Identification of proteins binding coding and non-coding human RNAs using protein microarrays

Siprashvili, Zurab; Webster, Dan E; Kretz, Markus; Johnston, Danielle; Rinn, John L; Chang, Howard Y; Khavari, Paul A

doi:10.1186/1471-2164-13-633

Table 1 Common RNA binding proteins and their conserved domains

From: Identification of proteins binding coding and non-coding human RNAs using protein microarrays

Gene name	Protein description (NCBI Protein)	Conserved	% of all RNAs significantly bound
Gene name	Protein description (NCBI Protein)	Domains	% of all RNAs significantly bound
CIRBP	Cold-inducible RNA-binding protein	RRM	90%
SFRS13A	FUSIP1 protein	RRM	85%
CPEB4	CPEB4 protein	RRM	85%
PTBP2	Polypyrimidine tract binding protein 2	RRM	80%
TIA1	TIA1 protein	RRM	80%
TIAL1	TIAL1 protein	RRM	75%
RBMS3	RNA-binding motif, single-stranded-interacting protein 3	RRM	95%
PTBP1	Polypyrimidine tract-binding protein 1 isoform c	RRM	95%
PCBP2	Poly(rC)-binding protein 2 isoform b	PCBP_like_KH, KH-I	100%
NOVA1	RNA-binding protein Nova-1 isoform 1	PCBP_like_KH,KH-I	90%
PCBP2	Poly(rC)-binding protein 2 isoform a	PCBP_like_KH, KH-I	90%
PCBP1	Poly(rC) binding protein 1	PCBP_like_KH, KH-I	80%
QKI	Protein quaking isoform HQK-6	SF1_like-KH	95%
QKI	Protein quaking isoform HQK-7B	SF1_like-KH	90%
QKI	Protein quaking isoform HQK-5	SF1_like-KH	80%
KHDRBS2	KH domain-containing,RNA-binding protein 2	SF1_like-KH	85%
KHDRBS3	KHDRBS3 protein	SF1_like-KH	75%
ZNF385b	ZNF385B protein	Zf-met	90%
MBNL1	Muscleblind-like protein 1 isoform a	Zf-CCCH	75%
ZC3H10	Zinc finger CCCH domain-containing protein 10	Zf-CCCH	95%
TARBP2	RISC-loading complex subunit TARBP2 isoform b	DSRM	95%
TARBP2	RISC-loading complex subunit TARBP2 isoform a	DSRM	100%
RPA1	Replication protein A 70 kDa DNA-binding subunit	RPA1N,RPA1_DBD_C	75%
UNG	Uracil-DNA glycosylase isoform UNG2	UDG_F1	95%
KCNAB1	Voltage-gated potassium channel subunit beta-1 isoform 1	Aldo_ket_red, Tas	95%
STK40	Serine/threonine-protein kinase 40	PKc_like	75%
PAGE1	G antigen family B member 1	GAGE	75%
NUDT16L1	Protein syndesmos isoform 1	None	75%

RRM – RNA recognition motif, PCBP_like_KH – Poly r(C) binding protein like K homology domain, KH – K homology RNA binding domain, KH-I – K homology RNA binding domain type I, SF1_like-KH – Splicing factor K homology RNA binding domain, Zf-CCCH – Zinc-finger of CCCH [C-x8-C-x5-Cx3-H] type, DSRM – Double-stranded RNA binding motif, Aldo_ket_red – Aldo-keto reductase, Tas – predicted oxidoreductase, UDG_F1 – family 1 of Uracil-DNA glycosylase, RPA1N – replication protein A N-terminal OB fold domain, RPA1_DBD_C – replication protein ssDNA binding domain DBD-C, PKc_like – Protein Kinase C family, GAGE – GAGE protein family.

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