List of the final 164 pseudogenes in ENCODE regions (Aug 2005):

id	encode-id	encode-start	encode-end	strand	length	parent-protein	parent-protein-length	type
ENCODE_YalePgene_1 	ENr111	350262	351109	+	848	ENSP00000301522	198	Processed
ENCODE_YalePgene_2 	ENr112	78535	79903	+	1369	ENSP00000219837	189	Processed
ENCODE_YalePgene_3 	ENr112	343693	343836	-	144	ENSP00000264376	174	Fragment
ENCODE_YalePgene_4 	ENr112	495320	495755	-	436	ENSP00000292314	166	Processed
ENCODE_YalePgene_5 	ENr113	87964	88812	+	849	ENSP00000346067	295	Processed
ENCODE_YalePgene_6 	ENr113	249602	250610	-	1009	ENSP00000242210	336	Processed
ENCODE_YalePgene_8 	ENr114	42330	43010	-	681	ENSP00000281508	284	Processed
ENCODE_YalePgene_9 	ENr121	397510	397800	-	291	ENSP00000234401	604	Fragment
ENCODE_YalePgene_13	ENr122	477997	478562	+	566	ENSP00000354739	191	Processed
ENCODE_YalePgene_14	ENr123	121839	122183	-	345	ENSP00000287038	115	Processed
ENCODE_YalePgene_15	ENr123	339882	340255	+	374	ENSP00000354499	513	Fragment
ENCODE_YalePgene_17	ENr131	2187	3365	-	1179	ENSP00000343838	530	Processed
ENCODE_YalePgene_18	ENr131	20370	21284	-	915	ENSP00000287677	528	Processed
ENCODE_YalePgene_19	ENr131	64748	65900	+	1153	ENSP00000343838	530	Duplicated
ENCODE_YalePgene_20	ENr131	138364	138888	-	525	ENSP00000355102	184	Processed
ENCODE_YalePgene_21	ENr131	160013	160300	-	288	ENSP00000316053	232	Fragment
ENCODE_YalePgene_22	ENr131	171360	172092	-	733	ENSP00000316053	232	Processed
ENCODE_YalePgene_23	ENr131	282960	285053	-	2094	ENSP00000312244	521	Processed
ENCODE_YalePgene_24	ENr132	494668	496292	+	1625	ENSP00000303043	597	Processed
ENCODE_YalePgene_26	ENr133	220463	221437	-	975	ENSP00000352228	362	Processed
ENCODE_YalePgene_27	ENr133	265984	266834	+	851	ENSP00000216463	89	Duplicated
ENCODE_YalePgene_28	ENr133	284723	285351	-	629	ENSP00000272839	218	Processed
ENCODE_YalePgene_29	ENr133	423060	426430	-	3371	ENSP00000346278	153	Processed
ENCODE_YalePgene_30	ENr211	201136	201492	-	357	ENSP00000233893	102	Processed
ENCODE_YalePgene_31	ENr211	493200	496551	-	3352	ENSP00000256497	657	Duplicated
ENCODE_YalePgene_32	ENr212	46296	46684	+	389	ENSP00000230050	132	Processed
ENCODE_YalePgene_34	ENr221	436080	436803	-	724	ENSP00000246071	225	Processed
ENCODE_YalePgene_36	ENr222	416250	418155	+	1906	ENSP00000310144	462	Processed
ENCODE_YalePgene_37	ENr223	31578	32892	+	1315	ENSP00000306191	254	Processed
ENCODE_YalePgene_38	ENr223	133898	134634	-	737	ENSP00000318102	196	Processed
ENCODE_YalePgene_40	ENr223	266847	267824	+	978	ENSP00000346067	295	Processed
ENCODE_YalePgene_41	ENr223	268435	269867	+	1433	ENSP00000220849	445	Processed
ENCODE_YalePgene_42	ENr223	299348	300029	+	682	ENSP00000245974	207	Processed
ENCODE_YalePgene_43	ENr223	303463	307544	+	4082	ENSP00000264221	451	Processed
ENCODE_YalePgene_44	ENr223	367522	368260	-	739	ENSP00000346006	249	Processed
ENCODE_YalePgene_47	ENr231	371863	372356	+	494	ENSP00000346060	165	Processed
ENCODE_YalePgene_48	ENr232	457115	457448	-	334	ENSP00000352033	604	Fragment
ENCODE_YalePgene_49	ENr233	208525	208692	+	168	ENSP00000300289	505	Fragment
ENCODE_YalePgene_50	ENr233	286443	305670	-	19228	ENSP00000299989	414	Duplicated
ENCODE_YalePgene_51	ENr233	435234	435674	-	441	ENSP00000218432	156	Processed
ENCODE_YalePgene_52	ENr311	202191	202776	+	586	ENSP00000346050	264	Processed
ENCODE_YalePgene_53	ENr312	430553	430972	-	420	ENSP00000353700	140	Processed
ENCODE_YalePgene_54	ENr313	114800	115202	+	403	ENSP00000339064	135	Processed
ENCODE_YalePgene_56	ENr322	50691	51340	-	650	ENSP00000346001	403	Processed
ENCODE_YalePgene_57	ENr323	42300	42520	-	221	ENSP00000264090	344	Fragment
ENCODE_YalePgene_58	ENr323	60803	62094	-	1292	ENSP00000346001	403	Processed
ENCODE_YalePgene_59	ENr323	374580	374882	+	303	ENSP00000346013	106	Processed
ENCODE_YalePgene_60	ENr323	428774	429429	-	656	ENSP00000349760	84	Processed
ENCODE_YalePgene_62	ENr324	116838	117238	+	401	ENSP00000295065	297	Processed
ENCODE_YalePgene_63	ENr324	136840	137570	+	731	ENSP00000349760	84	Processed
ENCODE_YalePgene_64	ENr324	230129	230900	-	772	ENSP00000262600	372	Fragment
ENCODE_YalePgene_66	ENr331	271395	272172	-	778	ENSP00000342283	208	Duplicated
ENCODE_YalePgene_67	ENr331	285190	285588	+	399	ENSP00000346039	140	Processed
ENCODE_YalePgene_69	ENr332	464696	465112	+	417	ENSP00000251453	146	Processed
ENCODE_YalePgene_70	ENr333	268819	269075	-	257	ENSP00000227495	329	Duplicated
ENCODE_YalePgene_71	ENr333	290617	290984	-	368	ENSP00000252543	105	Processed
ENCODE_YalePgene_72	ENr333	334712	335025	+	314	ENSP00000274242	97	Processed
ENCODE_YalePgene_74	ENr334	336632	337472	+	841	ENSP00000296930	294	Processed
ENCODE_YalePgene_77	ENm001	702983	705503	-	2521	ENSP00000299783	860	Processed
ENCODE_YalePgene_78	ENm001	705812	705910	-	99	ENSP00000256858	1104	Fragment
ENCODE_YalePgene_79	ENm001	801692	802449	-	758	ENSP00000340627	188	Duplicated
ENCODE_YalePgene_80	ENm001	1092641	1094417	-	1777	ENSP00000302894	378	Duplicated
ENCODE_YalePgene_81	ENm001	1269458	1270308	-	851	ENSP00000303518	239	Duplicated
ENCODE_YalePgene_82	ENm001	1317302	1317463	+	162	ENSP00000339064	135	Fragment
ENCODE_YalePgene_83	ENm001	1415730	1415970	-	241	ENSP00000242577	89	Processed
ENCODE_YalePgene_84	ENm001	1712397	1713703	+	1307	ENSP00000244437	164	Processed
ENCODE_YalePgene_86	ENm002	226764	226934	-	171	ENSP00000263556	534	Fragment
ENCODE_YalePgene_87	ENm002	279600	282200	+	2601	ENSP00000304743	1321	Processed
ENCODE_YalePgene_91	ENm003	449355	449697	-	343	ENSP00000314461	84	Processed
ENCODE_YalePgene_92	ENm004	112645	113726	-	1082	ENSP00000296417	128	Processed
ENCODE_YalePgene_93	ENm004	130388	130624	-	237	ENSP00000349784	115	Processed
ENCODE_YalePgene_94	ENm004	151519	152007	+	489	ENSP00000211372	152	Processed
ENCODE_YalePgene_95	ENm004	408760	409140	-	381	ENSP00000355102	184	Processed
ENCODE_YalePgene_96	ENm004	483148	483476	-	329	ENSP00000339861	101	Processed
ENCODE_YalePgene_97	ENm004	631523	631927	+	405	ENSP00000346045	135	Processed
ENCODE_YalePgene_98	ENm004	724340	724550	+	211	ENSP00000262325	939	Fragment
ENCODE_YalePgene_100	ENm004	789135	789422	-	288	ENSP00000249007	288	Fragment
ENCODE_YalePgene_101	ENm004	791952	792265	+	314	ENSP00000329312	213	Fragment
ENCODE_YalePgene_102	ENm004	861415	865141	+	3727	ENSP00000339353	1443	Processed
ENCODE_YalePgene_103	ENm004	948710	949030	-	321	ENSP00000347480	241	Processed
ENCODE_YalePgene_104	ENm004	968879	969185	+	307	ENSP00000304590	145	Processed
ENCODE_YalePgene_105	ENm004	978700	978910	+	211	ENSP00000290691	473	Fragment
ENCODE_YalePgene_106	ENm004	1486922	1487256	-	335	ENSP00000354554	378	Fragment
ENCODE_YalePgene_107	ENm005	122707	123274	+	568	ENSP00000323046	275	Processed
ENCODE_YalePgene_109	ENm005	247078	248038	+	961	ENSP00000305297	335	Processed
ENCODE_YalePgene_110	ENm005	467381	467756	-	376	ENSP00000341730	214	Fragment
ENCODE_YalePgene_111	ENm005	960525	961041	+	517	ENSP00000289790	310	Processed
ENCODE_YalePgene_112	ENm005	1107524	1108136	-	613	ENSP00000196551	204	Processed
ENCODE_YalePgene_113	ENm005	1144444	1145151	+	708	ENSP00000338516	162	Processed
ENCODE_YalePgene_116	ENm006	737479	738903	+	1425	ENSP00000310030	351	Processed
ENCODE_YalePgene_117	ENm006	779157	780581	+	1425	ENSP00000310030	351	Processed
ENCODE_YalePgene_118	ENm006	796815	805109	-	8295	ENSP00000263518	419	Duplicated
ENCODE_YalePgene_119	ENm006	973600	974460	-	861	ENSP00000288344	272	Processed
ENCODE_YalePgene_120	ENm006	1054400	1054900	-	501	ENSP00000300107	633	Processed
ENCODE_YalePgene_121	ENm006	1076405	1077015	-	611	ENSP00000310042	477	Processed
ENCODE_YalePgene_122	ENm006	1243017	1243180	-	164	ENSP00000339731	107	Fragment
ENCODE_YalePgene_123	ENm007	226986	227336	-	351	ENSP00000308782	620	Fragment
ENCODE_YalePgene_125	ENm007	381109	381518	-	410	ENSP00000352298	597	Fragment
ENCODE_YalePgene_126	ENm007	401093	402925	+	1833	ENSP00000314768	463	Processed
ENCODE_YalePgene_127	ENm007	418134	418364	-	231	ENSP00000270452	448	Duplicated
ENCODE_YalePgene_129	ENm007	440091	441564	+	1474	ENSP00000338176	716	Processed
ENCODE_YalePgene_130	ENm007	446912	447151	-	240	ENSP00000315997	652	Fragment
ENCODE_YalePgene_131	ENm007	466065	466243	-	179	ENSP00000291759	499	Fragment
ENCODE_YalePgene_132	ENm007	477361	477699	-	339	ENSP00000302948	287	Fragment
ENCODE_YalePgene_133	ENm007	499704	500717	-	1014	ENSP00000322339	353	Processed
ENCODE_YalePgene_134	ENm007	507790	508061	-	272	ENSP00000270464	368	Fragment
ENCODE_YalePgene_135	ENm007	509066	509903	-	838	ENSP00000301219	299	Fragment
ENCODE_YalePgene_136	ENm007	510807	510965	-	159	ENSP00000270452	448	Fragment
ENCODE_YalePgene_137	ENm007	626309	626392	+	84	ENSP00000296581	80	Fragment
ENCODE_YalePgene_138	ENm007	701000	701439	+	440	ENSP00000221567	227	Fragment
ENCODE_YalePgene_139	ENm007	713136	713561	+	426	ENSP00000343192	377	Fragment
ENCODE_YalePgene_140	ENm007	731453	731778	+	326	ENSP00000245620	631	Fragment
ENCODE_YalePgene_142	ENm007	827612	828530	+	919	ENSP00000322339	353	Processed
ENCODE_YalePgene_143	ENm007	850851	852301	+	1451	ENSP00000245620	631	Processed
ENCODE_YalePgene_144	ENm007	876792	878582	+	1791	ENSP00000245620	631	Processed
ENCODE_YalePgene_145	ENm007	880589	880886	+	298	ENSP00000251372	489	Duplicated
ENCODE_YalePgene_146	ENm007	883958	884193	+	236	ENSP00000340011	232	Fragment
ENCODE_YalePgene_148	ENm007	888903	889359	+	457	ENSP00000301219	299	Fragment
ENCODE_YalePgene_149	ENm007	919922	920263	+	342	ENSP00000344761	375	Fragment
ENCODE_YalePgene_150	ENm007	936500	947145	+	10646	ENSP00000344761	375	Duplicated
ENCODE_YalePgene_151	ENm007	951171	951611	+	441	ENSP00000342999	304	Fragment
ENCODE_YalePgene_154	ENm008	158920	159084	+	165	ENSP00000322421	142	Fragment
ENCODE_YalePgene_156	ENm008	18927	29467	-	10541	ENSP00000244174	521	Duplicated
ENCODE_YalePgene_158	ENm009	78929	79865	+	937	ENSP00000352305	302	Fragment
ENCODE_YalePgene_159	ENm009	123353	124305	+	953	ENSP00000322724	302	Fragment
ENCODE_YalePgene_160	ENm009	136395	137407	-	1013	ENSP00000352305	302	Fragment
ENCODE_YalePgene_161	ENm009	184173	185105	-	933	ENSP00000352305	302	Fragment
ENCODE_YalePgene_162	ENm009	219649	220614	-	966	ENSP00000352305	302	Fragment
ENCODE_YalePgene_163	ENm009	261949	262914	+	966	ENSP00000322593	314	Fragment
ENCODE_YalePgene_164	ENm009	283824	284804	+	981	ENSP00000328878	297	Fragment
ENCODE_YalePgene_165	ENm009	316383	317320	+	938	ENSP00000322088	325	Fragment
ENCODE_YalePgene_166	ENm009	322971	323931	-	961	ENSP00000326232	318	Fragment
ENCODE_YalePgene_167	ENm009	339487	340458	+	972	ENSP00000322088	325	Fragment
ENCODE_YalePgene_168	ENm009	350952	351892	+	941	ENSP00000322088	325	Fragment
ENCODE_YalePgene_172	ENm009	417174	418163	-	990	ENSP00000348350	297	Fragment
ENCODE_YalePgene_173	ENm009	489920	490351	-	432	ENSP00000292896	147	Duplicated
ENCODE_YalePgene_174	ENm009	538557	539191	-	635	ENSP00000300778	317	Processed
ENCODE_YalePgene_175	ENm009	561586	562528	-	943	ENSP00000333305	310	Fragment
ENCODE_YalePgene_176	ENm009	577369	578174	-	806	ENSP00000327540	312	Fragment
ENCODE_YalePgene_177	ENm009	601500	602390	+	891	ENSP00000348602	695	Processed
ENCODE_YalePgene_178	ENm009	609420	609773	+	354	ENSP00000257262	79	Processed
ENCODE_YalePgene_179	ENm009	677473	678413	-	941	ENSP00000348350	297	Fragment
ENCODE_YalePgene_181	ENm009	774034	774961	-	928	ENSP00000326232	318	Fragment
ENCODE_YalePgene_182	ENm009	798476	799407	-	932	ENSP00000326259	314	Fragment
ENCODE_YalePgene_183	ENm009	807754	808707	+	954	ENSP00000326259	314	Fragment
ENCODE_YalePgene_184	ENm009	813492	814436	-	945	ENSP00000326259	314	Fragment
ENCODE_YalePgene_185	ENm009	818059	819003	-	945	ENSP00000341826	372	Processed
ENCODE_YalePgene_186	ENm009	966113	967044	+	932	ENSP00000302422	314	Fragment
ENCODE_YalePgene_187	ENm009	973299	974269	+	971	ENSP00000337929	320	Fragment
ENCODE_YalePgene_188	ENm010	4209	5008	+	800	ENSP00000340366	266	Processed
ENCODE_YalePgene_189	ENm010	63804	65480	-	1677	ENSP00000339079	168	Processed
ENCODE_YalePgene_191	ENm010	105796	107057	+	1262	ENSP00000340627	188	Duplicated
ENCODE_YalePgene_192	ENm010	130234	130972	+	739	ENSP00000274606	153	Processed
ENCODE_YalePgene_193	ENm010	351420	351840	-	421	ENSP00000259469	123	Processed
ENCODE_YalePgene_194	ENm010	410680	411640	-	961	ENSP00000341826	372	Processed
ENCODE_YalePgene_195	ENm011	70360	70685	+	326	ENSP00000346012	106	Processed
ENCODE_YalePgene_196	ENm011	80849	81919	-	1071	ENSP00000349960	375	Semi-Processed
ENCODE_YalePgene_198	ENm012	3991	4357	-	367	ENSP00000252543	105	Processed
ENCODE_YalePgene_200	ENm012	843751	844084	-	334	ENSP00000258737	192	Fragment
ENCODE_YalePgene_203	ENm013	243358	243530	+	173	ENSP00000341072	56	Processed
ENCODE_YalePgene_204	ENm013	477530	479209	+	1680	ENSP00000305654	205	Processed
ENCODE_YalePgene_207	ENm013	952472	953608	+	1137	ENSP00000229983	173	Processed
ENCODE_YalePgene_208	ENm014	542366	543315	+	950	ENSP00000257849	141	Processed
ENCODE_YalePgene_211	ENm014	856950	857652	+	703	ENSP00000338065	210	Processed

The two ambiguous cases discussed in the paper -- these two loci were annotated as pseudogenes by us but as genes by GENCODE/HAVANA (as EGASP/2005):

ENCODE_YalePgene_12	ENr122	359278	362468	+	3191	ENSP00000331368	374	Duplicated
ENCODE_YalePgene_108	ENm005	200473	211501	-	11029	ENSP00000283507	307	Duplicated

Note, our annotation has been subsequently updated in Oct. 2005, resulting in a list of 167 pseudogenes. The new data is available as part of the ENCODE consensus pseudogene annotation.