. 2008 Nov 3;29(1):281–301. doi: 10.1128/MCB.01415-08

TABLE 1.

Protein composition of Drosophila spliceosomal B and C complexes^a

Human protein^b	GenBank accession no.	Drosophila melanogaster protein			Presence of or absolute no. of peptides sequenced for protein^c in indicated complex in:
		Drosophila melanogaster protein			HeLa nuclear extract			Kc nuclear extract							HeLa extract, C, PM5^d
		CG no.	Gene name	Mol mass (kDa)	B, MINX-M3^d	B, Ftz-M3		B, Ftz-M3		B, Zeste62-M3			C, M3-Ftz-longPYT
		CG no.	Gene name	Mol mass (kDa)	B, MINX-M3^d	1	2	1	2	1	2	3	1	2
Sm proteins
B	gi\|17136806	CG5352	SmB	21.0	•	10	12	22	11	11	12	12	12	11	•
D1	gi\|17864386	CG10753	snRNP69D	13.8	•	7	9	3	2	4	5	4	4	5	•
D2	gi\|21357623	CG1249	SmD2	13.5	•	17	17	19	10	18	16	10	14	12	•
D3	gi\|24652901	CG8427	SmD3	15.6	•	9	15	18	11	17	11	15	7	4	•
E	gi\|24582631	CG18591		11.1	•	9	5	5	8	11	6	9	8	6	•
F	gi\|22024001	CG16792	DebB	9.7	•	11	13	5					2	2	•
G	gi\|29428065	CG9742		12.7	•	2	3	6	3	4	3	4	3	3	•
U1 snRNP
U1-70K	gi\|17137278	CG8749	U1-70K	52.9	•	1	4	17	5	5	7	6	1
U1-A	gi\|17737284	CG4528	snf	24.6	•			12	4	4	2	4	5	5
U1-associated
S164/RBM25	gi\|18857955	CG4119		112.7		1	1	18	7	11	13	12
FBP11	gi\|24581324	CG3542		91.3				9	6	8	13	11
U2 snRNP
U2A′	gi\|19921760	CG1406	U2A	29.7	•	18	20	9	2	9	8	9	8	5	•
U2B″	gi\|17737284	CG4528	snf	24.6	•	5	7	12	4	4	2		5	5	•
SF3a120	gi\|24647566	CG16941		88.1	•	26	32	84	21	28	26	20	20	9	•
SF3a66	gi\|24663500	CG10754		30.3	•	2	5	4	3	6	5	4		2	•
SF3a60	gi\|17137118	CG2925	noi	58.4	•	14	19	28	16	15	15	17	9	3	•
SF3b155	gi\|45550087	CG2807		149.6	•	37	54	102	29	48	49	54	15	16	•
SF3b145	gi\|19920622	CG3605		84.8	•	20	30	25	13	17	22	13	10	9	•
SF3b130	gi\|24654874	CG13900		136.6	•	50	71	66	36	68	50	60	28	30	•
SF3b49	gi\|17530817	CG3780	spx	39.7	•	1	2				1				•
SF3b14a/p14	gi\|21357707	CG13298		14.2	•	14	6	7	8	8	6	6	5	6	•
SF3b14b	gi\|24582237	CG9548		12.5	•		6	9	3	5	6	5	4	3	•
SF3b10	gi\|24645240	CG11985		10.0	•	1	2	4		1
U2-related
hPRP43	gi\|19921728	CG11107		82.7	•	7	11	3		2	8	3	3	4	•
SPF45	gi\|116007460	CG17540		44.4	•					3	1
SPF30	gi\|16769358	CG17454	SPF30	28.2	•	2	2	4	2	7	7	5
U2AF65	gi\|17136764	CG9998	U2af50	46.7	•	6	2	8	7	9	11	8
U2AF35	gi\|17137284	CG3582	U2af38	29.9	•	2		4	1	3	2
PUF60	gi\|24655242	CG12085	pUf68	67.9			3	20	9	25	17	16	29	12
A proteins
RBM10	gi\|24580815	CG4887		114.2	•					1		1
SF1	gi\|24647704	CG5836	SF1	87.4				3	1	1	1
A/B proteins
DDX9	gi\|62474635	CG11680	mle	143.7	•	24	33
ZC3H18/LOC124245	gi\|24640344	CG1677		109.1	•	10	12	23	9	12	9	12	3		•
ASR2B	gi\|24585960	CG7843		107.2	•	15	23	50	18	24	22	29	8		•
TCERG1 (CA150)	gi\|116007968	CG33097		84.8	•	1	5	14	2	2		1	3	2
p68/DDX5 or DDX17	gi\|45551833	CG10279	Rm62	78.5	•		4	19	10	18	14	19	15	14	•
ELAV (HuR)	gi\|62471589	CG3151	Rbp9	70.5	•	1	4								•
RBM39/RNPC2	gi\|45550943	CG11266		66.5	•	7	6	20		16	14	23	4	1	•
NF45/ILF2	gi\|21357109	CG5641		43.7	•	15	31	23	6	3	2	1	1		•
YBX-1	gi\|24663131	CG5654	yps	38.9	•	16	15	11	4	4	3	6	2	9	•
TLS/FUS	gi\|24642436	CG3606	caz	38.8	•								3	6
HCNGP	gi\|19921898	CG2063		36.2						1	1		1
SR proteins
SFRS12	gi\|17137528	CG4602	Srp54	58.5				10	2	7	5	3	13	7
SRp55	gi\|28571701	CG10851	B52	42.8	•	2	1	8	3	8	10	6	9	3	•
hTra-2 b/SFRS10	gi\|45552623	CG10128	Tra2	31.0	•		3			3	2				•
SF2/ASF	gi\|21358097	CG6987	SF2	28.4	•	4	15	4	9	12	8	6	8	7	•
9G8	gi\|24582360	CG10203	xl6	27.9	•	7	15			1	1		2	3	•
SRp20	gi\|24641772	CG1987	Rbp1-like	16.8			1			2	1				•
SRp30c	▴^e				•	1	5								•
SRp38	▴				•	3	8								•
SR-related
SRm300	gi\|161080550	CG7971		127.3		9	13	19		3	3	1	41	19	•
SRm160	gi\|24663664	CG11274	SRm160	107.6	•			3		1	1	3	2		•
Cap binding complex
CBP80	gi\|24639721	CG7035	Cbp80	93.2	•	25	35	37	9	21	24	21	13	8	•
CBP20	gi\|17738031	CG12357	Cbp20	17.7	•	11	11	7	1	2	2	2	4	1	•
hnRNP
hnRNP A0					•	3	4
hnRNP A1	—^f				•	11	16								•
hnRNP A3	—				•	4	8								•
hnRNP AB	—				•	4	7
hnRNP A2/B1	—				•	10	23
hnRNP C	—				•	22	49								•
hnRNP D	—					4	4								•
hnRNP G	—				•	13	11								•
hnRNP K	—					1	3
hnRNP L	—					27	46
hnRNP Q	—				•	13	23								•
hnRNP R	—				•	44	41								•
hnRNP U	—					4	6								•
hnRPUL2/SAF-A2	—					4	2
PCBP1	—				•	3	7								•
RALY	—				•	5	8								•
—	gi\|22024201	CG30122		81.0						1		2
—	gi\|161078453	CG17838		76.9				8	1	2	7	6
—	gi\|24646609	CG16901	sqd	63.2									2	5
—	gi\|11040		hrp40.2	39.5						2	2
U5
220K	gi\|20129897	CG8877	prp8	279.4	•	92	140	149	71	123	150	161	202	104	•
200K	gi\|28574898	CG5931		244.5	•	86	120	134	54	136	99	113	171	108	•
116K	gi\|21357743	CG4849		110.7	•	33	46	61	42	41	34	46	90	43	•
102K	gi\|24666532	CG6841		105.2	•	30	75	44	21	30	21	26	6	3	•
100K	gi\|24584994	CG10333		94.6	•	26	27	26	19	23	21	18	3	2	•
52K	gi\|24583433	CG5198	LIN1	36.8	•	2	5
40K	gi\|24580577	CG3436		38.9	•	16	10	23	7	6	9	10	24	17	•
15K	gi\|28574029	CG3058		16.8	•	3	8	4	3	3	5	4
LSm proteins
LSm2	gi\|21358381	CG10418		10.7	•	9	6	5	2	2	7	5		1	•
LSm3	gi\|24649486	CG5926		11.9	•	2	4	2	2						•
LSm4	gi\|78706862	CG17764		30.6	•	2	6	7		2	1	3
LSm5^j	gi\|21358059	CG6610		10.1
LSm6^j	gi\|24656550	CG9344		9.0	•										•
LSm7	gi\|20129565	CG13277		12.2	•	2	3	3	2	3	3	4	2	2	•
LSm8	gi\|24655606	CG2021		10.4	•	4	1				1				•
U4/U6 snRNP
90K	gi\|24667067	CG7757		67.4	•	27	34	41	15	12	17	15			•
60K	gi\|21355245	CG6322		61.6	•	16	25	22	16	13	22	24	2		•
61K	gi\|21357435	CG6876		55.5	•	15	17	42	27	15	22	22			•
20K	gi\|24586038	CG17266		20.2	•	10	12	11	8	10	6	3			•
15.5K	gi\|17864298	CG3949	hoi-polloi	13.8	•	3	1	3	3	2	3	3			•
U4/U6.U5
110K	gi\|24583764	CG6686		112.6	•	37	31	19	12	12	12	11			•
65K	gi\|18859907	CG7288		57.5	•	11	18	20	9	14	16	16			•
27K	gi\|19922846	CG18426	ytr	21.5		2	5	10		6	4	3
TFIP11	gi\|24582006	CG7238	sip1	94.8	•	2	4	6		3	5	4	4	1	•
hPRP38	gi\|22024089	CG30342		40.1	•	13	10	19	7	7	11	8	7	6	•
hPRP19/CDC5L
CDC5L	gi\|19922992	CG6905	cdc5-like	93.1	•	18	20	21	7	24	19	16	46	28	•
Hsp73 (CCAP1)	gi\|28571721	CG4264	Hsc70-4	71.1	•	4	5					2	3	3	•
hPRP19	gi\|17647459	CG5519	Gbp	55.2	•	15	24	37	18	22	21	16	49	44	•
PRL1	gi\|18859793	CG1796	Tango4	52.7	•	9	13	8	5	4	7	14	29	19	•
SPF27	gi\|24650745	CG4980		31.3	•	6	4	11	2	5	7	5	11	17	•
AD002 (CCAP2)	gi\|21358119	CG12135	c12.1	28.4	•	2		3		3	2		8	13	•
Npw38BP	gi\|20128957	CG2685		61.0	•	9	10	6					2	1
Npw38	gi\|21356239	CG11820		27.1	•	2	5	2	2	2		1	1
hPRP19/CDC5L related
KIAA0560	gi\|45553341	CG31368		172.0	•	11	7	63	6	24	30	35	102	65	•
hSYF1 (XAB2)	gi\|20129961	CG6197		103.3	•	13	4	13	1	11	13	11	39	36	•
CRNKL1/Clf1	gi\|17137126	CG3193	crn	84.3	•	14	12	17	1	16	17	29	62	40	•
SKIP	gi\|24640727	CG8264	BX42	61.2	•	13	12	19	6	3	7	8	40	28	•
hECM2 (fSAP47)	gi\|28573264	CG14641		47.2	•	5	6	22	2	3	3	4	29	17	•
Cyp-E	gi\|17647301	CG4886	cyp33	33.3	•			5	3	7	6	6	20	21	•
hIsy1	gi\|78709073	CG9667		31.4	•	3	2	2		6	4	8	13	12	•
PPIL1	gi\|17986117	CG13892	Cypl	19.5	•	3	4	7	2	6	6	2	11	7	•
G10	gi\|17737310	CG1639	l(1)10Bb	17.0	•	9	8	5	2	5	6	7	12	9	•
RES complex
MGC13125	gi\|21355513	CG13625		76.5	•	7	3						2	2	•
SNIP1	gi\|62862214	CG17168		49.8	•	4	5								•
CGI-79	gi\|20129641	CG10466		17.8	•	4	1	1						1	•
B/B* proteins
hPRP4-kinase/PRPF4B	gi\|19922978	CG7028		104.0	•	7	10	18	4	5	10	6	2		•
hPRP2	gi\|19921526	CG10689		102.8	•	3		8		7	6	5	5	7	•
PPIL4	gi\|21355677	CG5808		75.5	•	2				1	1	1	1
RED	gi\|21355769	CG18005		61.4	•	10	8	17	3	9	5	9	9	1	•
PPIL2/Cyp-60	gi\|19922376	CG7747		59.0	•	7							5	1	•
hSmu-1	gi\|21356791	CG5451		57.3	•	20	22	16	8	7	7	14	12	4	•
MFAP1	gi\|21358323	CG1017		56.1	•	7	6	5		1	2	2	4		•
FBP21	gi\|24580725	CG4291		38.8	•	2	2	6		7	9	3
UBL5	gi\|24586084	CG3450	ubl	8.6	•	3	4
C proteins
hPRP22	gi\|20129977	CG8241	pea	142.0				2		3	2	5	54	28	•
PPIG, SR-Cyp	gi\|28571910	CG1866	Moca-cyp	116.4				1	1	2	1	2	12	2	•
Q9BRR8	gi\|24663949	CG8833	GPTC1	107.9						1		1	6	4	•
cactin (c19orf29)	gi\|45549144	CG1676	cactin	91.3									17	10	•
DDX35	gi\|19920696	CG3225		76.1				3		3	2	3	12	8	•
Abstrakt	gi\|17977678	CG14637	abs	69.5	•					1	3	4	42	17	•
hPRP17	gi\|21355805	CG6015		65.4	•	5	2	17	2	6	11	15	35	18	•
GCIP p29	gi\|24652559	CG12343		26.5	•			1		4	4	2	18	14	•
EJC/mRNP
eIF4AIII	gi\|24645031	CG7483	eIF4AIII	45.6		3		12	3	4	7	8	21	16	•
Y14	gi\|24651979	CG8781	tsu	19.0									3	1	•
Magoh	gi\|17136332	CG9401	mago	17.3	•			1		1			2	2	•
Acinus	gi\|24585110	CG10473	hkl	83.7							3	1	2		•
UAP56	gi\|24581956	CG7269	Hel25E	48.7	•	2	5								•
Pinin	gi\|161078140	CG8383	Pnn	35.9				1					2	1	•
Aly/REF (THOC4)	gi\|21356157	CG1101	Aly	27.9		1	2				1		1		•
SAP18	gi\|17738001	CG6046	bin1	17.3				3					2	1	•
ELG		NH				1	1
Miscellaneous Drosophila + HeLa
Spliceosomal^g
SKIV2L2	gi\|17864608	CG4152	lethal(2)35Df	118.9		2	5						6	1	•
GCFC	gi\|24644714	CG1965		102.6	•	2		3	1	7	6	8	3	3	•
ZFR2	gi\|28574893	CG5215	Zn72D	96.0		12	16	21	8	2	1		1
RBM15B	gi\|24586450	CG2910	nito	89.1		2		3	1	5	7
PABP	gi\|45552715	CG5119	PABP	69.9	•	2	6	14	12	13	13	22	15	10	•
HsKin17	gi\|24667403	CG5649	kin17	45.4	•	2	3	1	1						•
RACK1 (GNB2L1)	gi\|17137396	CG7111	RACK1	35.6		1	1	1		1	2	1	2	3	•
RBM42	gi\|21357051	CG2931		33.6		1	2	17	8	7	8	8	1		•
Novel^h
IGF2BP1	gi\|116007146	CG1691	IMP-1	63.4		10	12	40	18	10	18	20	10	4
PABP II	gi\|24586513	CG2163	Pabp2	25.0							1	1	1
Miscellaneous Drosophila only
Spliceosomal^g
PSF	gi\|62473776	CG4211	Bj6	82.0				8	2	9	8	7	8	2
NY-CO-10	gi\|21357249	CG10907		56.6	•		1	4	1	2		1	3	2	•
DGCR14	gi\|18858195	CG1474	ES2	56.0									12	6	•
NKAP	gi\|24650530	CG6066		52.9									8	2	•
RBM4	gi\|24659981	CG8597	lark	39.9	•			25	14	9	11	6	5	2
CDK10, PISSLRE	gi\|24652305	CG1362	cdc2rk	39.4						1			2	2	•
NOSIP	gi\|24643007	CG6179	NOSIPL	34.2									3	1	•
MORG1	gi\|24584567	CG4935		34.1						2	2	3	7	3	•
CXorf56	gi\|20129505	CG16865		27.7									4	4	•
Novel^h
CDC27	gi\|24659892	CG8610	Cdc27	101.3					2	11	7	8
PIWIL1	gi\|161076864	CG6137	aub	98.6				7		2	1	2	2	3
APTX	gi\|24648185	CG5316		76.5				8	3		2	1
MTHFSD	gi\|161078016	CG14648	growl	58.8				20	3	10	7	9	10	2
LUC7-like	gi\|24665973	CG7564		48.4				3	2	2	5	4
KHDRBS2	gi\|24658086	CG3613	QKR58E-1	42.3				4	1	3	2	2	1	1
PSME3	gi\|18860055	CG1591	REG	28.1						1	1	1	1	1
NH	gi\|45553181	CG6143	pep	78.1				4	1	6	9	6	2
NH	gi\|45550712	CG9684		71.9				78	42	8	12	6	1
NH	gi\|24656457	CG8994	exu	58.0				1	3		3	2
NH	gi\|24641752	CG15747		44.7				2			1		1	3
NH	gi\|19922308	CG11808		25.7						3			1	2
Miscellaneous Drosophila Ftz-M3 only, novel^h
EIF2AK4	gi\|17137328	CG1609	Gcn2	178.5				1					1	1
G3BP2	gi\|24646611	CG9412	rin	75.0				4	2			1	1
▿ⁱ	gi\|24649433	CG13597		59.2				2	1
PRPF38B	gi\|24641727	CG1622		45.4				1	1
NH	gi\|28571193	CG5877		114.2									2	1
NH	gi\|24653446	CG6209	mst101(2)	69.0				1					4	9
NH	gi\|24650092	CG12250		16.5				4					3	5
Miscellaneous Drosophila Zeste62-M3 only
Spliceosomal^g: AGGF1	gi\|24653802	CG8079		66.9						1	1
Novel^h
SLC7A2	gi\|116007820	CG7255		85.6							1	1
NCOA5	gi\|17647723	CG8614	Neos	42.6				1		2	2
DNAJC17	gi\|24645889	CG17187		34.7						2	3
TFIIB	gi\|19921082	CG5343		23.3						4	3		1
Miscellaneous HeLa only
Spliceosomal^g
GEMIN3/DDX20	gi\|17647335	CG6539	Dhh1	116.5		1	1
SON3	gi\|24645429	CG8273		88.6		2	2
GNL3	gi\|28572990	CG3983	GNL3	66.0		4	5								•
STRBP	▿					8	19
RBM7	▿				•	1	2								•
ZCC2	▿					4	5
Novel^h
Spen	gi\|24580579	CG18497	spen	600.0		7	15
RIMS1	gi\|62472639	CG33547	Rim	314.8		6	3
EXOSC10	gi\|161078302	CG7292	Rrp6	102.9		1	2
ZNF346, JAZ	gi\|24583489	CG17098		73.2		3	7
SNED1	▿					6	2

Proteins were identified by LC-MS-MS after separation by PAGE. Proteins identified in two out of two or two out of three preparations are shown (preparations are numbered 1, 2, and 3). Proteins not reproducibly detected are summarized in Table S1 in the supplemental material. Proteins generally accepted to be common contaminants, such as ribosomal proteins, are not shown. NH, no apparent/unambiguous homologue could be detected by BLAST searches at NCBI.

The name of the human protein is given to aid comparison with previous studies of human spliceosomal complexes. Proteins are grouped in organizational and/or functional subgroups.

The presence of a protein is indicated by a number which represents the absolute number of peptides sequenced for that protein (see Materials and Methods for details).

Data from previous proteomics studies of MS2-affinity-selected human B and C complexes formed on an adenovirus-derived pre-mRNA substrate (MINX) (11) or PM5 pre-mRNA (5), respectively, are also included. •, presence of a given protein in these previously analyzed complexes.

▴, homologues could not be assigned on the basis of BLAST data.

—, extensive homology between protein family members prevents assignment of Drosophila homologues on the basis of BLAST data.

Human homologue previously detected in one or more human spliceosomal complex.

Never detected in human spliceosomal complexes.

ⁱ

▿, homology with several proteins, but only within conserved domains.

LSm5 and LSm6 are difficult to detect by MS and have been included for completeness.