RNA Processing Factor Genes

Here, we present links to information about homologs of pre-mRNA processing factors in the Drosophila, human, yeast (Saccharomyces) and Arabidopsis genomes. In many cases, functional data are not available, and our assignments are based on the best match among genomes. Components of the RNA processing machinery are highly conserved. Very few factors identified in yeast are absent from the Drosophila or Arabidopsis genomes. In general, proteins involved in the mechanics of RNA processing are even more conserved than proteins involved in the interpretation of RNA processing signals.

An early form of this table appears in an article by Steve Mount and Helen Salz that was published in the Journal of Cell Biology in a special issue on the Drosophila genome. The reference is:

        Stephen M. Mount and Helen K. Salz
           Pre-messenger RNA Processing Factors in the Drosophila Genome
                 J. Cell Biol. 2000 150: F37-F44. Published online Jul 24 2000. [Abstract] [Full Text] [PDF] [PubMed] This web page differs from the table in the paper in that it has additional content and will be continuously updated. Most significantly, we have added links to homologs in Arabidopsis.

This page is perpetually under revision. Our original selection and organization of spliceosomal genes was based on that presented by Burge et al. in the second edition of the RNA World (1998. Gesteland, Cech and Atkins eds., CSHL Press, pg. 525). We have completed the incorporation of links to Arabidopsis for those proteins in the original analysis. We then reviewed specific genes that have multiple paralogs in some species (some of which are noted with an asterisk below). Our analysis of these is presented with a tree icon in the left-most column that presents an unrooted tree generated using clustalw at the EBI. There are also families of related splicing factors (e.g. the Sm core proteins or the SR proteins) conserved across species, in which case we present trees of related genes within a single species (tree icon at the top of a column). We also plan to incorporate additional proteins identified by Zhou et al. 2002 (Comprehensive proteomic analysis of the human spliceosome. Nature 419:182-5) using mass spectrometry. Those using this site may want to refer to that work (particularly the supplemental information).

Comments and suggestions are very much appreciated and should be sent to Steve Mount

We thank Jonathan Roberts, Jason Martineau, Wei Xian and Chau Nguyen for help creating this page.

Links in the following table are to flybase and GenBank accessions. In the case of Arabidopsis, links to TIGR and MIPS are for the single gene with the single best BLAST score. In some cases, there are multiple genes with significant scores. BLAST output from TAIR , The Arabidopsis Information Resourse is provided to allow the reader to make their own evaluations of other matches.


Steve Mount's home page	Model Organism Links	Bioinformatic Links	The RNA Society

Table: Genes for Proteins Involved in pre-mRNA Processing


Protein	Drosophila Flybase \| NCBI	Human homologs E value	Yeast (S.c.) E value	Arabidopsis

snRNP proteins

Core proteins
Protein	Drosophila Flybase \| NCBI	Human homologs E value	Yeast (S.c.) E value	Arabidopsis
snRNP core protein SmB	SmB \| NP_476921	E-38 6E-38	Smb1p, 2E-10	TIGR \| MIPS \| TAIR:7e-027 TIGR \| MIPS
LSM8, U6 snRNA-associated Sm core protein LSM8, (LSM1-like)	LSM8 \| NP_647660	LSM8, E-34 LSM1, 8E-05	Lsm8p, E-05 Lsm1p, 2E-06	TIGR \| MIPS \| TAIR:1e-029
snRNP core protein SmD1	SmD1 \| NP_524774	E-36	Smd1p, 5E-11	TIGR \| MIPS \| TAIR:5e-031 TIGR \| MIPS
LSM2	LSM2 \| NP_648570	3E-46	Lsm2p, 8E-28	TIGR \| MIPS \| TAIR:3e-035
snRNP core protein SmD2	SmD2 \| NP_649645	9E-46	Smd2p, 5E-25	TIGR \| MIPS \| TAIR:5e-039 TIGR \| MIPS
LSM3	LSM3 \| NP_651203	6E-29	Lsm3p, E-05	TIGR \| MIPS \| TAIR:3e-017 TIGR \| MIPS
snRNP core protein SmD3	SmD3 \| NP_725106	E-37	Smd3p, E-20	TIGR \| MIPS \| TAIR:2e-027 TIGR \| MIPS
LSM4, U6 snRNA-associated Sm-like	LSM4 \| NP_572211	3E-70	Lsm4p, E-10	TIGR \| MIPS \| TAIR:3e-041
snRNP core protein SmE	SmE \| NP_609162	8E-33	Sme1p, E-17	TIGR \| MIPS \| TAIR:7e-029 TIGR \| MIPS
LSM5	LSM5 \| NP_648022	5E-35	Lsm5p, E-13	TIGR \| MIPS \| TAIR:3e-028
snRNP core protein SmF	SmF \| NP_523708	6E-37	Smx3p, 3E-16	TIGR \| MIPS \| TAIR:6e-030
LSM6	LSM6 \| NP_611528	8E-33	Lsm6p, 7E-09	TIGR \| MIPS \| TAIR:2e-028 TIGR \| MIPS TIGR \| MIPS
snRNP core protein SmG	SmG \| NP_573139	7E-27	Smx2p, 7E-16	TIGR \| MIPS \| TAIR:9e-021 TIGR \| MIPS
LSM7	LSM7 \| NP_609807	8E-38	Lsm7p, 3E-16	TIGR \| MIPS \| TAIR:1e-029
Cancer-related Sm/LSM1	LSM1 \| NP_611559	LSM1, E-43 ; LSM8, E-10	Lsm1p, 7E-19	TIGR \| MIPS \| TAIR:1e-021 TIGR \| MIPS

U1snRNP
Protein	Drosophila Flybase \| NCBI	Human homologs E value	Yeast (S.c.) E value	Arabidopsis
U1-70k Subunit	U1-70K \| NP_477205	2E-62	Snp1p, 7E-31	TIGR \| MIPS \| TAIR:3e-041 TIGR \| MIPS
U1C Subunit	U1C \| NP_650767	8E-28	Yhc1p, 4E-06	TIGR \| MIPS \| TAIR:9e-018
U1A Subunit	U1A \| NP_511045	7E-32	Mud1p, 6E-04	TIGR \| MIPS \| TAIR:2e-051 TIGR \| MIPS TIGR \| MIPS
Luc7-like protein, unnamed	Luc7-like \| NP_648991	4E-84	Luc7p, 5E-24	TIGR \| MIPS \| TAIR:4e-024 * TIGR \| MIPS TIGR \| MIPS
related to Luc7-like protein, CG7564	Luc7-like \| NP_572337	3E-06	Luc7p, 3E-06	TIGR \| MIPS \| TAIR:9e-032
Prp39/Prp42	Prp39/Prp42 \| NP_651634	BAA92024, 2E-30 BAA91318, 9E-23	Prp39p, 2E-13 Prp42p, 1E-06	TIGR \| MIPS \| TAIR:7e-031 TIGR \| MIPS
Prp40-like protein	Prp40-like \| NP_722868	2E-98 (aka mouse Huntington yeast partner C E-100 )	Prp40p, 3E-14	TIGR \| MIPS \| TAIR:3e-054 TIGR \| MIPS

U2snRNP
Protein	Drosophila Flybase \| NCBI	Human homologs E value	Yeast (S.c.) E value	Arabidopsis
U2B" Subunit	U2B \| NP_511045	7E-68	Ms11p, 3E-05	TIGR \| MIPS \| TAIR:2e-051 TIGR \| MIPS TIGR \| MIPS
U2A' Subunit	U2A \| NP_610315	7E-54	Lea1p, 5E-05	TIGR \| MIPS \| TAIR:3e-039
SF3a60/SAP61 Subunit	SF3a60/SAP61 \| NP_477114	E-180	Prp9p, 3E-31	TIGR \| MIPS \| TAIR:1e-103
SF3a66/SAP62 Subunit	SF3a66/SAP62 \| NP_648603	E-100	Prp11, 1E-13	TIGR \| MIPS \| TAIR:6e-073
SF3a120/SAP114 Subunit	SF3a120/SAP114 \| NP_650583	E-155	Prp21p, 2E-11	TIGR \| MIPS \| TAIR:2e-068 TIGR \| MIPS TIGR \| MIPS
SF3b53/SAP49 Subunit	SF3b53/SAP49 \| NP_511058	E-109	Hsh49p, 1E-28	TIGR \| MIPS \| TAIR:1e-088 TIGR \| MIPS
SF3b150/SAP145 Subunit	SF3b150/SAP145 \| NP_608739	E-178	Cus1p, 5E-38	TIGR \| MIPS \| TAIR:7e-089 TIGR \| MIPS
SF3b120/SAP130 Subunit	SF3b120/SAP130 \| NP_728546	E=0	Rse1p, 8E-78	TIGR \| MIPS \| TAIR:0.0 TIGR \| MIPS TIGR \| MIPS
SF3b160/SAP155 Subunit	SF3b160/SAP155 \| NP_608534	E=0	Hsh155p, E=0	TIGR \| MIPS \| TAIR:0.0
FBP21-like protein that associates with U2 snRNPs	FBP21-like \| NP_608551	7E-28	Prp40p, 0.078	TIGR \| MIPS \| TAIR:2e-014

U5snRNP
Protein	Drosophila Flybase \| NCBI	Human homologs E value	Yeast (S.c.) E value	Arabidopsis
220kD Subunit	220KD Subunit \| NP_610735	E=0	Prp8p, E=0	TIGR \| MIPS \| TAIR:0.0 TIGR \| MIPS
200kD Subunit	200KD Subunit \| NP_650472	E=0	Slh1p, E=0 ; Brr2, E=0	TIGR \| MIPS \| TAIR:0.0 TIGR \| MIPS
40kD Subunit	40KD Subunit \| NP_608501	E-120 SPF38, 7E-99	unknown	TIGR \| MIPS \| TAIR:1e-106 TIGR \| MIPS
116 kD Subunit	116KD Subunit \| NP_651605	E=0 E=0 , mouse	unknown	TIGR \| MIPS \| TAIR:0.0 TIGR \| MIPS
Prp6-like	Prp6-like \| NP_649073	E=0	Prp6p, 6E-74	TIGR \| MIPS \| TAIR:0.0 TIGR \| MIPS
100kD Subunit	100KD Subunit \| NP_609888	E=0	Prp28p, 2E-92	TIGR \| MIPS \| TAIR:1e-166
15kD Subunit	15KD Subunit \| NP_608830	5E-78	Dib1p, 3E-48	TIGR \| MIPS \| TAIR:2e-069 TIGR \| MIPS

TrisnRNP
Protein	Drosophila Flybase \| NCBI	Human homologs E value	Yeast (S.c.) E value	Arabidopsis
SAP90	SAP90 \| NP_649156	E-144	Prp3p, 1E-23	TIGR \| MIPS \| TAIR:3e-069 TIGR \| MIPS TIGR \| MIPS
SAP60	SAP60 \| NP_648990	E-138	Prp4p, 9E-56	TIGR \| MIPS \| TAIR:1e-079 TIGR \| MIPS
15.5 kD Subunit	15.5KD Subunit \| NP_524714	4E-39	Snu13p, 9E-32	TIGR \| MIPS \| TAIR:3e-035 TIGR \| MIPS TIGR \| MIPS
20 kD cyclophilin	20KD Cyclophilin \| AAF57375	4E-80	unknown	TIGR \| MIPS \| TAIR:7e-069

Pre-spliceosome splicing factors
Protein	Drosophila Flybase \| NCBI	Human homologs E value	Yeast (S.c.) E value	Arabidopsis
Small subunit of U2AF	U2AF Subunit \| NP_477208	5E-88	unknown	TIGR \| MIPS \| TAIR:9e-060 TIGR \| MIPS TIGR \| MIPS
Related to small subunit of U2AF (Urp)	U2AF(Urp) Subunit \| NP_608857	1E-20	unknown	TIGR \| MIPS \| TAIR:5e-025 * TIGR \| MIPS TIGR \| MIPS
Large subunit of U2AF	U2AF Subunit \| NP_476891	E-146	Mud2p, 0.22	TIGR \| MIPS \| TAIR:8e-056 TIGR \| MIPS
SF1/BBP	SF1/BBP \| NP_524654	E-106	Msl5p, 4E-62	TIGR \| MIPS \| TAIR:3e-060
small subunit of nuclear cap binding protein	Nuclear cap \| NP_524396	4E-63	Cbc2p, 6E-37	TIGR \| MIPS \| TAIR:7e-052
large subunit of nuclear cap binding protein	Nuclear cap \| NP_726938	E=0	Sto1p, 3E-23	TIGR \| MIPS \| TAIR:4e-072
CBP80-like	CBP80-like \| NP_650969	1E-96	Sto1p, 1E-10	TIGR \| MIPS \| TAIR:3e-049 *
UAP56	UAP56 \| NP_723089	E=0	Sub2p, E-141	TIGR \| MIPS \| TAIR:1e-159 TIGR \| MIPS
Prp5-like	Prp5-like \| NP_573020	E=0	Prp5p, 4E-94	TIGR \| MIPS \| TAIR:1e-169 *

Catalytically active spliceosome splicing factors
Protein	Drosophila Flybase \| NCBI	Human homologs E value	Yeast (S.c.) E value	Arabidopsis
Prp31	Prp31 \| NP_648756	E-141	Prp31p, 3E-22	TIGR \| MIPS \| TAIR:9e-082 TIGR \| MIPS
pombe, cdc5-related protein	Pombe \| NP_612033	E=0	Cef1p, 4E-49	TIGR \| MIPS \| TAIR:1e-169
Prp2	Prp2 \| NP_609946	E=0 (64%)	Prp2p, E-172	TIGR \| MIPS \| TAIR:0.0 TIGR \| MIPS TIGR \| MIPS TIGR \| MIPS
Prp22	Prp22 \| NP_610928	E=0	Prp22p, E=0	TIGR \| MIPS \| TAIR:0.0 TIGR \| MIPS
Prp16	Prp16 \| NP_727764	E=0 (85%)	Prp16p, E-160	TIGR \| MIPS \| TAIR:0.0 *
Prp17	Prp17 \| NP_651005	E=0	Cdc40p, 1E-76	TIGR \| MIPS \| TAIR:1e-151 TIGR \| MIPS TIGR \| MIPS
Prp43	Prp43 \| NP_610269	E=0	Prp43p, E=0	TIGR \| MIPS \| TAIR:0.0 TIGR \| MIPS
Slu7	Slu7 \| NP_651659	E-128	Slu7p, 1E-12	TIGR \| MIPS \| TAIR:1e-097 TIGR \| MIPS TIGR \| MIPS
Prp18	Prp18 \| NP_650776	4E-93	Prp18p, 4E-05	TIGR \| MIPS \| TAIR:2e-047 TIGR \| MIPS
Srm160	Srm160 \| NP_648627	2E-43	unknown	TIGR \| MIPS \| TAIR:9e-028
Srm300	Srm300 \| NP_647642	2E-37	unknown	TIGR \| MIPS \| TAIR:0.036 *

SR proteins
Protein	Drosophila Flybase \| NCBI	Human homologs E value	Yeast (S.c.) E value	Arabidopsis
SC35	SC35 \| NP_652612	5E-53	Npl3, 3E-12	TIGR \| MIPS \| TAIR:3e-020 TIGR \| MIPS TIGR \| MIPS TIGR \| MIPS TIGR \| MIPS TIGR \| MIPS
ASF/SF2	ASF/SF2\| NP_652611	2E-80	Npl3, 7E-15	TIGR \| MIPS \| TAIR:6e-041 TIGR \| MIPS TIGR \| MIPS TIGR \| MIPS
B52	B52 \| NP_788668	SRp55, 2E-96 SRp75, 3E-96 Srp40/HRS, E-78	Npl3, 3E-14	TIGR \| MIPS \| TAIR:8e-026 *
9G8	\| NP_723226	4E-42	Npl3, 7E-05	TIGR \| MIPS \| TAIR:7e-019 * TIGR \| MIPS
RBP1	RBP1 \| NP_524307	2E-38	Nsr1p, E-07	TIGR \| MIPS \| TAIR:4e-015 TIGR \| MIPS
RBP1-like	PBP1-like \| NP_572880	4E-31	Nsr1p, 4E-14	TIGR \| MIPS \| TAIR:1e-014 *
SRp54	SRp54 \| NP_477347	2E-41	none significant	TIGR \| MIPS \| TAIR:7e-004

SR protein kinase homologs
Protein	Drosophila Flybase \| NCBI	Human homologs E value	Yeast (S.c.) E value	Arabidopsis
SR protein kinase (e-values relative to SRpK1)	SR protein Kinase 1 \| NP_725458 SR Protein Kinase 2 \| NP_649387 SR Protein Kinase 3 \| NP_573080	SRPK1, 9E-76 SRPK2, 3E-77	Sky1p, 5E-44	TIGR \| MIPS \| TAIR:1e-52 TIGR \| MIPS TIGR \| MIPS TIGR \| MIPS TIGR \| MIPS
Lammer, CLK kinase	Doa \| NP_477275	CLK2, E-151	Kns1p, 5E-61	TIGR \| MIPS \| TAIR:4e-92

Miscellaneous proteins
Protein	Drosophila Flybase \| NCBI	Human homologs E value	Yeast (S.c.) E value	Arabidopsis
crooked neck/CLF1	crn \| NP_477118	unknown	Clf1p, E-123	TIGR \| MIPS \| TAIR:0.0
poly-U binding protein	Poly-U binding Protein \| NP_525123	1E-81	unknown	TIGR \| MIPS \| TAIR:2e-017 *
poly-pyrimidine tract associated protein	Poly-pyrimidine \| NP_536740	5E-62	unknown	TIGR \| MIPS \| TAIR:2e-010 *
poly-pyrimidine tract binding protein (PTB), hnRNP I	hnRNP I \| NP_733461	E-150	none < E-4	TIGR \| MIPS \| TAIR:8e-027 * TIGR \| MIPS TIGR \| MIPS
Most similar to Survival of Motor Neuron Protein (SMN)	SMN \| NP_524112	1E-05		TIGR \| MIPS \| TAIR:1.9
SPF30, SMN-related	SPF30 \| AAF45352	3E-37		TIGR \| MIPS \| TAIR:3e-009 *
survival of motor neuron interacting protein (SIP1)	SIPI \| NP_649092	2E-18	Brr1p, E=0.05	TIGR \| MIPS \| TAIR:0.013
debranching enzyme	Debranching Enzyme \| NP_648175	E-113	Dbr1p, 2E-62	TIGR \| MIPS \| TAIR:1e-101
SR protein-like RRM	RSF1 \| NP_477001	SR-like RRM matches SR proteins. Acts as a repressor of splicing. See Bourbon et al.	RRM domain matches only	TIGR \| MIPS \| TAIR:1e-001

Cleavage and polyadenylation

General
Protein	Drosophila Flybase \| NCBI	Human homologs E value	Yeast (S.c.) E value	Arabidopsis

PolyA polymerase	PolyA Polymerase \| NP_536790	E-173	Pap1p, E-102	TIGR \| MIPS \| TAIR:1e-104 TIGR \| MIPS TIGR \| MIPS TIGR \| MIPS
PolyA binding protein	pAbp \| NP_725753	E-176 , mouse	Pab1p, E-106	TIGR \| MIPS \| TAIR:1e-123 * TIGR \| MIPS
PolyA binding protein II	Pabp2 \| NP_476902	2E-54	Sgn1p, 2E-18	TIGR \| MIPS \| TAIR:5e-035 TIGR \| MIPS TIGR \| MIPS
possible polyA binding protein	PolyA binding Protein \| NP_611924	9E-48 , mouse 8E-46 , human	Pab1p, 2E-24	TIGR \| MIPS \| TAIR:1e-045 *

CPSF (cleavage and polyadenylation specificity factor)
Protein	Drosophila Flybase \| NCBI	Human homologs E value	Yeast (S.c.) E value	Arabidopsis
CPSF-160 kd. Subunit	CPSF-160KD Subunit \| NP_725397	E=0	Cft1p, 4E-37	TIGR \| MIPS \| TAIR:1e-155
CPSF-100 kd. Subunit	CPSF-100KD Subunit \| NP_651658	E=0 , bovine	Ysh1p, E-32	TIGR \| MIPS \| TAIR:1e-139
CPSF-73 kd. Subunit	CPSF-73KD Subunit \| NP_650738	0	Ysh1p, E-146	TIGR \| MIPS \| TAIR:0.0
possible variant CPSF-73 kd. Subunit	CPSF-73KD Subunit \| NP_651721	7E-93	Ysh1p, E-73	TIGR \| MIPS \| TAIR:1e-155
related to CPSF-100 and -73	Related to CPSF \| NP_648838	0 E-113	Ysh1p, 6E-14	TIGR \| MIPS \| TAIR:1e-021
CPSF-30 kd. Subunit	Clp \| NP_477156	8E-89	Yth1p, 1E-34	TIGR \| MIPS \| TAIR:7e-021 * TIGR \| MIPS

cleavage-polyadenylation stimulation factor
Protein	Drosophila Flybase \| NCBI	Human homologs E value	Yeast (S.c.) E value	Arabidopsis
CstF-77 kd. Subunit	\| AAF45314	E=0	Rna14p, 2E-47	TIGR \| MIPS \| TAIR:4e-092
CstF-64 kd. Subunit	CstF-64KD Subunit \| NP_477453	E-71	Rna15p, 2E-18	TIGR \| MIPS \| TAIR:4e-040
CstF-50 kd. Subunit	CstF-50KD Subunit \| NP_651883	E-129	no known homolog.	TIGR \| MIPS \| TAIR:1e-066
symplekin	Symplekin \| NP_649580	E-173	Pta1p, 5E-04	TIGR \| MIPS \| TAIR:1e-052 TIGR \| MIPS

Cleavage factors I and II
Protein	Drosophila Flybase \| NCBI	Human homologs E value	Yeast (S.c.) E value	Arabidopsis
cleavage factor Im - 25 kd. Subunit	Im-25KD Subunit \| NP_648308	E-102	unknown	TIGR \| MIPS \| TAIR:2e-052 TIGR \| MIPS
cleavage factor Im - 68 kd. Subunit	Im-68KD Subunit \| NP_648206	3E-34	unknown	TIGR \| MIPS \| TAIR:7e-009 TIGR \| MIPS
Yeast cleavage and polyA factor IA homolog	IA Homolog \| NP_611565	7E-41	Pcf11p, 3E-9	TIGR \| MIPS \| TAIR:7e-013 *


Miscellaneous proteins not in published tables (under development)
Protein	Drosophila Flybase \| NCBI	Human homologs E value	Yeast (S.c.) E value	Arabidopsis
Splicing factor domains	BcDNA:GH01073 \| NP_651291	E-39	unknown	TIGR \| MIPS \| TAIR:5e-085
Splicing factor (CC1.3)	CC1.3 \| NP_723243	E-123 PUF60, 3E-18	unknown	TIGR \| MIPS \| TAIR:4e-066 TIGR \| MIPS
PSI protein (P somatic inhibitor)	PSI \| NP_477123	unknown	unknown	TIGR \| MIPS \| TAIR:2e-016

hnRNP proteins (under development)

Genes identified in Drosophila with roles in splicing (under development)

missing genes (under development)

* indicates Arabidopsis proteins that are the best match in the Arabidopsis genome to the Drosophila query but whose best match in Drosophila is not the query. These cases are currently being resolved by phylogenetic analysis, the results of which will soon be accessible from the first column via a tree icon.