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Protein

RNA-binding protein 8A

Gene

RBM8A

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Core component of the splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junctions on mRNAs. The EJC is a dynamic structure consisting of core proteins and several peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. The EJC marks the position of the exon-exon junction in the mature mRNA for the gene expression machinery and the core components remain bound to spliced mRNAs throughout all stages of mRNA metabolism thereby influencing downstream processes including nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). The MAGOH-RBM8A heterodimer inhibits the ATPase activity of EIF4A3, thereby trapping the ATP-bound EJC core onto spliced mRNA in a stable conformation. The MAGOH-RBM8A heterodimer interacts with the EJC key regulator PYM1 leading to EJC disassembly in the cytoplasm and translation enhancement of EJC-bearing spliced mRNAs by recruiting them to the ribosomal 48S preinitiation complex. Its removal from cytoplasmic mRNAs requires translation initiation from EJC-bearing spliced mRNAs. Associates preferentially with mRNAs produced by splicing. Does not interact with pre-mRNAs, introns, or mRNAs produced from intronless cDNAs. Associates with both nuclear mRNAs and newly exported cytoplasmic mRNAs. The MAGOH-RBM8A heterodimer is a component of the nonsense mediated decay (NMD) pathway. Involved in the splicing modulation of BCL2L1/Bcl-X (and probably other apoptotic genes); specifically inhibits formation of proapoptotic isoforms such as Bcl-X(S); the function is different from the established EJC assembly.6 Publications

GO - Molecular functioni

  • mRNA binding Source: UniProtKB
  • nucleotide binding Source: InterPro
  • poly(A) RNA binding Source: UniProtKB
  • RNA binding Source: UniProtKB

GO - Biological processi

  • mRNA 3'-end processing Source: Reactome
  • mRNA export from nucleus Source: Reactome
  • mRNA splicing, via spliceosome Source: UniProtKB
  • nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Source: UniProtKB
  • regulation of alternative mRNA splicing, via spliceosome Source: UniProtKB
  • regulation of translation Source: UniProtKB-KW
  • RNA export from nucleus Source: Reactome
  • termination of RNA polymerase II transcription Source: Reactome
Complete GO annotation...

Keywords - Biological processi

mRNA processing, mRNA splicing, mRNA transport, Nonsense-mediated mRNA decay, Translation regulation, Transport

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

ReactomeiR-HSA-109688. Cleavage of Growing Transcript in the Termination Region.
R-HSA-159236. Transport of Mature mRNA derived from an Intron-Containing Transcript.
R-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72187. mRNA 3'-end processing.
R-HSA-975957. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
SIGNORiQ9Y5S9.

Protein family/group databases

TCDBi3.A.18.1.1. the nuclear mrna exporter (mrna-e) family.

Names & Taxonomyi

Protein namesi
Recommended name:
RNA-binding protein 8A
Alternative name(s):
Binder of OVCA1-1
Short name:
BOV-1
RNA-binding motif protein 8A
RNA-binding protein Y14
Ribonucleoprotein RBM8A
Gene namesi
Name:RBM8A
Synonyms:RBM8
ORF Names:HSPC114, MDS014
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

HGNCiHGNC:9905. RBM8A.

Subcellular locationi

GO - Cellular componenti

  • catalytic step 2 spliceosome Source: UniProtKB
  • cytoplasm Source: UniProtKB
  • cytosol Source: Reactome
  • dendrite Source: Ensembl
  • exon-exon junction complex Source: UniProtKB
  • neuronal cell body Source: Ensembl
  • nuclear speck Source: UniProtKB-SubCell
  • nucleoplasm Source: HPA
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus, Spliceosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi82 – 832EE → RR: Impaired nonsense-mediated decay activity. 1 Publication
Mutagenesisi106 – 1083LDR → RDE: Complete loss of nonsense-mediated decay activity. 1 Publication
Mutagenesisi118 – 1181L → R: Complete loss of nonsense-mediated decay activity. 1 Publication
Mutagenesisi149 – 1502CF → KA: Complete loss of nonsense-mediated decay activity. 1 Publication

Organism-specific databases

MalaCardsiRBM8A.
Orphaneti3320. Thrombocytopenia - absent radius.
PharmGKBiPA34270.

Polymorphism and mutation databases

DMDMi10720244.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedCombined sources
Chaini2 – 174173RNA-binding protein 8APRO_0000081763Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanineCombined sources
Modified residuei24 – 241PhosphoserineCombined sources
Cross-linki27 – 27Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei42 – 421PhosphoserineCombined sources
Modified residuei56 – 561PhosphoserineCombined sources

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ9Y5S9.
MaxQBiQ9Y5S9.
PaxDbiQ9Y5S9.
PeptideAtlasiQ9Y5S9.
PRIDEiQ9Y5S9.

PTM databases

iPTMnetiQ9Y5S9.
PhosphoSiteiQ9Y5S9.

Miscellaneous databases

PMAP-CutDBQ9Y5S9.

Expressioni

Tissue specificityi

Ubiquitous.

Gene expression databases

BgeeiENSG00000131795.
CleanExiHS_RBM8A.
ExpressionAtlasiQ9Y5S9. baseline and differential.
GenevisibleiQ9Y5S9. HS.

Organism-specific databases

HPAiHPA018403.

Interactioni

Subunit structurei

Heterodimer with RBM8A. Part of the mRNA splicing-dependent exon junction complex (EJC) complex; the core complex contains CASC3, EIF4A3, MAGOH and RBM8A. Interacts with PYM1; the interaction is direct and dissociates the EJC from spliced mRNAs. Found in a post-splicing complex with NXF1, RBM8A, UPF1, UPF2, UPF3A, UPF3B and RNPS1. Interacts with BAT1, MAGOH, OVCA1, UPF3B, RNPS1, SRRM1 and ALYREF/THOC4. Interacts with IPO13; the interaction mediates the nuclear import of the MAGOH-RBM8A heterodimer. Identified in the spliceosome C complex. Associates with polysomes.18 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
EIF4A3P3891921EBI-447231,EBI-299104
MAGOHP6132626EBI-447231,EBI-299134
MAGOHBQ96A725EBI-447231,EBI-746778
SRPK1Q96SB42EBI-447231,EBI-539478
SRPK2P783622EBI-447231,EBI-593303
UPF3AQ9H1J14EBI-447231,EBI-521530
UPF3BQ9BZI79EBI-447231,EBI-372780

Protein-protein interaction databases

BioGridi115265. 105 interactions.
DIPiDIP-33070N.
IntActiQ9Y5S9. 61 interactions.
MINTiMINT-265248.
STRINGi9606.ENSP00000333001.

Structurei

Secondary structure

1
174
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi72 – 787Combined sources
Helixi86 – 938Combined sources
Helixi94 – 963Combined sources
Beta strandi99 – 1068Combined sources
Turni108 – 1103Combined sources
Beta strandi111 – 12212Combined sources
Helixi124 – 13411Combined sources
Beta strandi138 – 1436Combined sources
Beta strandi145 – 1539Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1P27X-ray2.00B/D50-155[»]
2HYIX-ray2.30B/H64-154[»]
2J0QX-ray3.20D/G66-174[»]
2J0SX-ray2.21D66-154[»]
2XB2X-ray3.40D/Z66-155[»]
3EX7X-ray2.30B/G51-174[»]
ProteinModelPortaliQ9Y5S9.
SMRiQ9Y5S9. Positions 12-155.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9Y5S9.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini73 – 15179RRMPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the RBM8A family.Curated
Contains 1 RRM (RNA recognition motif) domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG0130. Eukaryota.
ENOG4111IHM. LUCA.
GeneTreeiENSGT00730000111185.
HOGENOMiHOG000183826.
HOVERGENiHBG055173.
InParanoidiQ9Y5S9.
KOiK12876.
OMAiISVDWGF.
OrthoDBiEOG091G0PLI.
PhylomeDBiQ9Y5S9.
TreeFamiTF314933.

Family and domain databases

Gene3Di3.30.70.330. 1 hit.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR008111. RNA-bd_8.
IPR000504. RRM_dom.
[Graphical view]
PANTHERiPTHR23139:SF72. PTHR23139:SF72. 1 hit.
PfamiPF00076. RRM_1. 1 hit.
[Graphical view]
PRINTSiPR01738. RNABINDINGM8.
SMARTiSM00360. RRM. 1 hit.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 1 hit.
PROSITEiPS50102. RRM. 1 hit.
[Graphical view]

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: Q9Y5S9-1) [UniParc]FASTAAdd to basket
Also known as: BOV-1a

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
MADVLDLHEA GGEDFAMDED GDESIHKLKE KAKKRKGRGF GSEEGSRARM
60 70 80 90 100
REDYDSVEQD GDEPGPQRSV EGWILFVTGV HEEATEEDIH DKFAEYGEIK
110 120 130 140 150
NIHLNLDRRT GYLKGYTLVE YETYKEAQAA MEGLNGQDLM GQPISVDWCF
160 170
VRGPPKGKRR GGRRRSRSPD RRRR
Length:174
Mass (Da):19,889
Last modified:November 1, 1999 - v1
Checksum:i70BBD03CDDFEECFE
GO
Isoform 2 (identifier: Q9Y5S9-2) [UniParc]FASTAAdd to basket
Also known as: BOV-1b

The sequence of this isoform differs from the canonical sequence as follows:
     44-44: Missing.

Show »
Length:173
Mass (Da):19,760
Checksum:i6710C1BD9CFAF92E
GO

Sequence cautioni

The sequence AAG14951 differs from that shown. Reason: Erroneous initiation. Curated
The sequence AAG16782 differs from that shown.Chimeric cDNA. A chimeric cDNA originating from chromosomes 1 and 5.Curated
The sequence AAG16782 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti130 – 1301A → V in CAG46622 (Ref. 8) Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei44 – 441Missing in isoform 2. 2 PublicationsVSP_005810

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF127761 mRNA. Translation: AAD21089.1.
AF198620 mRNA. Translation: AAF37551.1.
AF231511 mRNA. Translation: AAG16781.1.
AF231512 mRNA. Translation: AAG16782.1. Different initiation.
AF299118 mRNA. Translation: AAG27091.1.
AF403012 Genomic DNA. Translation: AAL26999.1.
AF182415 mRNA. Translation: AAG14951.1. Different initiation.
AF161463 mRNA. Translation: AAF29078.1.
CR541823 mRNA. Translation: CAG46622.1.
CR541805 mRNA. Translation: CAG46604.1.
AK075009 mRNA. Translation: BAG52051.1.
AL160282 Genomic DNA. No translation available.
CH471244 Genomic DNA. Translation: EAW71419.1.
BC017088 mRNA. Translation: AAH17088.1.
CCDSiCCDS72872.1. [Q9Y5S9-1]
RefSeqiNP_005096.1. NM_005105.4. [Q9Y5S9-1]
UniGeneiHs.591455.

Genome annotation databases

EnsembliENST00000369307; ENSP00000358313; ENSG00000265241. [Q9Y5S9-2]
ENST00000583313; ENSP00000463058; ENSG00000265241. [Q9Y5S9-1]
ENST00000632555; ENSP00000488265; ENSG00000265241. [Q9Y5S9-1]
GeneIDi9939.
KEGGihsa:9939.
UCSCiuc031uto.2. human. [Q9Y5S9-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF127761 mRNA. Translation: AAD21089.1.
AF198620 mRNA. Translation: AAF37551.1.
AF231511 mRNA. Translation: AAG16781.1.
AF231512 mRNA. Translation: AAG16782.1. Different initiation.
AF299118 mRNA. Translation: AAG27091.1.
AF403012 Genomic DNA. Translation: AAL26999.1.
AF182415 mRNA. Translation: AAG14951.1. Different initiation.
AF161463 mRNA. Translation: AAF29078.1.
CR541823 mRNA. Translation: CAG46622.1.
CR541805 mRNA. Translation: CAG46604.1.
AK075009 mRNA. Translation: BAG52051.1.
AL160282 Genomic DNA. No translation available.
CH471244 Genomic DNA. Translation: EAW71419.1.
BC017088 mRNA. Translation: AAH17088.1.
CCDSiCCDS72872.1. [Q9Y5S9-1]
RefSeqiNP_005096.1. NM_005105.4. [Q9Y5S9-1]
UniGeneiHs.591455.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1P27X-ray2.00B/D50-155[»]
2HYIX-ray2.30B/H64-154[»]
2J0QX-ray3.20D/G66-174[»]
2J0SX-ray2.21D66-154[»]
2XB2X-ray3.40D/Z66-155[»]
3EX7X-ray2.30B/G51-174[»]
ProteinModelPortaliQ9Y5S9.
SMRiQ9Y5S9. Positions 12-155.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi115265. 105 interactions.
DIPiDIP-33070N.
IntActiQ9Y5S9. 61 interactions.
MINTiMINT-265248.
STRINGi9606.ENSP00000333001.

Protein family/group databases

TCDBi3.A.18.1.1. the nuclear mrna exporter (mrna-e) family.

PTM databases

iPTMnetiQ9Y5S9.
PhosphoSiteiQ9Y5S9.

Polymorphism and mutation databases

DMDMi10720244.

Proteomic databases

EPDiQ9Y5S9.
MaxQBiQ9Y5S9.
PaxDbiQ9Y5S9.
PeptideAtlasiQ9Y5S9.
PRIDEiQ9Y5S9.

Protocols and materials databases

DNASUi9939.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000369307; ENSP00000358313; ENSG00000265241. [Q9Y5S9-2]
ENST00000583313; ENSP00000463058; ENSG00000265241. [Q9Y5S9-1]
ENST00000632555; ENSP00000488265; ENSG00000265241. [Q9Y5S9-1]
GeneIDi9939.
KEGGihsa:9939.
UCSCiuc031uto.2. human. [Q9Y5S9-1]

Organism-specific databases

CTDi9939.
GeneCardsiRBM8A.
GeneReviewsiRBM8A.
HGNCiHGNC:9905. RBM8A.
HPAiHPA018403.
MalaCardsiRBM8A.
MIMi605313. gene.
neXtProtiNX_Q9Y5S9.
Orphaneti3320. Thrombocytopenia - absent radius.
PharmGKBiPA34270.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0130. Eukaryota.
ENOG4111IHM. LUCA.
GeneTreeiENSGT00730000111185.
HOGENOMiHOG000183826.
HOVERGENiHBG055173.
InParanoidiQ9Y5S9.
KOiK12876.
OMAiISVDWGF.
OrthoDBiEOG091G0PLI.
PhylomeDBiQ9Y5S9.
TreeFamiTF314933.

Enzyme and pathway databases

ReactomeiR-HSA-109688. Cleavage of Growing Transcript in the Termination Region.
R-HSA-159236. Transport of Mature mRNA derived from an Intron-Containing Transcript.
R-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72187. mRNA 3'-end processing.
R-HSA-975957. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
SIGNORiQ9Y5S9.

Miscellaneous databases

ChiTaRSiRBM8A. human.
EvolutionaryTraceiQ9Y5S9.
GeneWikiiRBM8A.
GenomeRNAii9939.
PMAP-CutDBQ9Y5S9.
PROiQ9Y5S9.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000131795.
CleanExiHS_RBM8A.
ExpressionAtlasiQ9Y5S9. baseline and differential.
GenevisibleiQ9Y5S9. HS.

Family and domain databases

Gene3Di3.30.70.330. 1 hit.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR008111. RNA-bd_8.
IPR000504. RRM_dom.
[Graphical view]
PANTHERiPTHR23139:SF72. PTHR23139:SF72. 1 hit.
PfamiPF00076. RRM_1. 1 hit.
[Graphical view]
PRINTSiPR01738. RNABINDINGM8.
SMARTiSM00360. RRM. 1 hit.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 1 hit.
PROSITEiPS50102. RRM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRBM8A_HUMAN
AccessioniPrimary (citable) accession number: Q9Y5S9
Secondary accession number(s): B3KQI9
, Q6FHD1, Q6IQ40, Q9GZX8, Q9NZI4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: November 1, 1999
Last modified: September 7, 2016
This is version 190 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.