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Protein

RNA-binding protein 8A

Gene

Rbm8a

Organism
Mus musculus (Mouse)
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; the function is different from the established EJC assembly (By similarity).By similarity

GO - Molecular functioni

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

GO - Biological processi

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

Names & Taxonomyi

Protein namesi
Recommended name:
RNA-binding protein 8A
Alternative name(s):
RNA-binding motif protein 8A
Ribonucleoprotein RBM8A
Gene namesi
Name:Rbm8a
Synonyms:Rbm8
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 3

Organism-specific databases

MGIiMGI:1913129. Rbm8a.

Subcellular locationi

  • Nucleus By similarity
  • Nucleus speckle By similarity
  • Cytoplasm By similarity

  • Note: Nucleocytoplasmic shuttling protein. Travels to the cytoplasm as part of the exon junction complex (EJC) bound to mRNA. Colocalizes with the core EJC, ALYREF/THOC4, NXF1 and UAP56 in the nucleus and nuclear speckles (By similarity).By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus, Spliceosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedBy similarity
Chaini2 – 174173RNA-binding protein 8APRO_0000081764Add
BLAST

Amino acid modifications

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

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ9CWZ3.
MaxQBiQ9CWZ3.
PaxDbiQ9CWZ3.
PRIDEiQ9CWZ3.

PTM databases

iPTMnetiQ9CWZ3.
PhosphoSiteiQ9CWZ3.

Expressioni

Gene expression databases

BgeeiQ9CWZ3.
CleanExiMM_RBM8A.
ExpressionAtlasiQ9CWZ3. baseline and differential.

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 (By similarity).By similarity

Protein-protein interaction databases

BioGridi208557. 37 interactions.
IntActiQ9CWZ3. 38 interactions.
MINTiMINT-4131956.
STRINGi10090.ENSMUSP00000044548.

Structurei

3D structure databases

ProteinModelPortaliQ9CWZ3.
SMRiQ9CWZ3. Positions 12-155.
ModBaseiSearch...
MobiDBiSearch...

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.
InParanoidiQ9CWZ3.
KOiK12876.
OrthoDBiEOG7C5MB6.
PhylomeDBiQ9CWZ3.
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: Q9CWZ3-1) [UniParc]FASTAAdd to basket

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 GSKEGSRARM
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):19,888
Last modified:July 7, 2009 - v3
Checksum:i70B666394BF6CCFE
GO
Isoform 2 (identifier: Q9CWZ3-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     43-43: Missing.

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

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti14 – 141D → N in BAB26605 (PubMed:16141072).Curated
Sequence conflicti43 – 431K → E in BAC38693 (PubMed:16141072).Curated
Sequence conflicti51 – 511R → Q in BAE24142 (PubMed:16141072).Curated
Sequence conflicti51 – 511R → Q in AAI32652 (PubMed:15489334).Curated
Sequence conflicti51 – 511R → Q in AAI32654 (PubMed:15489334).Curated
Sequence conflicti58 – 581E → K in BAE24142 (PubMed:16141072).Curated
Sequence conflicti58 – 581E → K in AAI32652 (PubMed:15489334).Curated
Sequence conflicti58 – 581E → K in AAI32654 (PubMed:15489334).Curated
Sequence conflicti61 – 611G → S in BAE24142 (PubMed:16141072).Curated
Sequence conflicti61 – 611G → S in AAI32652 (PubMed:15489334).Curated
Sequence conflicti61 – 611G → S in AAI32654 (PubMed:15489334).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei43 – 431Missing in isoform 2. 2 PublicationsVSP_010251

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK009953 mRNA. Translation: BAB26605.1.
AK010284 mRNA. Translation: BAB26820.1.
AK082925 mRNA. Translation: BAC38693.1.
AK139805 mRNA. Translation: BAE24142.1.
CH466620 Genomic DNA. Translation: EDL38900.1.
BC020086 mRNA. Translation: AAH20086.1.
BC058376 mRNA. Translation: AAH58376.1.
BC132651 mRNA. Translation: AAI32652.1.
BC132653 mRNA. Translation: AAI32654.1.
CCDSiCCDS79983.1. [Q9CWZ3-2]
RefSeqiNP_001095877.1. NM_001102407.1.
NP_080151.2. NM_025875.2. [Q9CWZ3-2]
UniGeneiMm.261972.
Mm.441390.

Genome annotation databases

EnsembliENSMUST00000048915; ENSMUSP00000044548; ENSMUSG00000038374. [Q9CWZ3-2]
GeneIDi60365.
KEGGimmu:60365.
UCSCiuc007dty.3. mouse. [Q9CWZ3-1]
uc008qnk.2. mouse. [Q9CWZ3-2]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK009953 mRNA. Translation: BAB26605.1.
AK010284 mRNA. Translation: BAB26820.1.
AK082925 mRNA. Translation: BAC38693.1.
AK139805 mRNA. Translation: BAE24142.1.
CH466620 Genomic DNA. Translation: EDL38900.1.
BC020086 mRNA. Translation: AAH20086.1.
BC058376 mRNA. Translation: AAH58376.1.
BC132651 mRNA. Translation: AAI32652.1.
BC132653 mRNA. Translation: AAI32654.1.
CCDSiCCDS79983.1. [Q9CWZ3-2]
RefSeqiNP_001095877.1. NM_001102407.1.
NP_080151.2. NM_025875.2. [Q9CWZ3-2]
UniGeneiMm.261972.
Mm.441390.

3D structure databases

ProteinModelPortaliQ9CWZ3.
SMRiQ9CWZ3. Positions 12-155.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi208557. 37 interactions.
IntActiQ9CWZ3. 38 interactions.
MINTiMINT-4131956.
STRINGi10090.ENSMUSP00000044548.

PTM databases

iPTMnetiQ9CWZ3.
PhosphoSiteiQ9CWZ3.

Proteomic databases

EPDiQ9CWZ3.
MaxQBiQ9CWZ3.
PaxDbiQ9CWZ3.
PRIDEiQ9CWZ3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000048915; ENSMUSP00000044548; ENSMUSG00000038374. [Q9CWZ3-2]
GeneIDi60365.
KEGGimmu:60365.
UCSCiuc007dty.3. mouse. [Q9CWZ3-1]
uc008qnk.2. mouse. [Q9CWZ3-2]

Organism-specific databases

CTDi9939.
MGIiMGI:1913129. Rbm8a.

Phylogenomic databases

eggNOGiKOG0130. Eukaryota.
ENOG4111IHM. LUCA.
GeneTreeiENSGT00730000111185.
HOGENOMiHOG000183826.
HOVERGENiHBG055173.
InParanoidiQ9CWZ3.
KOiK12876.
OrthoDBiEOG7C5MB6.
PhylomeDBiQ9CWZ3.
TreeFamiTF314933.

Enzyme and pathway databases

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

Miscellaneous databases

ChiTaRSiRbm8a. mouse.
NextBioi314841.
PROiQ9CWZ3.
SOURCEiSearch...

Gene expression databases

BgeeiQ9CWZ3.
CleanExiMM_RBM8A.
ExpressionAtlasiQ9CWZ3. baseline and differential.

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...

Publicationsi

  1. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
    Strain: C57BL/6J.
    Tissue: Egg and Tongue.
  2. Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.
    Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
    Strain: C57BL/6J.
    Tissue: Brain and Mammary tumor.
  4. "The phagosomal proteome in interferon-gamma-activated macrophages."
    Trost M., English L., Lemieux S., Courcelles M., Desjardins M., Thibault P.
    Immunity 30:143-154(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  5. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-56, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Brain, Brown adipose tissue, Heart, Kidney, Liver, Lung, Pancreas, Spleen and Testis.

Entry informationi

Entry nameiRBM8A_MOUSE
AccessioniPrimary (citable) accession number: Q9CWZ3
Secondary accession number(s): Q3UT38, Q6GTD4, Q9D6U5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 10, 2004
Last sequence update: July 7, 2009
Last modified: April 13, 2016
This is version 130 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. 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.