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Protein

RNA-binding protein with serine-rich domain 1

Gene

RNPS1

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

Functioni

Part of pre- and post-splicing multiprotein mRNP complexes. Auxiliary component of the splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction 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. Component of the ASAP and PSAP complexes which bind RNA in a sequence-independent manner and are proposed to be recruited to the EJC prior to or during the splicing process and to regulate specific excision of introns in specific transcription subsets. The ASAP complex can inhibit RNA processing during in vitro splicing reactions. The ASAP complex promotes apoptosis and is disassembled after induction of apoptosis. Enhances the formation of the ATP-dependent A complex of the spliceosome. Involved in both constitutive splicing and, in association with SRP54 and TRA2B/SFRS10, in distinctive modulation of alternative splicing in a substrate-dependent manner. 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 activity is different from the established EJC assembly and function. Participates in mRNA 3'-end cleavage. Involved in UPF2-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.10 Publications

GO - Molecular functioni

  • mRNA 3'-UTR 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: Reactome
  • negative regulation of mRNA splicing, via spliceosome Source: UniProtKB
  • nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Source: UniProtKB
  • positive regulation of apoptotic process Source: UniProtKB
  • regulation of alternative mRNA splicing, via spliceosome Source: UniProtKB
  • RNA export from nucleus Source: Reactome
  • RNA splicing Source: ProtInc
  • termination of RNA polymerase II transcription Source: Reactome
  • transcription, DNA-templated Source: ProtInc

Keywordsi

Molecular functionRNA-binding
Biological processmRNA processing, mRNA splicing, Nonsense-mediated mRNA decay

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-9010553 Regulation of expression of SLITs and ROBOs
R-HSA-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)

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 with serine-rich domain 1
Alternative name(s):
SR-related protein LDC2
Gene namesi
Name:RNPS1
Synonyms:LDC2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 16

Organism-specific databases

EuPathDBiHostDB:ENSG00000205937.11
HGNCiHGNC:10080 RNPS1
MIMi606447 gene
neXtProtiNX_Q15287

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

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi53S → A: Abolishes phosphorylation by CSNK2A1 and partially reduces splicing stimulation. Does not abolish interaction with CSNK2A1 and subcellular localization. 1 Publication1
Mutagenesisi53S → E: Partially reduces splicing stimulation. Does not abolish interaction with CSNK2A1 and subcellular localization. 1 Publication1
Mutagenesisi171N → R: Impairs interaction with SAP18. 1 Publication1
Mutagenesisi205Y → A: Abolishes exon-skipping. 1 Publication1
Mutagenesisi207Y → A: Abolishes exon-skipping. 1 Publication1

Organism-specific databases

DisGeNETi10921
OpenTargetsiENSG00000205937
PharmGKBiPA34453

Polymorphism and mutation databases

DMDMi74754492

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000818161 – 305RNA-binding protein with serine-rich domain 1Add BLAST305

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki7Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki15Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei53Phosphoserine; by CK21 Publication1
Modified residuei155PhosphoserineCombined sources1
Modified residuei157PhosphoserineCombined sources1
Modified residuei161PhosphothreonineCombined sources1
Modified residuei218N6-acetyllysineCombined sources1

Post-translational modificationi

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 and translation stimulation activity in vitro.1 Publication

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ15287
MaxQBiQ15287
PaxDbiQ15287
PeptideAtlasiQ15287
PRIDEiQ15287

PTM databases

iPTMnetiQ15287
PhosphoSitePlusiQ15287
SwissPalmiQ15287

Expressioni

Tissue specificityi

Ubiquitous.1 Publication

Gene expression databases

BgeeiENSG00000205937
CleanExiHS_RNPS1
ExpressionAtlasiQ15287 baseline and differential
GenevisibleiQ15287 HS

Organism-specific databases

HPAiHPA044014

Interactioni

Subunit structurei

Found in mRNA splicing-dependent exon junction complexes (EJC). Found in a post-splicing complex with NXF1, RBM8A, UPF1, UPF2, UPF3A, UPF3B and RNPS1. Component of the heterotrimeric ASAP (apoptosis- and splicing-associated protein) and PSAP complexes consisting of RNPS1, SAP18 and either ACIN1 or PNN, respectively; the ASAP and PSAP complexes probably are formed mutually exclusive. Component of the active spliceosome. Associates with polysomes. Interacts with the cleaved p110 isoform of CDC2L1, CSNK2A1, PNN, SART3, SRP54, SRRM1 and TRA2B/SFRS10.14 Publications

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi116125, 198 interactors
CORUMiQ15287
DIPiDIP-32943N
IntActiQ15287, 167 interactors
MINTiQ15287
STRINGi9606.ENSP00000301730

Structurei

Secondary structure

1305
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi162 – 166Combined sources5
Helixi174 – 182Combined sources9
Beta strandi187 – 191Combined sources5
Beta strandi198 – 202Combined sources5
Beta strandi204 – 212Combined sources9
Helixi213 – 223Combined sources11
Beta strandi234 – 238Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4A8XX-ray1.90A159-244[»]
ProteinModelPortaliQ15287
SMRiQ15287
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini161 – 240RRMPROSITE-ProRule annotationAdd BLAST80

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 220Necessary for interaction with the cleaved p110 isoform of CDC2L1Add BLAST220
Regioni1 – 161Necessary for interaction with SRP54, nuclear localization and exon-skipping1 PublicationAdd BLAST161
Regioni69 – 121Necessary for interactions with UPF2 and UPF3B and UPF2-dependent NMDAdd BLAST53
Regioni156 – 242Necessary for interaction with PNN and exon-skippingAdd BLAST87
Regioni159 – 244Interaction with SAP18 and ACIN11 PublicationAdd BLAST86
Regioni238 – 305Necessary for interaction with TRA2B, nuclear localization and exon-skipping1 PublicationAdd BLAST68

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi7 – 64Lys-richAdd BLAST58
Compositional biasi67 – 141Ser-richAdd BLAST75
Compositional biasi128 – 154Arg-richAdd BLAST27
Compositional biasi241 – 298Arg/Pro-richAdd BLAST58

Domaini

The RRM domain is required for the formation of the ASAP complex.

Sequence similaritiesi

Belongs to the splicing factor SR family.Curated

Phylogenomic databases

eggNOGiKOG4209 Eukaryota
ENOG4111PFV LUCA
GeneTreeiENSGT00730000111029
HOVERGENiHBG053138
InParanoidiQ15287
KOiK14325
OMAiPNFGRGV
OrthoDBiEOG091G14LV
PhylomeDBiQ15287
TreeFamiTF314165

Family and domain databases

CDDicd12365 RRM_RNPS1, 1 hit
Gene3Di3.30.70.330, 1 hit
InterProiView protein in InterPro
IPR012677 Nucleotide-bd_a/b_plait_sf
IPR035979 RBD_domain_sf
IPR034201 RNPS1_RRM
IPR000504 RRM_dom
PfamiView protein in Pfam
PF00076 RRM_1, 1 hit
SMARTiView protein in SMART
SM00360 RRM, 1 hit
SUPFAMiSSF54928 SSF54928, 1 hit
PROSITEiView protein in PROSITE
PS50102 RRM, 1 hit

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q15287-1) [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
MDLSGVKKKS LLGVKENNKK SSTRAPSPTK RKDRSDEKSK DRSKDKGATK
60 70 80 90 100
ESSEKDRGRD KTRKRRSASS GSSSTRSRSS STSSSGSSTS TGSSSGSSSS
110 120 130 140 150
SASSRSGSSS TSRSSSSSSS SGSPSPSRRR HDNRRRSRSK SKPPKRDEKE
160 170 180 190 200
RKRRSPSPKP TKVHIGRLTR NVTKDHIMEI FSTYGKIKMI DMPVERMHPH
210 220 230 240 250
LSKGYAYVEF ENPDEAEKAL KHMDGGQIDG QEITATAVLA PWPRPPPRRF
260 270 280 290 300
SPPRRMLPPP PMWRRSPPRM RRRSRSPRRR SPVRRRSRSP GRRRHRSRSS

SNSSR
Length:305
Mass (Da):34,208
Last modified:November 1, 1996 - v1
Checksum:i930C9D36C2486144
GO
Isoform 2 (identifier: Q15287-2) [UniParc]FASTAAdd to basket

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

Show »
Length:282
Mass (Da):31,709
Checksum:iD3F7AAD16B6309F4
GO
Isoform 3 (identifier: Q15287-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     2-24: Missing.
     69-82: Missing.

Show »
Length:268
Mass (Da):30,354
Checksum:i9058DEEC9B433103
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti32K → E in BAG56859 (PubMed:14702039).Curated1
Sequence conflicti66R → G in AAC39791 (PubMed:9580558).Curated1
Sequence conflicti249R → G in BAG56859 (PubMed:14702039).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0162432 – 24Missing in isoform 2 and isoform 3. 2 PublicationsAdd BLAST23
Alternative sequenceiVSP_03760169 – 82Missing in isoform 3. 1 PublicationAdd BLAST14

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L37368 mRNA Translation: AAA92859.1
AF015608 mRNA Translation: AAC39791.1
AF274003 mRNA Translation: AAL56665.1
AK289955 mRNA Translation: BAF82644.1
AK293343 mRNA Translation: BAG56859.1
AK303100 mRNA Translation: BAG64209.1
AK316132 mRNA Translation: BAH14503.1
AC009065 Genomic DNA No translation available.
CH471112 Genomic DNA Translation: EAW85516.1
BC001659 mRNA Translation: AAH01659.1
BC001838 mRNA Translation: AAH01838.1
BC108316 mRNA Translation: AAI08317.1
AF247662 mRNA Translation: AAF72519.1
CCDSiCCDS10465.1 [Q15287-1]
CCDS66907.1 [Q15287-2]
PIRiJC4525
RefSeqiNP_001273554.1, NM_001286625.1 [Q15287-1]
NP_001273555.1, NM_001286626.1 [Q15287-2]
NP_001273556.1, NM_001286627.1
NP_006702.1, NM_006711.4 [Q15287-1]
NP_542161.1, NM_080594.3 [Q15287-1]
XP_005255105.1, XM_005255048.1 [Q15287-1]
XP_005255106.1, XM_005255049.3 [Q15287-1]
XP_016878363.1, XM_017022874.1 [Q15287-1]
UniGeneiHs.355643
Hs.507343
Hs.733012

Genome annotation databases

EnsembliENST00000301730; ENSP00000301730; ENSG00000205937 [Q15287-1]
ENST00000320225; ENSP00000315859; ENSG00000205937 [Q15287-1]
ENST00000397086; ENSP00000380275; ENSG00000205937 [Q15287-1]
ENST00000565678; ENSP00000457723; ENSG00000205937 [Q15287-1]
ENST00000566458; ENSP00000456352; ENSG00000205937 [Q15287-2]
ENST00000568631; ENSP00000457820; ENSG00000205937 [Q15287-1]
GeneIDi10921
KEGGihsa:10921
UCSCiuc002cpt.5 human [Q15287-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiRNPS1_HUMAN
AccessioniPrimary (citable) accession number: Q15287
Secondary accession number(s): A8K1P0
, B4DDU8, B4DZU7, B7ZA17, O75308, Q32P25, Q8WY42, Q9NYG3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 22, 2005
Last sequence update: November 1, 1996
Last modified: April 25, 2018
This is version 179 of the entry and version 1 of the sequence. See 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
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Main funding by: National Institutes of Health