading of RNA Export Factors Shapes the Human Transcriptome.
In both ORF57 and ICP27 the interaction sites for ALYREF and UIF partially overlap, suggestive of mutually exclusive binding. The data provide a map of the binding sites responsible for promoting herpes virus mRNA export, enabling future studies to accurately probe these interactions and reveal the functional consequences for UIF and ALYREF redundancy
Title: Overlapping motifs on the herpes viral proteins ICP27 and ORF57 mediate interactions with the mRNA export adaptors ALYREF and UIF.
Dysregulation of ALYREF-mediated mRNA export upon NSUN2 depletion could be restored by reconstitution of wild-type but not methyltransferase-defective NSUN2.
Title: 5-methylcytosine promotes mRNA export - NSUN2 as the methyltransferase and ALYREF as an m(5)C reader.
ALYREF mainly binds to the 5' and the 3' regions of the mRNA. ALYREF is likely recruited to mRNAs by PABPN1 and the 3' processing machinery.
Title: ALYREF mainly binds to the 5' and the 3' regions of the mRNA in vivo.

Submit: New GeneRIF Correction See all GeneRIFs (31)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	Tandem affinity purification and mass spectrometry analysis identify Aly/REF export factor (ALYREF; THO complex subunit 4, THOC4), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Gag-Pol	gag-pol	Tandem affinity purification and mass spectrometry analysis identify Aly/REF export factor (ALYREF; THO complex subunit 4, THOC4), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Nef	nef	Tandem affinity purification and mass spectrometry analysis identify Aly/REF export factor (ALYREF; THO complex subunit 4, THOC4), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Pr55(Gag)	gag	Tandem affinity purification and mass spectrometry analysis identify Aly/REF export factor (ALYREF; THO complex subunit 4, THOC4), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Rev	rev	HIV-1 Rev specifically inhibits the association of ALY/REF and UAP56 with spliced RRE-containing RNA	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D17S723 (e-PCR)
- UniSTS:38918

RH44900 (e-PCR)
- UniSTS:44835

NoName (e-PCR)
- UniSTS:481341

ALY_7964 (e-PCR)
- UniSTS:467553

RH65676 (e-PCR)
- UniSTS:37993

SIRT7_1731 (e-PCR)
- UniSTS:277714

RH65274 (e-PCR)
- UniSTS:45027

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables C5-methylcytidine-containing RNA reader activity	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	HDA more info	PubMed
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA export from nucleus	IDA Inferred from Direct Assay more info	PubMed
involved_in RNA splicing	IEA Inferred from Electronic Annotation more info
involved_in mRNA export from nucleus	IBA Inferred from Biological aspect of Ancestor more info
involved_in mRNA export from nucleus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in osteoblast differentiation	HDA more info	PubMed

Component	Evidence Code	Pubs
part_of catalytic step 2 spliceosome	IDA Inferred from Direct Assay more info	PubMed
colocalizes_with chromosome, telomeric region	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
part_of exon-exon junction complex	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular exosome	HDA more info	PubMed
located_in membrane	HDA more info	PubMed
located_in nuclear speck	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
part_of transcription export complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: THO complex subunit 4

Names: THO complex 4; ally of AML-1 and LEF-1; bZIP enhancing factor; bZIP-enhancing factor BEF; tho4; transcriptional coactivator Aly/REF

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_005782.4 → NP_005773.3 THO complex subunit 4

Status: REVIEWED

Source sequence(s)

BC052302, BU624466

Consensus CDS

CCDS32768.2

UniProtKB/Swiss-Prot

O43672, Q86V81

UniProtKB/TrEMBL

E9PB61

Related

ENSP00000421592.2, ENST00000505490.3

Conserved Domains (3) summary

COG0724
Location:114 → 210

RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]

cd12680
Location:114 → 187

RRM_THOC4; RNA recognition motif in THO complex subunit 4 (THOC4) and similar proteins

pfam07078
Location:4 → 23

FYTT; Forty-two-three protein