Markup | Genome Research

Table 4.

Distributions of Processed Pseudogenes Among RP Genes

Gene name[i]	SWISSPROT ID[ii]	mRNA length[iii]	CDS length[iv]	CDS GC content[v]	# Processed	# Fragments
RPL21	RL21_HUMAN	568	483	0.43	145	13
RPL23A	RL2B_HUMAN	546	471	0.49	85	11
RPL7	RL7_HUMAN	838	747	0.43	83	19
RPL7A	RL7A_HUMAN	890	801	0.54	73	13
RPL31	RL31_HUMAN	442	378	0.47	71	5
RPSA	RSP4_HUMAN	1039	888	0.53	67	12
RPS26	RS26_HUMAN	459	348	0.53	65	5
RPS3A	RS3A_HUMAN	921	795	0.43	60	15
RPL17	RL17_HUMAN	898	555	0.46	59	11
RPS2	RS2_HUMAN	978	882	0.58	57	10
RPL39	RL39_HUMAN	401	156	0.42	56	8
RPL36A	RL44_HUMAN	425	321	0.47	54	6
RPL12A	RL12_HUMAN	632	498	0.52	49	3
RPL34	RL34_HUMAN	849	354	0.45	44	3
RPS15A	RS1A_HUMAN	541	393	0.47	43	4
RPL29	RL29_HUMAN	737	480	0.56	40	3
RPL26	RL26_HUMAN	525	438	0.45	39	3
RPS27	RS27_HUMAN	344	255	0.49	38	0
RPL5	RL5_HUMAN	1033	894	0.44	37	8
RPS20	RS20_HUMAN	539	360	0.45	36	0
RPL35A	R35A_HUMAN	511	333	0.47	36	2
RPL32	RL32_HUMAN	521	408	0.51	36	7
RPS29	RS29_HUMAN	346	171	0.53	36	2
RPS12	RS12_HUMAN	534	399	0.46	33	8
RPS10	RS10_HUMAN	598	498	0.55	33	4
RPL9	RL9_HUMAN	716	579	0.44	31	6
RPS24	RS24_HUMAN	537	402	0.44	30	13
RPL6	RL6_HUMAN	950	867	0.47	30	5
RPS6	RS6_HUMAN	829	750	0.47	27	1
RPL37	RL37_HUMAN	371	294	0.51	27	3
RPL13A	R13A_HUMAN	1142	612	0.58	26	3
RPS27A	R27A_HUMAN	551	471	0.44	24	1
RPL36	RL36_HUMAN	428	318	0.6	24	2
RPS4	RS4_HUMAN	916	792	0.48	23	5
RPL22	RL22_HUMAN	574	387	0.44	22	1
RPL19	RL19_HUMAN	698	591	0.54	22	4
RPL15	RL15_HUMAN	2018	615	0.54	21	5
RPS7	RS7_HUMAN	729	585	0.48	18	5
RPS17	RS17_HUMAN	515	408	0.51	18	3
RPP1	RLA1_HUMAN	512	345	0.54	17	3
RPL18A	RL1X_HUMAN	618	531	0.6	17	7
RPL30	RL30_HUMAN	524	348	0.45	16	1
RPS16	RS16_HUMAN	570	441	0.57	16	1
RPL10A	R10A_HUMAN	700	654	0.51	14	4
RPL10	RL10_HUMAN	2188	645	0.55	14	32
RPL18	RL18_HUMAN	648	567	0.59	14	1
RPS18	RS18_HUMAN	549	459	0.56	13	3
RPL13	RL13_HUMAN	1110	636	0.62	13	1
RPL23	RL23_HUMAN	493	423	0.49	11	1
RPL27	RL27_HUMAN	513	411	0.49	11	4
RPS8	RS8_HUMAN	705	627	0.52	11	3
RPP0	RLA0_HUMAN	1116	954	0.54	11	4
RPS28	RS28_HUMAN	398	210	0.62	11	2
RPS5	RS5_HUMAN	725	615	0.58	10	1
RPS15	RS15_HUMAN	515	438	0.63	10	1
RPS23	RS23_HUMAN	506	432	0.45	9	1
RPS25	RS25_HUMAN	514	378	0.47	9	0
RPL37A	R37A_HUMAN	392	279	0.52	9	1
RPL40[vi]	RL40_HUMAN	501	387	0.54	9	1
RPS21	RS21_HUMAN	356	252	0.54	9	0
RPL3	RL3_HUMAN	1311	1212	0.55	9	5
RPL35	RL35_HUMAN	455	372	0.57	9	2
RPS13	RS13_HUMAN	529	456	0.46	8	4
RPL24	RL24_HUMAN	556	474	0.48	8	9
RPS14	RS14_HUMAN	589	456	0.54	8	2
RPP2	RLA2_HUMAN	482	348	0.56	8	0
RPL38	RL38_HUMAN	368	213	0.46	7	4
RPS3	RS3_HUMAN	843	732	0.54	7	3
RPL4	RL4_HUMAN	1449	1284	0.49	6	5
RPS11	RS11_HUMAN	594	477	0.51	6	3
RPL27A[vi]	RL2A_HUMAN	514	447	0.54	6	5
RPS19	RS19_HUMAN	569	438	0.58	6	0
RPL28	RL28_HUMAN	500	414	0.6	6	1
RPL41	RL41_HUMAN	478	78	0.5	5	0
RPL11	RL11_HUMAN	609	537	0.51	4	3
RPS30[vi]	RS30_HUMAN	574	402	0.59	4	1
RPS9	RS9_HUMAN	691	585	0.6	4	1
RPL8	RL8_HUMAN	894	774	0.61	4	3
RPL14	RL14_HUMAN	843	651	0.5	3	3
Total		685	511	0.51	26	4.5
Correlation		−0.01[vii]	0.04[viii]	−0.41[ix]
p-value		0.93	0.73	0.0002

[i] The SWISSPROT ID (Bairoch and Apweiler 2000) for the human RP protein.

[ii] The standard mammalian RP gene nomenclature.

[iii] Number of nucleotides for RP mRNA.

[iv] Number of nucleotides for RP coding sequence (CDS).

[v] GC content of the RP coding sequence.

[vi] RPS27a, RPL40, and RPS30 are carboxyl extensions of ubiquitin or ubiquitin-like proteins.

[vii] Correlation between number of processed pseudogenes and mRNA length.

[viii] Correlation between number of processed pseudogenes and CDS length.

[ix] Correlation between number of processed pseudogenes and CDS GC-content.