ASpdb: an integrative knowledgebase of human protein isoforms from experimental and AI-predicted structures

Home

Download

Statistics

Examples

Help

Contact

	Protein Summary
	AS Summary
	Protein Functional Features
	Gene Isoform Structures and Expression Levels
	Protein Structures
	pLDDT Score Distribution
	Ramachandran Plot of Protein Structures
	Potential Active Site Information
	Protein Structure and Feature Comparision
	Protein-Protein Interaction
	Related Drugs
	Related Diseases
	Clinically Important Variants

Protein:RNPS1

Protein Summary

Gene summary

Gene name: RNPS1
ASpdb.0 ID: 10921
	Gene
Gene symbol	RNPS1
Gene ID	10921
Gene name	RNA binding protein with serine rich domain 1
Synonyms	E5.1
Cytomap	16p13.3
Type of gene	protein-coding
Description	RNA-binding protein with serine-rich domain 1RNA binding protein with serine-rich domainRNA-binding protein S1, serine-rich domainSR proteinSR-related protein LDC2
Modification date	20240407
UniProtAcc	Q15287

Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Gene	RNPS1	GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	11546874
Gene	RNPS1	GO:0003723	RNA binding	22388736
Gene	RNPS1	GO:0003730	mRNA 3'-UTR binding	11546874
Gene	RNPS1	GO:0005634	nucleus	11546874
Gene	RNPS1	GO:0005654	nucleoplasm	-
Gene	RNPS1	GO:0005737	cytoplasm	11546874
Gene	RNPS1	GO:0043065	positive regulation of apoptotic process	12665594
Gene	RNPS1	GO:0048025	negative regulation of mRNA splicing, via spliceosome	12665594
Gene	RNPS1	GO:0061574	ASAP complex	12665594

AS Summary

Information of the canonical protein with experimentally identified structure from PDB (2023).

UniProt Acc	File name	PDB ID	Method	Resolution	Chain	Start	End
Q15287-1	Q15287-1_4a8x_A.pdb	4A8X	X-ray	1.9	A	159	244

ASpdb's canonical and alternatively spliced isoform information.

accession_id

gene_name

canonical_id

alternative_id

canonical_length

alternative_length

canonical_start

canonical_end

type

originalSEQ

variationSEQ

alternative_start

alternative_end

Q15287

RNPS1

Q15287-1

Q15287-2

305

282

Deletion

none

Q15287

RNPS1

Q15287-1

Q15287-3

305

268

Deletion

none

Q15287

RNPS1

Q15287-1

Q15287-3

305

268

Deletion

none

Multiple sequence alignment of our canonical and alternatively spliced RNPS1

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of RNPS1

UniProt-id	ENSG	ENST	ENSP
Q15287-1	ENSG00000205937.12	ENST00000301730.12	ENSP00000301730.8
Q15287-1	ENSG00000205937.12	ENST00000320225.10	ENSP00000315859.5
Q15287-1	ENSG00000205937.12	ENST00000397086.6	ENSP00000380275.2
Q15287-1	ENSG00000205937.12	ENST00000565678.5	ENSP00000457723.1
Q15287-1	ENSG00000205937.12	ENST00000568631.5	ENSP00000457820.1
Q15287-2	ENSG00000205937.12	ENST00000566458.5	ENSP00000456352.1

UniProt-id	NM ID	NP ID
Q15287-1	NM_001286625.1	NP_001273554.1
Q15287-1	NM_006711.4	NP_006702.1
Q15287-1	NM_080594.3	NP_542161.1
Q15287-1	XM_005255048.1	XP_005255105.1
Q15287-1	XM_005255049.3	XP_005255106.1
Q15287-2	NM_001286626.1	NP_001273555.1

Amino acid sequences of our canonical and alternatively spliced RNPS1

accession_id	Protein sequence
Q15287-1	MDLSGVKKKSLLGVKENNKKSSTRAPSPTKRKDRSDEKSKDRSKDKGATKESSEKDRGRDKTRKRRSASSGSSSTRSRSSSTSSSGSSTS TGSSSGSSSSSASSRSGSSSTSRSSSSSSSSGSPSPSRRRHDNRRRSRSKSKPPKRDEKERKRRSPSPKPTKVHIGRLTRNVTKDHIMEI FSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVLAPWPRPPPRRFSPPRRMLPPPPMWRRSPPRM
Q15287-2	MAPSPTKRKDRSDEKSKDRSKDKGATKESSEKDRGRDKTRKRRSASSGSSSTRSRSSSTSSSGSSTSTGSSSGSSSSSASSRSGSSSTSR SSSSSSSSGSPSPSRRRHDNRRRSRSKSKPPKRDEKERKRRSPSPKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSK GYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVLAPWPRPPPRRFSPPRRMLPPPPMWRRSPPRMRRRSRSPRRRSPVRRRSRSPGRR
Q15287-3	MAPSPTKRKDRSDEKSKDRSKDKGATKESSEKDRGRDKTRKRRSASSSGSSTSTGSSSGSSSSSASSRSGSSSTSRSSSSSSSSGSPSPS RRRHDNRRRSRSKSKPPKRDEKERKRRSPSPKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAE

Protein Functional Features

Main function of this protein. (from UniProt)

RNPS1 (go to UniProt):Q15287

Retention analysis result of protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at
download page
* Minus value of BPloci means that the break pointn is located before the CDS.

- Retained protein feature among the 13 regional features.

Accession_id	Subsection	Start	End	Funcitonal feature	Splicing information
Q15287	Region	1	220	Note=Necessary for interaction with the cleaved p110 isoform of CDC2L1	Type=Deletion;Start=2;End=24
Q15287	Region	1	220	Note=Necessary for interaction with the cleaved p110 isoform of CDC2L1	Type=Deletion;Start=2;End=24
Q15287	Region	1	220	Note=Necessary for interaction with the cleaved p110 isoform of CDC2L1	Type=Deletion;Start=69;End=82
Q15287	Region	1	170	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=2;End=24
Q15287	Region	1	170	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=2;End=24
Q15287	Region	1	170	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=69;End=82
Q15287	Region	1	161	Note=Necessary for interaction with SRP54%2C nuclear localization and exon-skipping;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:14729963;Dbxref=PMID:14729963	Type=Deletion;Start=2;End=24
Q15287	Region	1	161	Note=Necessary for interaction with SRP54%2C nuclear localization and exon-skipping;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:14729963;Dbxref=PMID:14729963	Type=Deletion;Start=2;End=24
Q15287	Region	1	161	Note=Necessary for interaction with SRP54%2C nuclear localization and exon-skipping;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:14729963;Dbxref=PMID:14729963	Type=Deletion;Start=69;End=82
Q15287	Region	69	121	Note=Necessary for interactions with UPF2 and UPF3B and UPF2-dependent NMD	Type=Deletion;Start=69;End=82
Q15287	Compositional bias	68	126	Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=69;End=82

Gene Isoform Structures and Expression Levels for RNPS1

Gene structures of our canonical and alternative spliced genes of RNPS1
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Expression levels of gene isoforms across GTEx.

Expression levels of gene isoforms across TCGA.

Protein Structures

PDB and CIF files of the predicted protein structures
* Here we show the 3D structure of the proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.

3D view using mol* of Q15287-1

3D view using mol* of Q15287-2

3D view using mol* of Q15287-3

pLDDT Score Distribution

pLDDT score distribution of the predicted protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

pLDDT distribution across the protein length of Q15287-1

pLDDT distribution across the protein length of Q15287-2

pLDDT distribution across the protein length of Q15287-3

Ramachandran Plot of Protein Structures

Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this protein peptide.

Ramachandran plot of Q15287-1

Ramachandran plot of Q15287-2

Potential Active Site Information

The potential binding sites of these proteins were identified using SiteMap, a module of the Schrodinger suite.

UniProt-id	Site score	Size	D score	Volume	Exposure	Enclosure	Contact	Phobic	Philic	Balance	Don/Acc	Residues
Q15287-1	0.304	8	0.195	4.459	0.795	0.438	0.722	0.085	1.024	0.083	0.267	254,255,256,257
Q15287-2	0.395	8	0.323	45.962	0.897	0.489	0.572	0.105	0.725	0.145	1.167	150,151,152,169,179
Q15287-3	0.429	10	0.376	33.614	0.846	0.477	0.603	0.241	0.635	0.379	2.087	133,136,155,157,162,163,165

Protein Structure and Feature Comparision

Protein Structure Comparision Using Template Modeling Scores (TM-score).

Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Canonical validated structure (PDB)(green)

3D view using mol* of Q15287-1_Q15287-1_4a8x_A.pdb

Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green)

3D view using mol* of Q15287-1_4a8x_A_Q15287-2.pdb

3D view using mol* of Q15287-1_4a8x_A_Q15287-3.pdb

Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green)

3D view using mol* of Q15287-1_Q15287-2.pdb

3D view using mol* of Q15287-1_Q15287-3.pdb

Protein Feature Comparison of the protein sequendary structures among the protiens.

./stats/secondary_structure/figure/Q15287-1_vs_Q15287-2.png

./stats/secondary_structure/figure/Q15287-1_vs_Q15287-3.png

Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens.

./stats/relative_asa/Q15287-1_vs_Q15287-2.png

./stats/relative_asa/Q15287-1_vs_Q15287-3.png

Protein-Protein Interaction

Interactors from UniProt.

Accession_id	Subsection	Start	End	Funcitonal feature	Splicing information
Q15287	Region	1	220	Note=Necessary for interaction with the cleaved p110 isoform of CDC2L1	Type=Deletion;Start=2;End=24
Q15287	Region	1	220	Note=Necessary for interaction with the cleaved p110 isoform of CDC2L1	Type=Deletion;Start=2;End=24
Q15287	Region	1	220	Note=Necessary for interaction with the cleaved p110 isoform of CDC2L1	Type=Deletion;Start=69;End=82
Q15287	Region	1	161	Note=Necessary for interaction with SRP54%2C nuclear localization and exon-skipping;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:14729963;Dbxref=PMID:14729963	Type=Deletion;Start=2;End=24
Q15287	Region	1	161	Note=Necessary for interaction with SRP54%2C nuclear localization and exon-skipping;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:14729963;Dbxref=PMID:14729963	Type=Deletion;Start=2;End=24
Q15287	Region	1	161	Note=Necessary for interaction with SRP54%2C nuclear localization and exon-skipping;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:14729963;Dbxref=PMID:14729963	Type=Deletion;Start=69;End=82
Q15287	Region	69	121	Note=Necessary for interactions with UPF2 and UPF3B and UPF2-dependent NMD	Type=Deletion;Start=69;End=82

Interactors from STRING.

Gene name

Interactors

Related Drugs to RNPS1

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession

Gene name

DrugBank ID

Drug name

Drug group

Actions

Related Diseases to RNPS1

Previous studies relating to the alternative splicing of RNPS1 and disease information from the MeSH term (PubMed)

Gene	PMID	Title	Abstract	MeSH ID	MeSH term
RNPS1	24711643	Identifying biological pathways that underlie primordial short stature using network analysis.	Mutations in CUL7, OBSL1 and CCDC8, leading to disordered ubiquitination, cause one of the commonest primordial growth disorders, 3-M syndrome. This condition is associated with i) abnormal p53 function, ii) GH and/or IGF1 resistance, which may relate to failure to recycle signalling molecules, and iii) cellular IGF2 deficiency. However the exact molecular mechanisms that may link these abnormalities generating growth restriction remain undefined. In this study, we have used immunoprecipitation/mass spectrometry and transcriptomic studies to generate a 3-M 'interactome', to define key cellular pathways and biological functions associated with growth failure seen in 3-M. We identified 189 proteins which interacted with CUL7, OBSL1 and CCDC8, from which a network including 176 of these proteins was generated. To strengthen the association to 3-M syndrome, these proteins were compared with an inferred network generated from the genes that were differentially expressed in 3-M fibroblasts compared with controls. This resulted in a final 3-M network of 131 proteins, with the most significant biological pathway within the network being mRNA splicing/processing. We have shown using an exogenous insulin receptor (INSR) minigene system that alternative splicing of exon 11 is significantly changed in HEK293 cells with altered expression of CUL7, OBSL1 and CCDC8 and in 3-M fibroblasts. The net result is a reduction in the expression of the mitogenic INSR isoform in 3-M syndrome. From these preliminary data, we hypothesise that disordered ubiquitination could result in aberrant mRNA splicing in 3-M; however, further investigation is required to determine whether this contributes to growth failure.	D004392	Dwarfism
RNPS1	24711643	Identifying biological pathways that underlie primordial short stature using network analysis.	Mutations in CUL7, OBSL1 and CCDC8, leading to disordered ubiquitination, cause one of the commonest primordial growth disorders, 3-M syndrome. This condition is associated with i) abnormal p53 function, ii) GH and/or IGF1 resistance, which may relate to failure to recycle signalling molecules, and iii) cellular IGF2 deficiency. However the exact molecular mechanisms that may link these abnormalities generating growth restriction remain undefined. In this study, we have used immunoprecipitation/mass spectrometry and transcriptomic studies to generate a 3-M 'interactome', to define key cellular pathways and biological functions associated with growth failure seen in 3-M. We identified 189 proteins which interacted with CUL7, OBSL1 and CCDC8, from which a network including 176 of these proteins was generated. To strengthen the association to 3-M syndrome, these proteins were compared with an inferred network generated from the genes that were differentially expressed in 3-M fibroblasts compared with controls. This resulted in a final 3-M network of 131 proteins, with the most significant biological pathway within the network being mRNA splicing/processing. We have shown using an exogenous insulin receptor (INSR) minigene system that alternative splicing of exon 11 is significantly changed in HEK293 cells with altered expression of CUL7, OBSL1 and CCDC8 and in 3-M fibroblasts. The net result is a reduction in the expression of the mitogenic INSR isoform in 3-M syndrome. From these preliminary data, we hypothesise that disordered ubiquitination could result in aberrant mRNA splicing in 3-M; however, further investigation is required to determine whether this contributes to growth failure.	D006130	Growth Disorders
RNPS1	24711643	Identifying biological pathways that underlie primordial short stature using network analysis.	Mutations in CUL7, OBSL1 and CCDC8, leading to disordered ubiquitination, cause one of the commonest primordial growth disorders, 3-M syndrome. This condition is associated with i) abnormal p53 function, ii) GH and/or IGF1 resistance, which may relate to failure to recycle signalling molecules, and iii) cellular IGF2 deficiency. However the exact molecular mechanisms that may link these abnormalities generating growth restriction remain undefined. In this study, we have used immunoprecipitation/mass spectrometry and transcriptomic studies to generate a 3-M 'interactome', to define key cellular pathways and biological functions associated with growth failure seen in 3-M. We identified 189 proteins which interacted with CUL7, OBSL1 and CCDC8, from which a network including 176 of these proteins was generated. To strengthen the association to 3-M syndrome, these proteins were compared with an inferred network generated from the genes that were differentially expressed in 3-M fibroblasts compared with controls. This resulted in a final 3-M network of 131 proteins, with the most significant biological pathway within the network being mRNA splicing/processing. We have shown using an exogenous insulin receptor (INSR) minigene system that alternative splicing of exon 11 is significantly changed in HEK293 cells with altered expression of CUL7, OBSL1 and CCDC8 and in 3-M fibroblasts. The net result is a reduction in the expression of the mitogenic INSR isoform in 3-M syndrome. From these preliminary data, we hypothesise that disordered ubiquitination could result in aberrant mRNA splicing in 3-M; however, further investigation is required to determine whether this contributes to growth failure.	D009123	Muscle Hypotonia

Clinically important variants in RNPS1

(ClinVar, 04/20/2024)

accession_id

uniprot_id

gene_name

Type

Variant

Clinical_significance