Alyref Aly/REF export factor [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Alyrefprovided by MGI
Official Full Name: Aly/REF export factorprovided by MGI
Primary source: MGI:MGI:1341044
See related: Ensembl:ENSMUSG00000025134 AllianceGenome:MGI:1341044
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Aly; Ref1; Tho4; Thoc4; Ref1-I; Refbp1
Summary: Enables RNA binding activity and single-stranded DNA binding activity. Predicted to be involved in several processes, including mRNA export from nucleus; regulation of nucleobase-containing compound metabolic process; and viral mRNA export from host cell nucleus. Predicted to act upstream of or within RNA splicing; mRNA processing; and mRNA transport. Predicted to be located in cytoplasm. Predicted to be part of catalytic step 2 spliceosome; exon-exon junction complex; and transcription export complex. Predicted to be active in nucleus. Predicted to colocalize with chromosome, telomeric region. Is expressed in several structures, including branchial arch; central nervous system; genitourinary system; hemolymphoid system gland; and sensory organ. Orthologous to human ALYREF (Aly/REF export factor). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in CNS E11.5 (RPKM 97.1), liver E14 (RPKM 68.0) and 24 other tissues See more
Orthologs: human all
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Genomic context

Location:: 11 E2; 11 84.31 cM

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	11	NC_000077.7 (120485330..120489342, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	11	NC_000077.6 (120594504..120598399, complement)

Chromosome 11 - NC_000077.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Incomplete activation of Alyref and Gabpb1 leads to preimplantation arrest in cloned mouse embryos.
Title: Incomplete activation of Alyref and Gabpb1 leads to preimplantation arrest in cloned mouse embryos.
Structure of the nuclear factor ALY provides insights into post-transcriptional regulatory and mRNA nuclear export processes.
Title: Structure of the nuclear factor ALY: insights into post-transcriptional regulatory and mRNA nuclear export processes.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (3)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Refbp2 (e-PCR), detects polymorphism
- UniSTS:479247

Thoc4 (e-PCR), detects polymorphism
- UniSTS:479293

NoName (e-PCR)
- UniSTS:491367

NoName (e-PCR)
- UniSTS:236797

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables C5-methylcytidine-containing RNA reader activity	ISO Inferred from Sequence Orthology more info
enables RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA folding chaperone	EXP Inferred from Experiment more info	PubMed
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables molecular adaptor activity	EXP Inferred from Experiment more info	PubMed
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info
enables single-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA export from nucleus	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within 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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within mRNA processing	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within mRNA transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of catalytic step 2 spliceosome	ISO Inferred from Sequence Orthology more info
colocalizes_with chromosome, telomeric region	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
part_of exon-exon junction complex	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	TAS Traceable Author Statement more info	PubMed
part_of spliceosomal complex	IEA Inferred from Electronic Annotation more info
part_of transcription export complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: THO complex subunit 4

Names: RNA and export factor binding protein 1; THO complex 4; Tcra enhancer-binding factor interacting protein 1; ally of AML-1 and LEF-1; 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.