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.
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
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