This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to find a list of all proteins involved in Alternative splicing regulation

I am an intern entering my third year and I am currently tasked with finding all the proteins directly involved in splicing regulation. I am currently looking through published papers after failing with QuickGO and Uniprot. Any help with this would be appreciated.

alternative-splicing

2 answers

You could also use the web interface at UniProt. Limit the queries based on your needs with right keywords.

Everything : https://www.uniprot.org/uniprotkb?query=splicing+regulation
"Splicing + Regulation" : https://www.uniprot.org/uniprotkb?query=%22splicing+regulation%22
Only for "human": https://www.uniprot.org/uniprotkb?query=%22splicing+regulation%22&facets=model_organism%3A9606

Alternative splicing regulation: https://www.uniprot.org/uniprotkb?query=%22Alternative+splicing+regulation%22
Only for "human": https://www.uniprot.org/uniprotkb?query=%22Alternative+splicing+regulation%22&facets=model_organism%3A9606

Once you have a result you like (use various filters, terms in the left column), customize the results columns and then download as a table or as sequences.

using uniprot+sparql : https://sparql.uniprot.org/

PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX GO: <http://purl.obolibrary.org/obo/GO_>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
PREFIX up: <http://purl.uniprot.org/core/>
SELECT DISTINCT
   ?gene ?geneName
WHERE
{   
    ?protein rdf:type up:Protein ;
             up:organism taxon:9606 ;
             up:classifiedWith|(up:classifiedWith/rdfs:subClassOf) GO:0043484 .
        ?protein up:encodedBy ?gene .
        ?gene skos:prefLabel ?geneName .


}
A2BP1 
AAR2 
ACIN1 
AFF2 
AHNAK 
AHNAK2 
AKAP17A 
ANGEL2 
ARB2A 
ARGLU1 
ATXN7 
ATXN7L3 
BRDT 
C1QBP 
CCAR2 
CCDC55 
CCNL1 
CCNL2 
CDK11A 
CDK11B 
CELF1 
CELF2 
CELF3 
CELF4 
CELF5 
CELF6 
CLK1 
CLK2 
CLK3 
CLK4 
CLNS1A 
CWC22 
DAZAP1 
DDX17 
DDX5 
DKFZp547L059 
DKFZp686F20131 
DKFZp781C0423 
DYRK1A 
EFTUD2 
ENY2 
ERN1 
ESRP1 
ESRP2 
FAM50A 
FASTK 
FMR1 
FUS 

GRSF1 
H1-2 
H1-3 
HABP4 
HNRNPA1 
HNRNPF 
HNRNPH1 
HNRNPH2 
HNRNPH3 
HNRNPK 
HNRNPL 
HNRNPLL 
HNRNPU 
HOXB-AS3 
HSPA1A 
ILDR1 
ILDR2 
JMJD6 
KAT2A 
KAT2B 
KHDRBS1 
KHDRBS2 
KHDRBS3 
LARP7 
MAGOH 
MBNL1 
MBNL2 
MBNL3 
METTL16 
METTL4 
MYOD1 
NCBP1 
NOVA1 
NOVA2 
NSRP1 
NUP98 
PCBP4 
PIK3R1 
POLR2A 
PQBP1 
PRDX6 
PRMT5 
PRPF8 
PRX 
PTBP1 
PTBP2 
PTBP3 
PUF60 
QKI 
RBFOX1 
RBFOX2 
RBFOX3 
RBM11 
RBM12 
RBM12B 
RBM14 
RBM15 
RBM15B 
RBM19 
RBM20 
RBM22 
RBM23 
RBM24 
RBM25 
RBM38 
RBM39 
RBM4 
RBM47 
RBM4B 
RBM5 
RBM7 
RBM8A 
RBMX 
RBMY1A1 
RBMY1C 
RBPMS 
RBPMS2 
REST 
RNPS1 
RPS13 
RPS26 
RRP1B 
SAP18 
SAP30BP 
SETX 
SF3B3 
SF3B5 
SFSWAP 
SGF29 
SLC38A2 
SMU1 
SNRNP200 
SNRNP70 
SNRPB 
SNRPD1 
SNRPD2 
SNRPD3 
SNRPE 
SNRPF 
SNRPG 
SNW1 
SON 
SRPK1 
SRPK2 
SRRM1 
SRRM4 
SRSF1 
SRSF10 
SRSF12 
SRSF2 
SRSF3 
SRSF4 
SRSF5 
SRSF6 
SRSF7 
SRSF8 
SRSF9 
SRSP 
STH 
SUPT20H 
SUPT3H 
SUPT7L 
TADA1 
TADA2B 
TADA3 
TAF10 
TAF12 
TAF5L 
TAF6L 
TAF9 
THRAP3 
THUMPD2 
TIA1 
TIAL1 
TMBIM6 
TRA2B 
TRRAP 
U2AF2 
USP22 
WDR77 
WTAP 
YTHDC1 
ZBTB7A 
ZC3H10 
ZNF326 
ZNF638 
ZPR1

Log in to answer this question.