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Protein

RNA-binding protein with serine-rich domain 1

Gene

RNPS1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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
  • nucleotide binding Source: InterPro
  • poly(A) RNA binding Source: UniProtKB
  • RNA binding Source: ProtInc

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
Complete GO annotation...

Keywords - Biological processi

mRNA processing, mRNA splicing, Nonsense-mediated mRNA decay

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciZFISH:ENSG00000167971-MONOMER.
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).

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

HGNCiHGNC:10080. RNPS1.

Subcellular locationi

  • Nucleus
  • Nucleus speckle
  • Cytoplasm

  • Note: Nucleocytoplasmic shuttling protein. Colocalizes with the core EJC, ALYREF/THOC4, NXF1 and UAP56 in the nucleus and nuclear speckles.

GO - Cellular componenti

  • ASAP complex Source: UniProtKB
  • cytoplasm Source: UniProtKB
  • cytosol Source: Reactome
  • nuclear speck Source: UniProtKB-SubCell
  • nucleoplasm Source: HPA
  • nucleus Source: UniProtKB
Complete GO annotation...

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
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, Phosphoprotein

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

WithEntry#Exp.IntActNotes
SART3Q150205EBI-395959,EBI-308619
SRPK1Q96SB42EBI-395959,EBI-539478
SRPK2P783623EBI-395959,EBI-593303

Protein-protein interaction databases

BioGridi116125. 182 interactors.
DIPiDIP-32943N.
IntActiQ15287. 77 interactors.
MINTiMINT-1474621.
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
Contains 1 RRM (RNA recognition motif) domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG4209. Eukaryota.
ENOG4111PFV. LUCA.
GeneTreeiENSGT00730000111029.
HOVERGENiHBG053138.
InParanoidiQ15287.
KOiK14325.
OMAiPTKVHLG.
OrthoDBiEOG091G14LV.
PhylomeDBiQ15287.
TreeFamiTF314165.

Family and domain databases

Gene3Di3.30.70.330. 1 hit.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF00076. RRM_1. 1 hit.
[Graphical view]
SMARTiSM00360. RRM. 1 hit.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 1 hit.
PROSITEiPS50102. RRM. 1 hit.
[Graphical view]

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

Cross-referencesi

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.

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...

Protein-protein interaction databases

BioGridi116125. 182 interactors.
DIPiDIP-32943N.
IntActiQ15287. 77 interactors.
MINTiMINT-1474621.
STRINGi9606.ENSP00000301730.

Protein family/group databases

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

PTM databases

iPTMnetiQ15287.
PhosphoSitePlusiQ15287.
SwissPalmiQ15287.

Polymorphism and mutation databases

DMDMi74754492.

Proteomic databases

EPDiQ15287.
MaxQBiQ15287.
PaxDbiQ15287.
PeptideAtlasiQ15287.
PRIDEiQ15287.

Protocols and materials databases

DNASUi10921.
Structural Biology KnowledgebaseSearch...

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]

Organism-specific databases

CTDi10921.
DisGeNETi10921.
GeneCardsiRNPS1.
H-InvDBHIX0031789.
HGNCiHGNC:10080. RNPS1.
HPAiHPA044014.
MIMi606447. gene.
neXtProtiNX_Q15287.
OpenTargetsiENSG00000205937.
PharmGKBiPA34453.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG4209. Eukaryota.
ENOG4111PFV. LUCA.
GeneTreeiENSGT00730000111029.
HOVERGENiHBG053138.
InParanoidiQ15287.
KOiK14325.
OMAiPTKVHLG.
OrthoDBiEOG091G14LV.
PhylomeDBiQ15287.
TreeFamiTF314165.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000167971-MONOMER.
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).

Miscellaneous databases

ChiTaRSiRNPS1. human.
GeneWikiiRNPS1.
GenomeRNAii10921.
PROiQ15287.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000205937.
CleanExiHS_RNPS1.
ExpressionAtlasiQ15287. baseline and differential.
GenevisibleiQ15287. HS.

Family and domain databases

Gene3Di3.30.70.330. 1 hit.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF00076. RRM_1. 1 hit.
[Graphical view]
SMARTiSM00360. RRM. 1 hit.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 1 hit.
PROSITEiPS50102. RRM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRNPS1_HUMAN
AccessioniPrimary (citable) accession number: Q15287
Secondary accession number(s): A8K1P0
, B4DDU8, B4DZU7, B7ZA17, O75308, Q32P25, Q8WY42, Q9NYG3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 22, 2005
Last sequence update: November 1, 1996
Last modified: November 30, 2016
This is version 166 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 16
    Human chromosome 16: 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.