The ASRG database: identification and survey of Arabidopsis thalianagenes involved in pre-mRNA splicing

Wang, Bing-Bing; Brendel, Volker

doi:10.1186/gb-2004-5-12-r102

Table 1 Arabidopsis snRNA genes

From: The ASRG database: identification and survey of Arabidopsis thalianagenes involved in pre-mRNA splicing

Gene	GeneID	Chromosome	Strand	From	To	Length (nucleotides)	e-value	Similarity	GenBank ID
atU1a*	At5g49054	5	-	19903323	19903158	166	1E-89	1-166, 100%	gi17660
atU1-2	At4g23415	4	+	12225621	12225786	166	1E-58	1-166, 92%	gi22293582
atU1-3	At5g51675	5	+	21013986	21014149	164	4E-55	3-166, 91%
atU1-4	At5g25774	5	-	8972971	8972807	165	2E-51	1-166, 90%	gi22293583
atU1-5	At1g08115	1	-	2538238	2538073	166	1E-46	1-166, 89%	gi22293581
atU1-6	At3g05695	3	+	1681815	1681977	163	4E-40	4-166, 87%
atU1-7	At3g05672	3	+	1657766	1657928	163	4E-40	4-166, 87%	gi22293580
atU1-8	At5g27764	5	+	9832576	9832740	165	1E-39	1-166, 87%
atU1-9	At5g26694	5	-	9494594	9494430	165	1E-27	1-166, 84%
atU1-10	At1g11884	1	-	4007396	4007236	161	1E-18	4-61, 93%; 80-166, 88%
atU1-11p	At4g16645	4	+	9370786	9370841	56	7E-17	4-59, 94%
atU1-12p	At4g23565	4	-	12298871	12298802	70	1E-15	94-163, 90%
atU1-13p	At5g49524	5	-	20112431	20112275	157	2E-14	4-50, 91%; 91-166, 88%
atU1-14p	At1g35354	1	+	12986822	12986908	87	1E-06	10-60, 88%; 84-118, 88%
atU2-1	At1g16825	1	+	5758381	5758575	195	2E-88	1-196, 96%
atU2.2*	At3g57645	3	+	21357718	21357913	196	1E-107	1-196, 100%	gi17661
atU2.3	At3g57765	3	-	21408595	21408400	196	1E-95	1-196, 97%	gi17662
atU2.4	At3g56825	3	-	21052994	21052800	195	5E-86	1-196, 95%	gi17663
atU2.5	At5g09585	5	+	2975013	2975208	196	7E-79	1-196, 93%	gi17664
atU2.6	At3g56705	3	+	21015472	21015667	196	1E-83	1-196, 94%	gi17665
atU2.7	At5g61455	5	-	24730829	24730634	196	5E-86	1-196, 95%	gi17666
atU2-8	At5g67555	5	+	26966884	26967079	196	5E-86	1-196, 95%
atU2.9	At4g01885	4	+	815273	815466	194	2E-82	1-194, 94%	gi17667
atU2-10	At2g02938	2	+	849777	849972	196	3E-93	1-196, 96%	gi22293586
atU2-10b/12	At2g02940	2	+	852859	853054	196	3E-93	1-196, 96%
atU2-11	At1g09805/09895	1	-	3180736	3180547	190	8E-85	1-190, 95%
atU2-13	At2g20405	2	+	8809169	8809364	196	3E-81	1-196, 94%	gi22293584
atU2-14	At1g14165	1	+	4842274	4842469	196	3E-81	1-196, 94%	gi22293585
atU2-15	At5g62415	5	+	25083790	25083985	196	4E-74	1-196, 92%
atU2-16	At5g57835	5	-	23448717	23448522	196	2E-67	1-196, 92%
atU2-17	At5g14545	5	-	4690105	4690008	98	3E-44	1-98, 97%
atU2-18p	At3g26815	3	+	9881236	9881303	68	2E-14	1-68, 89%
atU4.1*	At5g49056	5	-	19902970	19902817	154	4E-80	1-154, 99%	gi17673
atU4.2	At3g06900	3	-	2178343	2178190	154	2E-75	1-154, 98%	gi17674
atU4.3p	At5g49526	5	-	20112072	20112030	43	2E-11	15-57, 95%	gi17675
atU4-4	At1g49242/49235	1	-	18222354	18222201	154	2E-75	1-154, 98%	gi22293588
atU4-5	At5g25776	5	-	8972618	8972465	154	1E-70	1-154, 96%
atU4-6	At1g11886	1	-	4007020	4006867	154	1E-70	1-154, 96%	gi22293587
atU4-7	At5g27766	5	+	9832934	9833083	150	7E-66	1-150, 96%
atU4-8	At5g26996	5	-	9494230	9494081	150	7E-66	1-150, 96%
atU4-9	At1g79965	1	+	30086031	30086168	138	9E-47	18-154, 92%
atU4-10	At1g35356	1	+	12987189	12987313	125	3E-34	1-124, 90%
atU4-11p	At1g68395	1	+	25647322	25647396	75	9E-07	18-37, 100%; 60-102, 90%
atU5.1*	At3g55865	3	-	20740607	20740503	105	6E-35	1-105, 94%	gi17676
atU5.1b	At3g55855	3	-	20736881	20736780	102	7E-38	1-102, 96%	gi22293592
atU5-2	At1g65115	1	+	24194482	24194586	105	1E-39	1-105, 96%
atU5-3	At1g70185	1	+	26433396	26433497	102	7E-38	1-102, 96%	gi22293590
atU5-4	At3g55645	3	+	20653843	20653947	105	3E-37	1-105, 95%
atU5-5	At1g24105/24095	1	-	8525204	8525103	102	2E-35	1-102, 95%	gi22293591
atU5-6	At1g04475	1	-	1215831	1215730	102	2E-35	1-102, 95%	gi22293589
atU5-7	At4g02535	4	-	1114629	1114528	102	1E-30	2-103, 93%
atU5-8	At3g25445	3	-	9227212	9227116	97	1E-20	5-101, 89%
atU5-9	At1g79545	1	-	29928543	29928447	97	1E-20	5-101, 89%
atU5-10	At5g14547	5	-	4690412	4690370	43	3E-12	24-67, 97%
atU5-11	At5g54065	5	-	21957066	21957023	44	2E-10	20-64, 95%
atU5-12	At1g71355	1	+	26895255	26895298	44	2E-10	20-64, 95%
atU5-13	At5g53745	5	-	21829988	21829943	46	3E-09	24-70, 93%
atU6.1*	At3g14735	3	+	4951596	4951697	102	1E-51	1-102, 100%	gi16516
atU6.26	At3g13855	3	+	4561111	4561212	102	2E-49	1-102, 99%	gi16517
atU6.29	At5g46315	5	+	18804616	18804717	102	2E-49	1-102, 99%	gi16518
atU6-2	At5g62995	5	+	25296825	25296926	102	1E-51	1-102, 100%
atU6-3	At4g27595	4	+	13782215	13782316	102	1E-51	1-102, 100%
atU6-4	At4g03375	4	-	1483121	1483020	102	1E-51	1-102, 100%
atU6-5	At4g33085	4	-	15965258	15965158	101	8E-37	1-101, 94%
atU6-6	At4g35225	4	+	16754836	16754931	96	1E-32	1-102, 93%
atU6-7	At2g15532	2	+	6784793	6784869	77	7E-25	4-80, 93%
atU6-8p	At1g52605	1	+	19596398	19596476	96	2E-19	4-99, 87%
atU6-9p	At1g53465	1	-	19960538	19960485	54	9E-09	21-74, 88%
atU6-10p	At3g45705	3	+	16792802	16792888	87	2E-06	1-46, 89%; 62-100, 89%
atU6-11p	At5g11085	5	-	3522167	3522143	25	9E-06	1-25, 100%
atU12*	At1g61275	1	+	22606785	22606960	176	1E-95	1-176, 100%	^†gi22293600
atU6atac*	At5g40395	5	-	16183534	16183413	122	1E-63	1-122, 100%	^†
atU6atac-2	At1g21395	1	-	7491489	7491378	112	5E-20	1-65, 95%; 81-110, 93%
atU4atac	At4g16065	4	+	9096374	9096532	159	N/A	N/A

Chromosomal locations were determined by conducting BLAST searches against the Arabidopsis genome (Release 5.0). *The gene used for query in the BLAST search; ^†atU12 and atU6atac sequences, which were experimentally identified [28]. Their sequences were compiled manually from the cited paper. The GenBank gi numbers for the chromosome sequences used are as follows: chromosome 1, 42592260; chromosome 2, 30698031; chromosome 3, 30698537; chromosome 4, 30698542; chromosome 5, 30698605.

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