Additional verification of PRESTA promoters.

Reliability of PRESTA-annotated promoters can be further supported by using promoter-prediction tools. As seen from the similar analysis of the EPD database, lack of prediction does not imply that the promoter is mismapped!

Analysis of PRESTA human promoters not supported by 5' EST mapping
Analysis of PRESTA mouse promoters not supported by 5' EST mapping
Analysis of EPD human promoters imported by PRESTA

Name: Sequence name in either PRESTA or EPD database
PRESTA: PRESTA position of the transcription start site. As for EPD sequences imported by PRESTA, PRESTA used EPD information to download the EMBL sequence.
Promoter Inspector: Extend of the promoter region predicted by Promoter Inspector.
FirstEF: Extend of the promoter region predicted by FirstEF
EpoNINE: Transcription start site position predicted by EpoNINE

The maximum length of an individual examined sequence was 1000 (upstream) + 500 (downstream) bp. Programs were used with default parameters.

Predicted promoters in the human PRESTA sequences not confirmed by 5' EST mapping

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Name	PRESTA	Promoter Inspector	FirstEF	EpoNINE
AB008681	1000	369 : 1116	72 : 641	923 : 925 946 : 951
AB013139	1000	NONE	NONE	NONE
AB016194	1000	833 : 1164	293 : 862	NONE
AB024498_1	619	461 : 744	NONE	482 : 482 497 : 503 521 : 523 543 : 549 563 : 573 586 : 592 597 : 604 620 : 626
AC004782_1	382	NONE	NONE	NONE
AF022722	487	29 : 552	NONE	484 : 494 788 : 790
AF035584	1000	NONE	NONE	NONE
AF061785_0	1000	133 : 976	NONE	209 : 213 322 : 324 818 : 822
AF067143	973	NONE	NONE	NONE
AF076613	929	729 : 996	105 : 674	NONE
AF077526	548	557 : 908	NONE	805 : 808
AF083425	218	NONE	NONE	NONE
AF095703	1000	969 : 1212	NONE	1015 : 1022
AF095901	1000	681 : 940	NONE	NONE
AF096769	705	NONE	NONE	NONE
AF098463	713	NONE	NONE	NONE
AF120988	252	173 : 752	NONE	267 : 270 338 : 342 398 : 404 603 : 606 702 : 702
AF127089	1000	NONE	NONE	NONE
AF127916	1000	NONE	NONE	NONE
AF158748_1	1000	761 : 988	168 : 737	885 : 892 915 : 919
AF200209	1000	NONE	NONE	1353 : 1361
AF208532	1000	NONE	NONE	NONE
AF228497	659	NONE	NONE	NONE
AF263016	226	NONE	NONE	NONE
AF267982	1000	565 : 996	NONE	699 : 700 715 : 715
AF271721	834	NONE	NONE	NONE
AF285633	1000	NONE	NONE	NONE
AF288992	1000	245 : 676	108 : 677 108 : 677	378 : 379 394 : 394
AF294007	244	NONE	NONE	NONE
AF294019	208	NONE	NONE	NONE
AF297519	1000	889 : 1088	NONE	NONE
AF319643	1000	NONE	NONE	NONE
AF361547	1000	765 : 1036	NONE	NONE
AF375663	1000	889 : 1200	NONE	1040 : 1047
AF395829	1000	517 : 1288	248 : 817	678 : 687 998 : 1002 1028 : 1030
AP001727_4	1000	NONE	NONE	NONE
AP001747	983	NONE	NONE	NONE
AP001748_3	1000	NONE	NONE	NONE
AX067148	1000	NONE	115 : 684	NONE
D85731	264	NONE	NONE	NONE
D86087S01	360	217 : 620	NONE	353 : 359
HS04636	831	NONE	131 : 700	NONE
HS17084	1000	1001 : 1420	NONE	NONE
HS202301	1000	NONE	NONE	NONE
HS229043	983	NONE	NONE	NONE
HS258161	1000	953 : 1380	401 : 970	709 : 710 946 : 953 982 : 985 1009 : 1021
HS264251	1000	929 : 1320	NONE	1172 : 1174
HS272661	807	NONE	NONE	NONE
HS299531	1000	NONE	NONE	NONE
HS2OD1	1000	NONE	NONE	NONE
HS43901_0	526	NONE	NONE	NONE
HS6824	1000	249 : 476 817 : 1008	NONE	836 : 841
HSA08062	1000	NONE	NONE	NONE
HSA243425	1000	429 : 808 1013 : 1232	258 : 827	NONE
HSA250044	257	NONE	NONE	NONE
HSA298926	1000	745 : 980	NONE	1153 : 1153
HSA315934	1000	765 : 1044	12 : 581	1067 : 1070
HSA400626	1000	781 : 1424	349 : 918	955 : 957 1061 : 1067 1173 : 1179 1218 : 1224 1244 : 1253 1270 : 1287 1339 : 1345
HSA6345_0	866	425 : 908	217 : 786	761 : 763
HSA6952	700	NONE	NONE	NONE
HSAB1523_0	1000	601 : 1076	168 : 737	565 : 569 667 : 673 857 : 861
HSACKI10	1000	NONE	NONE	NONE
HSACYP11B	603	NONE	NONE	NONE
HSADOR01	1000	NONE	NONE	NONE
HSAFP3	1000	NONE	NONE	NONE
HSALDG1	608	57 : 608	NONE	296 : 300 392 : 394
HSALDHX01	1000	853 : 1052	NONE	695 : 699
HSALPL13	1000	NONE	NONE	NONE
HSAPOCIA	492	NONE	NONE	NONE
HSAPOCIB	854	NONE	NONE	NONE
HSAPX35	891	NONE	NONE	337 : 338
HSAQP501	406	277 : 904	NONE	391 : 395 420 : 425 570 : 576 776 : 785
HSATPSY1_0	1000	NONE	NONE	NONE
HSBGLOP	323	NONE	NONE	NONE
HSBN51PRO	1000	845 : 1048	NONE	1004 : 1007
HSCALCAC	1000	NONE	NONE	NONE
HSCFCGRI1	271	NONE	NONE	NONE
HSCR1SF01	1000	NONE	NONE	NONE
HSCRYGBC_0	1000	NONE	NONE	NONE
HSCYP2DG	725	NONE	NONE	NONE
HSD087S01	360	217 : 620	NONE	353 : 359
HSEMP01	232	NONE	NONE	NONE
HSERB5FR_0	1000	NONE	NONE	NONE
HSERCC25	300	97 : 356	NONE	NONE
HSFABP_0	1000	NONE	NONE	NONE
HSFIXG	1000	NONE	NONE	NONE
HSFURIN	1000	NONE	NONE	NONE
HSGAA1	572	485 : 808	NONE	316 : 318 625 : 627
HSGCAP2	978	NONE	NONE	NONE
HSGCSFG	328	NONE	NONE	NONE
HSGHCSA_0	1000	NONE	NONE	NONE
HSGLPEX	1000	NONE	324 : 893	1000 : 1004
HSGNAS1_0	452	1 : 832	NONE	481 : 490 561 : 566 612 : 614 620 : 622 670 : 675 693 : 699
HSCHON01	132	NONE	NONE	213 : 219
HSIGFBP	1000	829 : 1348	435 : 1004	1025 : 1034
HSIGGFCII_0	1000	NONE	NONE	NONE
HSIGHVU_1	336	NONE	NONE	NONE
HSLZF1	929	729 : 996	105 : 674	NONE
HSMETHYL1	252	173 : 752	NONE	267 : 270 338 : 342 398 : 404 603 : 606 702 : 702
HSMHCP52	198	NONE	NONE	NONE
HSMKXX	993	589 : 1280	127 : 696	575 : 579 752 : 754 966 : 969 993 : 998
HSMLCKKRP5	705	NONE	NONE	NONE
HSMOGG	763	NONE	NONE	NONE
HSMPD2S1_1	222	145 : 344	NONE	225 : 228
HSMPD3S04_1	737	NONE	NONE	NONE
HSNCAM5R_1	1000	NONE	NONE	NONE
HSP53G	816	NONE	NONE	NONE
HSPABPS01	378	1 : 436	NONE	NONE
HSPAIA	1000	NONE	NONE	NONE
HSPDHBET	1000	945 : 1148	NONE	NONE
HSPF4V1A	213	NONE	NONE	NONE
HSPF7	1000	NONE	NONE	NONE
HSPPP2R01	218	NONE	NONE	NONE
HSPR22	1000	NONE	NONE	NONE
HSPRELP01	1000	NONE	NONE	NONE
HSQP501	406	277 : 904	NONE	391 : 395 420 : 425 570 : 576 776 : 785
HSRPBG1	784	605 : 928	82 : 651	708 : 715 755 : 763 784 : 793
HSSD11K1_1	1000	65 : 540 753 : 1132	NONE	297 : 301 322 : 326 386 : 387 451 : 458 992 : 996 1078 : 1082
HSSODB	387	1 : 576	NONE	162 : 162 193 : 199 388 : 396
HSTFAP2GN	390	369 : 588	NONE	NONE
HSTGFBG1	1000	821 : 1480	330 : 899	958 : 963
HSTGL1	864	NONE	NONE	NONE
HSTPAA1_1	266	NONE	NONE	NONE
HSTPAA1_2	401	NONE	NONE	NONE
HSU04636	831	NONE	131 : 700	NONE
HSU16815	1000	NONE	NONE	1080 : 1084
HSU17084	1000	1001 : 1420	NONE	NONE
HSU20230	1000	NONE	NONE	NONE
HSU25134	522	NONE	NONE	NONE
HSU26425	1000	901 : 1296	NONE	1146 : 1148
HSU27266	807	NONE	NONE	NONE
HSU36755	1000	161 : 444 905 : 1132	NONE	252 : 259
HSU52852_0	1000	NONE	NONE	NONE
HSUHON01	132	NONE	NONE	213 : 219
HSULDHX01	1000	853 : 1052	NONE	695 : 699
HSVATPB2R	693	549 : 912	NONE	879 : 884
HUMCR1SF01	1000	NONE	NONE	NONE
HUMCYPBB	603	NONE	NONE	NONE
HUMEMP01	232	NONE	NONE	NONE
HUMGLPEX	1000	NONE	324 : 893	1000 : 1004
PLCB3X01	992	1005 : 1400	NONE	1250 : 1252

Predicted promoters in the mouse PRESTA sequences not confirmed by 5' EST mapping

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Name	PRESTA	Promoter Inspector	FirstEF	EpoNINE
AB040292	984	1205 : 1464	NONE	1041 : 1044 1320 : 1325
AB063281	359	177 : 568	NONE	176 : 182 232 : 238 276 : 282 335 : 341 378 : 385
AF012870	265	1 : 232	NONE	89 : 99 151 : 155 183 : 185 197 : 210
AF016099	1000	NONE	NONE	NONE
AF026469	964	805 : 1084	393 : 962	904 : 913 927 : 942 972 : 978 1001 : 1004
AF027301	289	NONE	NONE	NONE
AF033356	1000	NONE	NONE	NONE
AF035777	398	NONE	NONE	NONE
AF046864	1000	NONE	NONE	1138 : 1144
AF052291	830	733 : 944	154 : 723	NONE
AF063666	1000	789 : 1132	NONE	NONE
AF067191	864	NONE	NONE	NONE
AF093878	1000	NONE	NONE	NONE
AF098460	570	NONE	NONE	NONE
AF117109	999	389 : 1344	412 : 981	865 : 869 915 : 921 996 : 1008 1028 : 1028 1075 : 1077
AF128459	351	NONE	NONE	NONE
AF152375	1000	501 : 1292	87 : 656	999 : 999 1027 : 1037 1061 : 1062 1113 : 1115 1129 : 1135
AF203031	1000	NONE	NONE	NONE
AF224341	1000	781 : 1224	374 : 943	NONE
AF254575S1	100	NONE	NONE	NONE
AF298116	1000	NONE	NONE	NONE
D78171	1000	NONE	155 : 724	887 : 889
MMGHGPRO	1000	NONE	NONE	NONE
MMGLURB01	1000	861 : 1068	396 : 965	NONE
MMH1CA	631	NONE	NONE	NONE
MMILCH	175	NONE	NONE	NONE
MMK13CPG	1000	NONE	NONE	NONE
MMKROX1_0	1000	309 : 504 805 : 1012	84 : 653	NONE
MMMHD2D	391	NONE	NONE	397 : 400
MMMOR1	1000	NONE	NONE	NONE
MMPEBP2B	700	577 : 904	NONE	948 : 957
MMPIM1	1000	453 : 1060	209 : 778	755 : 757
MMPLB4_0	1000	NONE	NONE	NONE
MMRETDEHY	1000	NONE	NONE	NONE
MMSR1	1000	NONE	NONE	NONE
MMTNFAB_0	1000	NONE	NONE	NONE
MMTNFBG	1000	NONE	NONE	NONE
MMTRAA	1000	NONE	NONE	NONE
MMU11680	1000	NONE	NONE	NONE
MMU12235	876	NONE	NONE	NONE
MMU20164	636	489 : 776	NONE	552 : 557 586 : 594 635 : 641 712 : 717
MMU252156	897	NONE	NONE	NONE
MMU271911	1000	NONE	NONE	NONE
MMU277444	1000	877 : 1068	289 : 858	NONE
MMU78796	443	NONE	NONE	NONE
MMU86783_0	1000	1121 : 1328	NONE	NONE
MUSIGHVTG1	332	NONE	NONE	NONE
MUSIGHVTG2	178	NONE	NONE	NONE
MUSSVA	722	NONE	NONE	NONE

Predicted promoters in the human EPD promoter sequences imported by PRESTA

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NOTE: Presta imports only subset of EPD sequences

Name	PRESTA	Promoter Inspector	FirstEF	EpoNINE
HS_A1AG	599	NONE	NONE	NONE
HS_A1AH	1000	NONE	NONE	NONE
HS_A1AT_2	1000	NONE	NONE	NONE
HS_A1AT_3	1000	NONE	NONE	NONE
HS_ALBU	1000	NONE	NONE	NONE
HS_ALFA_1	1000	NONE	NONE	NONE
HS_ALFA_2	1000	NONE	NONE	NONE
HS_ALFA_3	1000	365 : 1172	4 : 573	5 : 7
HS_ALFA_4	1000	309 : 1116	NONE	917 : 920 949 : 955
HS_AMYP_A	725	NONE	NONE	NONE
HS_AMYP_B	681	NONE	NONE	NONE
HS_ANT3	1000	NONE	NONE	NONE
HS_APA2	1000	NONE	NONE	NONE
HS_APB	898	NONE	NONE	NONE
HS_APE	1000	NONE	NONE	NONE
HS_ARF1	857	561 : 896	NONE	616 : 616 698 : 700 712 : 720
HS_ARF3	1000	849 : 1068	NONE	NONE
HS_ARGI	748	NONE	NONE	NONE
HS_B2AR	1000	789 : 1008	NONE	NONE
HS_BCL2__2	1000	1065 : 1256	NONE	209 : 214
HS_C4BP	550	NONE	NONE	NONE
HS_CA11	1000	NONE	NONE	NONE
HS_CA13	1000	NONE	NONE	NONE
HS_CA21	1000	389 : 588	160 : 729	NONE
HS_CCEM	1000	NONE	NONE	NONE
HS_CD3D	342	NONE	NONE	NONE
HS_CGD1	1000	773 : 972	NONE	787 : 792
HS_CGHB	363	NONE	NONE	NONE
HS_CGM6	473	NONE	NONE	NONE
HS_CPT7	1000	NONE	NONE	NONE
HS_CRP	164	NONE	NONE	NONE
HS_CSF1	570	NONE	NONE	NONE
HS_CSF2	625	NONE	NONE	NONE
HS_CSF3	326	NONE	NONE	NONE
HS_DBDD	814	NONE	NONE	NONE
HS_DCUP	1000	NONE	NONE	NONE
HS_DYR	1000	445 : 1092	NONE	NONE
HS_EGFR_1	856	565 : 1356	NONE	NONE
HS_EGFR_2	950	565 : 1384	347 : 916	883 : 887
HS_ESR1	1000	NONE	NONE	NONE
HS_ETBR	1000	NONE	NONE	NONE
HS_FIBB	1000	NONE	NONE	NONE
HS_FIBG	1000	NONE	NONE	NONE
HS_FOS	1000	457 : 1012	NONE	NONE
HS_FRIH	1000	785 : 1472	NONE	NONE
HS_FRIL	106	NONE	NONE	NONE
HS_HA2R	1000	NONE	NONE	NONE
HS_HB21	1000	NONE	NONE	NONE
HS_HBA_B	1000	525 : 1036	199 : 768	700 : 704
HS_HBB	1000	NONE	NONE	NONE
HS_HBD	1000	NONE	NONE	NONE
HS_HBE	1000	NONE	NONE	NONE
HS_HBG_A	1000	NONE	NONE	NONE
HS_HBG_B	1000	NONE	NONE	NONE
HS_HEM3_1	1000	NONE	NONE	NONE
HS_HEM3_2	1000	NONE	NONE	NONE
HS_HG17	1000	689 : 1084 1289 : 1500	235 : 804	NONE
HS_HG2A	791	NONE	NONE	NONE
HS_HS71	275	NONE	NONE	NONE
HS_HS7C	226	NONE	NONE	NONE
HS_HSP1	1000	NONE	NONE	NONE
HS_HSP2	1000	NONE	NONE	NONE
HS_IL1B	1000	NONE	NONE	NONE
HS_IL2A_1	1000	NONE	NONE	NONE
HS_IL2A_2	1000	NONE	NONE	NONE
HS_IL8B	1000	NONE	NONE	NONE
HS_INI2	603	NONE	NONE	NONE
HS_INS	1000	357 : 564	NONE	NONE
HS_K122	107	NONE	NONE	NONE
HS_K2C1	685	NONE	NONE	NONE
HS_KCRB	807	581 : 1188	94 : 663	NONE
HS_KITH	458	245 : 880	NONE	NONE
HS_KV1I	108	NONE	NONE	NONE
HS_LCAT	808	NONE	NONE	NONE
HS_LCK_1	750	NONE	NONE	NONE
HS_LCK_2	730	NONE	NONE	NONE
HS_LDVR	696	553 : 992	98 : 667	NONE
HS_LIPH	1000	NONE	NONE	NONE
HS_MT1E	411	NONE	NONE	NONE
HS_MT1F	419	NONE	NONE	NONE
HS_MT1G	350	NONE	NONE	NONE
HS_MT2	765	525 : 796	59 : 628	NONE
HS_MYC_1	1000	801 : 1252	156 : 725	538 : 542
HS_MYC_2	1000	661 : 1092	NONE	1 : 2 376 : 380 797 : 803
HS_MYCN_2	1000	1025 : 1300	137 : 706	NONE
HS_MYCN_3	1000	873 : 1144	NONE	NONE
HS_NFL	1000	901 : 1132	NONE	NONE
HS_NUCL	1000	617 : 940	287 : 856 338 : 907	731 : 732 778 : 782 795 : 800
HS_ODBA	1000	NONE	NONE	NONE
HS_OPSD	1000	NONE	NONE	NONE
HS_PEPA_A	1000	NONE	NONE	NONE
HS_PEPC	1000	NONE	NONE	NONE
HS_PGK1	1000	853 : 1060	381 : 950	NONE
HS_PHU1	432	NONE	NONE	NONE
HS_PS2	703	NONE	NONE	NONE
HS_PSG5	682	NONE	NONE	NONE
HS_PSPC	585	NONE	NONE	NONE
HS_PU16	224	NONE	NONE	NONE
HS_RASH_2	908	737 : 1408	301 : 870	NONE
HS_RASH_3	1000	649 : 1420	211 : 780	788 : 788 827 : 829 840 : 849 861 : 866 898 : 899
HS_RNPE	729	NONE	NONE	NONE
HS_RS14	218	421 : 640	NONE	NONE
HS_RS17	172	NONE	NONE	NONE
HS_S108	1000	NONE	NONE	NONE
HS_SMS	1000	NONE	NONE	NONE
HS_SODC	1000	717 : 1500	NONE	NONE
HS_STP1	1000	NONE	NONE	NONE
HS_TCR8	1000	NONE	NONE	NONE
HS_TCRA	1000	NONE	NONE	NONE
HS_TCRB	1000	NONE	NONE	NONE
HS_TDT	930	NONE	NONE	NONE
HS_THYG	530	NONE	NONE	NONE
HS_THYL	242	1 : 268	NONE	49 : 50
HS_TPIS	1000	693 : 1016	NONE	NONE
HS_TTP	548	NONE	NONE	NONE
HS_TY3H	516	NONE	NONE	NONE
HS_U2	1000	NONE	262 : 831	554 : 558
HS_U3	537	NONE	NONE	NONE
HS_U4C	270	NONE	NONE	NONE
HS_UBIQ	1000	829 : 1344	NONE	174 : 179