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Protein

THO complex subunit 4

Gene

Alyref

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

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. 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.

GO - Molecular functioni

  • RNA binding Source: MGI
  • single-stranded DNA binding Source: MGI

GO - Biological processi

Keywordsi

Molecular functionChaperone, RNA-binding
Biological processmRNA processing, mRNA splicing, mRNA transport, Transport

Names & Taxonomyi

Protein namesi
Recommended name:
THO complex subunit 4
Short name:
Tho4
Alternative name(s):
Ally of AML-1 and LEF-1
Aly/REF export factor
REF1-I
RNA and export factor-binding protein 1
Transcriptional coactivator Aly/REF
Gene namesi
Name:Alyref
Synonyms:Aly, Ref1, Refbp1, THOC4
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 11

Organism-specific databases

MGIiMGI:1341044 Alyref

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus, Spliceosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedBy similarity
ChainiPRO_00000819752 – 255THO complex subunit 4Add BLAST254

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylalanineBy similarity1
Modified residuei8PhosphoserineBy similarity1
Modified residuei38Asymmetric dimethylarginine; alternateCombined sources1
Modified residuei38Omega-N-methylarginine; alternateCombined sources1
Modified residuei50Omega-N-methylated arginineBy similarity1
Modified residuei58Omega-N-methylarginineBy similarity1
Modified residuei63Omega-N-methylarginineBy similarity1
Modified residuei70Omega-N-methylarginineBy similarity1
Modified residuei85N6-acetyllysineCombined sources1
Modified residuei93PhosphoserineBy similarity1
Modified residuei140Citrulline1 Publication1
Modified residuei196Asymmetric dimethylarginine; alternateCombined sources1
Modified residuei196Omega-N-methylarginine; alternateCombined sources1
Modified residuei203Asymmetric dimethylarginine; alternateBy similarity1
Modified residuei203Dimethylated arginine; alternateBy similarity1
Modified residuei203Omega-N-methylarginine; alternateCombined sources1
Modified residuei203Omega-N-methylated arginine; alternateBy similarity1
Modified residuei218Omega-N-methylarginineBy similarity1
Modified residuei233N6-methyllysineBy similarity1
Modified residuei237PhosphoserineBy similarity1

Post-translational modificationi

Arg-50 and Arg-203 are dimethylated, probably to asymmetric dimethylarginine. Arginine methylation reduces RNA binding (By similarity).By similarity
Citrullinated by PADI4.1 Publication

Keywords - PTMi

Acetylation, Citrullination, Methylation, Phosphoprotein

Proteomic databases

EPDiO08583
MaxQBiO08583
PaxDbiO08583
PeptideAtlasiO08583
PRIDEiO08583
TopDownProteomicsiO08583-1 [O08583-1]

PTM databases

iPTMnetiO08583
PhosphoSitePlusiO08583

Expressioni

Tissue specificityi

Highly expressed in heart, brain, spleen, lung, liver, skeletal muscle, kidney and testis.1 Publication

Gene expression databases

BgeeiENSMUSG00000025134 Expressed in 300 organ(s), highest expression level in maxillary prominence
CleanExiMM_THOC4
GenevisibleiO08583 MM

Interactioni

Subunit structurei

Homomultimer (By similarity). Is part of several complexes involved in mRNA processing and export (By similarity). 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 (By similarity). Found in mRNA splicing-dependent exon junction complexes (EJC) (By similarity). Identified in the spliceosome C complex (By similarity). Found in a mRNP complex with UPF3A and UPF3B (By similarity). Interacts with RBM8A, NCBP1, THOC5, LEF1, RUNX1, EIF4A3, RNPS1, SRRM1, IWS1 and EXOSC1 (By similarity). Interacts with RBM15B. Interacts with NXF1; the interaction is direct (PubMed:10786854).By similarity1 Publication

Protein-protein interaction databases

BioGridi204102, 8 interactors
DIPiDIP-59977N
IntActiO08583, 7 interactors
MINTiO08583
STRINGi10090.ENSMUSP00000026125

Structurei

Secondary structure

1255
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliO08583
SMRiO08583
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO08583

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini105 – 182RRMPROSITE-ProRule annotationAdd BLAST78

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni16 – 37Sufficient for RNA-binding, interaction with NXF1-NXT1 heterodimerBy similarityAdd BLAST22

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi21 – 229Ala/Arg/Gly-richAdd BLAST209

Sequence similaritiesi

Belongs to the THOC4 family.Curated

Phylogenomic databases

eggNOGiKOG0533 Eukaryota
ENOG4111JAW LUCA
GeneTreeiENSGT00410000025615
HOGENOMiHOG000239962
HOVERGENiHBG054806
InParanoidiO08583
KOiK12881
OMAiRNDYPRD
OrthoDBiEOG091G0T4Z
PhylomeDBiO08583
TreeFamiTF313312

Family and domain databases

Gene3Di3.30.70.330, 1 hit
InterProiView protein in InterPro
IPR025715 FoP_C
IPR012677 Nucleotide-bd_a/b_plait_sf
IPR035979 RBD_domain_sf
IPR000504 RRM_dom
PfamiView protein in Pfam
PF13865 FoP_duplication, 1 hit
PF00076 RRM_1, 1 hit
SMARTiView protein in SMART
SM01218 FoP_duplication, 1 hit
SM00360 RRM, 1 hit
SUPFAMiSSF54928 SSF54928, 1 hit
PROSITEiView protein in PROSITE
PS50102 RRM, 1 hit

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket
Isoform 1 (identifier: O08583-1) [UniParc]FASTAAdd to basket
Also known as: Refbp1-I

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide
        10         20         30         40         50
MADKMDMSLD DIIKLNRSQR GGRGGGRGRG RAGSQGGRGG AVQAAARVNR
60 70 80 90 100
GGGPMRNRPA IARGAAGGGR NRPAPYSRPK QLPDKWQHDL FDSGFGGGAG
110 120 130 140 150
VETGGKLLVS NLDFGVSDAD IQELFAEFGT LKKAAVHYDR SGRSLGTADV
160 170 180 190 200
HFERKADALK AMKQYNGVPL DGRPMNIQLV TSQIDTQRRP AQSINRGGMT
210 220 230 240 250
RNRGSGGFGG GGTRRGTRGG SRGRGRGTGR NSKQQLSAEE LDAQLDAYNA

RMDTS
Length:255
Mass (Da):26,940
Last modified:January 23, 2007 - v3
Checksum:iF597235EBDD47C17
GO
Isoform 2 (identifier: O08583-2) [UniParc]FASTAAdd to basket
Also known as: Refbp1-II

The sequence of this isoform differs from the canonical sequence as follows:
     14-105: Missing.

Show »
Length:163
Mass (Da):17,682
Checksum:iD212F3ACD29C8B13
GO

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_00859714 – 105Missing in isoform 2. 1 PublicationAdd BLAST92

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U89876 mRNA Translation: AAC53117.1
AJ252140 mRNA Translation: CAB76383.1
AL663030 Genomic DNA Translation: CAM27086.1
CH466558 Genomic DNA Translation: EDL34770.1
BC120588 mRNA Translation: AAI20589.1
BC137658 mRNA Translation: AAI37659.1
AK035721 mRNA Translation: BAC29168.1
CCDSiCCDS25744.1 [O08583-1]
RefSeqiNP_035698.1, NM_011568.1 [O08583-1]
UniGeneiMm.1886

Genome annotation databases

EnsembliENSMUST00000026125; ENSMUSP00000026125; ENSMUSG00000025134 [O08583-1]
GeneIDi21681
KEGGimmu:21681
UCSCiuc007mtl.1 mouse [O08583-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U89876 mRNA Translation: AAC53117.1
AJ252140 mRNA Translation: CAB76383.1
AL663030 Genomic DNA Translation: CAM27086.1
CH466558 Genomic DNA Translation: EDL34770.1
BC120588 mRNA Translation: AAI20589.1
BC137658 mRNA Translation: AAI37659.1
AK035721 mRNA Translation: BAC29168.1
CCDSiCCDS25744.1 [O08583-1]
RefSeqiNP_035698.1, NM_011568.1 [O08583-1]
UniGeneiMm.1886

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1NO8NMR-A77-182[»]
ProteinModelPortaliO08583
SMRiO08583
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi204102, 8 interactors
DIPiDIP-59977N
IntActiO08583, 7 interactors
MINTiO08583
STRINGi10090.ENSMUSP00000026125

PTM databases

iPTMnetiO08583
PhosphoSitePlusiO08583

Proteomic databases

EPDiO08583
MaxQBiO08583
PaxDbiO08583
PeptideAtlasiO08583
PRIDEiO08583
TopDownProteomicsiO08583-1 [O08583-1]

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000026125; ENSMUSP00000026125; ENSMUSG00000025134 [O08583-1]
GeneIDi21681
KEGGimmu:21681
UCSCiuc007mtl.1 mouse [O08583-1]

Organism-specific databases

CTDi10189
MGIiMGI:1341044 Alyref

Phylogenomic databases

eggNOGiKOG0533 Eukaryota
ENOG4111JAW LUCA
GeneTreeiENSGT00410000025615
HOGENOMiHOG000239962
HOVERGENiHBG054806
InParanoidiO08583
KOiK12881
OMAiRNDYPRD
OrthoDBiEOG091G0T4Z
PhylomeDBiO08583
TreeFamiTF313312

Miscellaneous databases

EvolutionaryTraceiO08583
PROiPR:O08583
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000025134 Expressed in 300 organ(s), highest expression level in maxillary prominence
CleanExiMM_THOC4
GenevisibleiO08583 MM

Family and domain databases

Gene3Di3.30.70.330, 1 hit
InterProiView protein in InterPro
IPR025715 FoP_C
IPR012677 Nucleotide-bd_a/b_plait_sf
IPR035979 RBD_domain_sf
IPR000504 RRM_dom
PfamiView protein in Pfam
PF13865 FoP_duplication, 1 hit
PF00076 RRM_1, 1 hit
SMARTiView protein in SMART
SM01218 FoP_duplication, 1 hit
SM00360 RRM, 1 hit
SUPFAMiSSF54928 SSF54928, 1 hit
PROSITEiView protein in PROSITE
PS50102 RRM, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiTHOC4_MOUSE
AccessioniPrimary (citable) accession number: O08583
Secondary accession number(s): Q0VBL5, Q8CBM4, Q9JJW7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 10, 2003
Last sequence update: January 23, 2007
Last modified: November 7, 2018
This is version 157 of the entry and version 3 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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