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Reviewed, UniProtKB/Swiss-Prot Q15287 (RNPS1_HUMAN)

Last modified November 25, 2008. Version 73. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data | Customize display text xml rdf/xml gff fasta
Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Alternative products · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein namesRecommended name:
    RNA-binding protein with serine-rich domain 1
Alternative name(s):
    SR-related protein LDC2
Gene names
Name: RNPS1
Synonyms: LDC2
OrganismHomo sapiens (Human)
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

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Protein attributes

Sequence length305 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is not processed.
Protein existenceEvidence at protein level.

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General annotation (Comments)

Function

Part of pre- and post-splicing multiprotein mRNP complexes. Enhances the formation of the ATP-dependent A complex of the spliceosome. Involved in both constitutive splicing and, in association with SRP54 and SFRS10, in distinctive modulation of alternative splicing in a substrate-dependent manner. Participates in mRNA 3'-end cleavage. Involved in RENT2-dependent nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. Also mediates increase of mRNA abundance and translational efficiency. Binds spliced mRNA 20-25 nt upstream of exon-exon junctions.

Subunit structure

Component of the active spliceosome. Associates with polysomes. Found in a mRNA splicing-dependent exon junction complex (EJC) with DEK, RBM8A, RNPS1, SRRM1 and THOC4. Found in a post-splicing complex with NXF1, RBM8A, RENT1, RENT2, RENT3A, RENT3B and RNPS1. Interacts with the cleaved p110 isoform of CDC2L1, CSNK2A1, PNN, SART3, SFRS10, SRP54 and SRRM1.

Subcellular location

Nucleus speckle. Cytoplasm. Note= Nucleocytoplasmic shuttling protein.

Tissue specificity

Ubiquitous.

Post-translational modification

Phosphorylated on one or more of the four Ser/Thr residues (Ser-43, Thr-49, Ser-52 or Ser-53). Ser-53 phosphorylation site is important for splicing stimulation activity in vitro.

Sequence similarities

Belongs to the splicing factor SR family.

Contains 1 RRM (RNA recognition motif) domain.

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Binary interactions

With

Entry

#Exp.

IntAct

Notes

AP2B1P630101EBI-395959,EBI-432924
ARS2Q9BXP51EBI-395959,EBI-712721
ASCC3L1O756431EBI-395959,EBI-1045395
C14orf102Q9H7Z31EBI-395959,EBI-1042642
C20orf11Q9NWU21EBI-395959,EBI-1051077
CDC2L1P211271EBI-395959,EBI-1298
CPSF2Q9P2I01EBI-395959,EBI-1043224
CPSF6Q166301EBI-395959,EBI-358410
CROPO952321EBI-395959,EBI-395671
CSNK2A1P684001EBI-395959,EBI-347804
CSNK2A2P197841EBI-395959,EBI-347451
CSNK2BP678701EBI-395959,EBI-348169
DDX20Q9UHI61EBI-395959,EBI-347658
DDX23Q9BUQ81EBI-395959,EBI-540096
DDX41Q9UJV91EBI-395959,EBI-1046350
DHX38Q926201EBI-395959,EBI-1043041
EFTUD2Q150291EBI-395959,EBI-357897
GEMIN4P576781EBI-395959,EBI-356700
KHKP500531EBI-395959,EBI-1053974
LUC7LQ9NQ291EBI-395959,EBI-473747
LUC7L2Q9Y3831EBI-395959,EBI-352851
MKLN1Q9UL631EBI-395959,EBI-1048053
NUDT21O438091EBI-395959,EBI-355720
PNNQ9H3071EBI-395959,EBI-681904
PRPF3O433951EBI-395959,EBI-744322
PRPF40AO754001EBI-395959,EBI-473291
PRPF6O949061EBI-395959,EBI-536755
PSME3P612891EBI-395959,EBI-355546
PUF60Q9UHX11EBI-395959,EBI-1053259
RANBP9Q96S591EBI-395959,EBI-636085
RARSP541361EBI-395959,EBI-355482
SART3Q150204EBI-395959,EBI-308619
SF3B1O755331EBI-395959,EBI-876542
SF3B3Q153931EBI-395959,EBI-346977
SFRS1Q079551EBI-395959,EBI-398920
SFRS10P629951EBI-395959,EBI-725485
SFRS12Q8WXA91EBI-395959,EBI-1044237
SFRS2Q011301EBI-395959,EBI-627047
SFRS8Q128721EBI-395959,EBI-1055938
SIP1O148931EBI-395959,EBI-443648
SNRP70P086211EBI-395959,EBI-1049228
SNRPAP090121EBI-395959,EBI-607085
SRPK1Q96SB41EBI-395959,EBI-539478
SRPK2P783621EBI-395959,EBI-593303
SRRM1Q8IYB31EBI-395959,EBI-1055880
SRRM2Q9UQ351EBI-395959,EBI-1050142
STRAPQ9Y3F41EBI-395959,EBI-727414
THRAP3Q9Y2W11EBI-395959,EBI-352039
U2AF2Q96HC51EBI-395959,EBI-742339
USP7Q930091EBI-395959,EBI-302474
WDR33Q9C0J81EBI-395959,EBI-712637

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Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q15287-1)

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.
Isoform 2 (identifier: Q15287-2)

The sequence of this isoform differs from the canonical sequence as follows:
     2-24: Missing.

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Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 305305RNA-binding protein with serine-rich domain 1
PRO_0000081816

Regions

Domain161 – 24080RRM
Region1 – 220220Necessary for interaction with the cleaved p110 isoform of CDC2L1
Region1 – 161161Necessary for interaction with SRP54, nuclear localization and exon-skipping
Region69 – 12153Necessary for interactions with RENT2 and REN3B and RENT2-dependent NMD
Region156 – 24287Necessary for interaction with PNN and exon-skipping
Region238 – 30568Necessary for interaction with SFRS10, nuclear localization and exon-skipping
Compositional bias7 – 6458Lys-rich
Compositional bias67 – 14175Ser-rich
Compositional bias128 – 15427Arg-rich
Compositional bias241 – 29858Arg/Pro-rich

Amino acid modifications

Modified residue271Phosphoserine
Modified residue531Phosphoserine; by CK2
Modified residue1251Phosphoserine
Modified residue1551Phosphoserine
Modified residue1571Phosphoserine
Modified residue2051Phosphotyrosine
Modified residue2511Phosphoserine
Modified residue2661Phosphoserine
Modified residue2871Phosphoserine
Modified residue2891Phosphoserine

Natural variations

Alternative sequence2 – 2423Missing in isoform 2.
VSP_016243

Experimental info

Mutagenesis531S → A: Abolishes phosphorylation by CSNK2A1 and partially reduces splicing stimulation. Does not abolish interaction with CSNK2A1 and subcellular localization
Mutagenesis531S → E: Partially reduces splicing stimulation. Does not abolish interaction with CSNK2A1 and subcellular localization
Mutagenesis2051Y → A: Abolishes exon-skipping
Mutagenesis2071Y → A: Abolishes exon-skipping
Sequence conflict661R → G in AAC39791. Ref.2

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Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified November 1, 1996. Version 1.
Checksum: 930C9D36C2486144

FASTA30534,208
        10         20         30         40         50         60 
MDLSGVKKKS LLGVKENNKK SSTRAPSPTK RKDRSDEKSK DRSKDKGATK ESSEKDRGRD 

        70         80         90        100        110        120 
KTRKRRSASS GSSSTRSRSS STSSSGSSTS TGSSSGSSSS SASSRSGSSS TSRSSSSSSS 

       130        140        150        160        170        180 
SGSPSPSRRR HDNRRRSRSK SKPPKRDEKE RKRRSPSPKP TKVHIGRLTR NVTKDHIMEI 

       190        200        210        220        230        240 
FSTYGKIKMI DMPVERMHPH LSKGYAYVEF ENPDEAEKAL KHMDGGQIDG QEITATAVLA 

       250        260        270        280        290        300 
PWPRPPPRRF SPPRRMLPPP PMWRRSPPRM RRRSRSPRRR SPVRRRSRSP GRRRHRSRSS 


SNSSR

« Hide

Isoform 2 [UniParc].

Checksum: D3F7AAD16B6309F4
Show »

28231,709

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References

« Hide 'large scale' references
[1]"Identification and characterisation of a novel human RNA-binding protein."
Badolato J., Gardiner E., Morrison N., Eisman J.
Gene 166:323-327(1995) [PubMed: 8543184] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), TISSUE SPECIFICITY.
Tissue: Brain.
[2]"The RNP protein, RNPS1, associates with specific isoforms of the p34cdc2-related PITSLRE protein kinases in vivo."
Loyer P., Trembley J.H., Lahti J.M., Kidd V.J.
J. Cell Sci. 111:1495-1506(1998) [PubMed: 9580558] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), INTERACTION WITH CDC2L1, SUBCELLULAR LOCATION.
Tissue: B-cell.
[3]"Identification of an alternatively spliced form of RNPS1."
Harada K., Yang D., Yamada A., Shichijo S., Itoh K.
Submitted (MAY-2000) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
[4]"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: 15489334] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
Tissue: Muscle and Skin.
[5]"Direct interaction of LDC2, a SR-related protein with pinin."
Lee D.-C., Ouyang P.
Submitted (MAR-2000) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 78-305.
Tissue: Kidney.
[6]"Purification and characterization of human RNPS1: a general activator of pre-mRNA splicing."
Mayeda A., Badolato J., Kobayashi R., Zhang M.Q., Gardiner E.M., Krainer A.R.
EMBO J. 18:4560-4570(1999) [PubMed: 10449421] [Abstract]
Cited for: FUNCTION IN PRE-MRNA SPLICING, ASSOCIATION WITH THE SPLICEOSOME, SUBCELLULAR LOCATION.
[7]"The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions."
Le Hir H., Izaurralde E., Maquat L.E., Moore M.J.
EMBO J. 19:6860-6869(2000) [PubMed: 11118221] [Abstract]
Cited for: IDENTIFICATION IN A MRNA SPLICING-DEPENDENT EXON JUNCTION COMPLEX (EJC) WITH DEK; RBM8A; SRRM1 AND THOC4.
[8]"Binding of a SART3 tumor-rejection antigen to a pre-mRNA splicing factor RNPS1: a possible regulation of splicing by a complex formation."
Harada K., Yamada A., Yang D., Itoh K., Shichijo S.
Int. J. Cancer 93:623-628(2001) [PubMed: 11477570] [Abstract]
Cited for: INTERACTION WITH SART3, SUBCELLULAR LOCATION.
[9]"Communication of the position of exon-exon junctions to the mRNA surveillance machinery by the protein RNPS1."
Lykke-Andersen J., Shu M.-D., Steitz J.A.
Science 293:1836-1839(2001) [PubMed: 11546874] [Abstract]
Cited for: FUNCTION IN NONSENSE-MEDIATED MRNA DECAY (NMD), IDENTIFICATION IN A POST-SPLICING COMPLEX WITH NXF1; RBM8A; RENT1; RENT2; RENT3A AND RENT3B, RNA-BINDING, SUBCELLULAR LOCATION.
[10]"An evolutionarily conserved role for SRm160 in 3'-end processing that functions independently of exon junction complex formation."
McCracken S., Longman D., Johnstone I.L., Caceres J.F., Blencowe B.J.
J. Biol. Chem. 278:44153-44160(2003) [PubMed: 12944400] [Abstract]
Cited for: FUNCTION IN MRNA 3'-END FORMATION, INTERACTION WITH SRRM1.
[11]"Nuclear Pnn/DRS protein binds to spliced mRNPs and participates in mRNA processing and export via interaction with RNPS1."
Li C., Lin R.-I., Lai M.-C., Ouyang P., Tarn W.-Y.
Mol. Cell. Biol. 23:7363-7376(2003) [PubMed: 14517304] [Abstract]
Cited for: IDENTIFICATION IN A MRNP COMPLEX WITH PININ, INTERACTION WITH PNN, SUBCELLULAR LOCATION.
[12]"Splicing enhances translation in mammalian cells: an additional function of the exon junction complex."
Nott A., Le Hir H., Moore M.J.
Genes Dev. 18:210-222(2004) [PubMed: 14752011] [Abstract]
Cited for: FUNCTION IN TRANSLATIONAL ACTIVITY AND NONSENSE-MEDIATED MRNA DECAY (NMD), ASSOCIATION WITH POLYSOMES.
[13]"A simple whole cell lysate system for in vitro splicing reveals a stepwise assembly of the exon-exon junction complex."
Kataoka N., Dreyfuss G.
J. Biol. Chem. 279:7009-7013(2004) [PubMed: 14625303] [Abstract]
Cited for: IDENTIFICATION IN A MRNA SPLICING-DEPENDENT EXON JUNCTION COMPLEX (EJC) WITH RBM8A AND SRRM1.
[14]"Human RNPS1 and its associated factors: a versatile alternative pre-mRNA splicing regulator in vivo."
Sakashita E., Tatsumi S., Werner D., Endo H., Mayeda A.
Mol. Cell. Biol. 24:1174-1187(2004) [PubMed: 14729963] [Abstract]
Cited for: FUNCTION IN ALTERNATIVE PRE-MRNA SPLICING, INTERACTION WITH PNN; SFRS10 AND SRP54, MUTAGENESIS OF TYR-205 AND TYR-207, SUBCELLULAR LOCATION.
[15]"Large-scale characterization of HeLa cell nuclear phosphoproteins."
Beausoleil S.A., Jedrychowski M., Schwartz D., Elias J.E., Villen J., Li J., Cohn M.A., Cantley L.C., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 101:12130-12135(2004) [PubMed: 15302935] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-125; SER-155 AND SER-157, MASS SPECTROMETRY.
Tissue: Epithelium.
[16]"Activation of pre-mRNA splicing by human RNPS1 is regulated by CK2 phosphorylation."
Trembley J.H., Tatsumi S., Sakashita E., Loyer P., Slaughter C.A., Suzuki H., Endo H., Kidd V.J., Mayeda A.
Mol. Cell. Biol. 25:1446-1457(2005) [PubMed: 15684395] [Abstract]
Cited for: FUNCTION IN PRE-MRNA SPLICING, ASSOCIATION WITH THE ACTIVE SPLICEOSOME, PHOSPHORYLATION, PHOSPHORYLATION AT SER-53, MASS SPECTROMETRY, INTERACTION WITH CSNK2A1, MUTAGENESIS OF SER-53, SUBCELLULAR LOCATION.
[17]"Exon-junction complex components specify distinct routes of nonsense-mediated mRNA decay with differential cofactor requirements."
Gehring N.H., Kunz J.B., Neu-Yilik G., Breit S., Viegas M.H., Hentze M.W., Kulozik A.E.
Mol. Cell 20:65-75(2005) [PubMed: 16209946] [Abstract]
Cited for: FUNCTION IN A RENT2-DEPENDENT NONSENSE-MEDIATED MRNA DECAY (NMD), IDENTIFICATION IN A COMPLEX WITH RENT2 AND RENT3B.
[18]"Immunoaffinity profiling of tyrosine phosphorylation in cancer cells."
Rush J., Moritz A., Lee K.A., Guo A., Goss V.L., Spek E.J., Zhang H., Zha X.-M., Polakiewicz R.D., Comb M.J.
Nat. Biotechnol. 23:94-101(2005) [PubMed: 15592455] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-205, MASS SPECTROMETRY.
[19]"Global, in vivo, and site-specific phosphorylation dynamics in signaling networks."
Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M.
Cell 127:635-648(2006) [PubMed: 17081983] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-27; SER-251; SER-266; SER-287 AND SER-289, MASS SPECTROMETRY.
Tissue: Epithelium.
[20]"Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry."
Molina H., Horn D.M., Tang N., Mathivanan S., Pandey A.
Proc. Natl. Acad. Sci. U.S.A. 104:2199-2204(2007) [PubMed: 17287340] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-155 AND SER-157, MASS SPECTROMETRY.
[21]"A quantitative atlas of mitotic phosphorylation."
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed: 18669648] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-251, MASS SPECTROMETRY.
+Additional computationally mapped references.

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Cross-references

Sequence databases

L37368 mRNA. Translation: AAA92859.1.
AF015608 mRNA. Translation: AAC39791.1.
AF274003 mRNA. Translation: AAL56665.1.
BC001659 mRNA. Translation: AAH01659.1.
BC001838 mRNA. Translation: AAH01838.1.
BC108316 mRNA. Translation: AAI08317.1.
AF247662 mRNA. Translation: AAF72519.1.
PIRJC4525.
RefSeqNP_006702.1.
NP_542161.1.
UniGeneHs.355643

3D structure databases

HSSPHSSP built from PDB template 1HL6 based on UniProtKB Q9V535.
ModBaseSearch...

Protein-protein interaction databases

IntActQ15287.

PTM databases

PhosphoSiteQ15287.

Genome annotation databases

EnsemblENSG00000205937. Homo sapiens. [Contig view]
GeneID10921.
KEGGhsa:10921.

Organism-specific databases

H-InvDBHIX0012719.
HIX0031789.
HGNCHGNC:10080. RNPS1.
MIM606447. gene.
PharmGKBPA34453.
GenAtlasSearch...
GeneCardsSearch...

Phylogenomic databases

HOGENOMQ15287.
HOVERGENQ15287.

Enzyme and pathway databases

ReactomeREACT_1675. mRNA Processing.
REACT_1788. Transcription.
REACT_6167. Influenza Infection.
REACT_71. Gene Expression.

Gene expression databases

ArrayExpressQ15287.
CleanExHS_RNPS1.
GermOnlineENSG00000205937. Homo sapiens.

Family and domain databases

InterProIPR012677. a_b_plait_nuc_bd.
IPR000504. RRM_RNP1.
[Graphical view]
Gene3DG3DSA:3.30.70.330. a_b_plait_nuc_bd. 1 hit.
PfamPF00076. RRM_1. 1 hit.
[Graphical view]
SMARTSM00360. RRM. 1 hit.
[Graphical view]
PROSITEPS50102. RRM. 1 hit.
[Graphical view]
ProtoNetSearch...

Other Resources

NextBio41487.
SOURCESearch...

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Entry information

Entry nameRNPS1_HUMAN
AccessionPrimary (citable) accession number: Q15287
Secondary accession number(s): O75308 expand/collapse secondary AC list , Q32P25, Q8WY42, Q9NYG3
Entry history
Integrated into UniProtKB/Swiss-Prot: November 22, 2005
Last sequence update: November 1, 1996
Last modified: November 25, 2008
This is version 73 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation projectHPI (Human Proteome Initiative)

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Relevant documents

Human chromosome 16

Human chromosome 16: entries, gene names and cross-references to MIM

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

SIMILARITY comments

Index of protein domains and families

Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Alternative products · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents