--------------------------------------------------------------------------------------------------------- Human constitutive and alternative splice junctions that failed to make gapped alignment on mouse draft genome sequence: 39 (= 35 constitutive and 4 alternative entries in total) --------------------------------------------------------------------------------------------------------- I. Showing good gapped alignment but to a chr region different from the one with which other related splice junctions match (1 constitutive entry). >IDB61794-26809-27415-splicePos-69 7 62 16.13000001-14000000 729779 729834 RF 56 100.00 [const] >IDB61794-26809-27415-splicePos-69 77 132 16.13000001-14000000 728547 728602 RF 56 100.00 [const] Other related splice junctions match to 15.78000001-79000000. A detailed blast of this sequence shows a weak 5p match (1-70 with 15.78000001-79000000 at 505327-505258 at 80% pid) with the chr region to which other related splice junctions match. II. Showing only 5p or 3p match (25 = 21 constitutive and 4 alternative entries) >>IDB60047-12237-13509-splicePos-38 [const] 17.34000001-35000000 38-108 618712-618772 FF 99% >>IDB60208-2589-2702-splicePos-43 [const] 11.6000001-7000000 41-110 302303-302372 FF 100% >>IDB60543-1994-6073-splicePos-70 [const] 9.60000001-61000000 1-70 211261-211330 FF 100% >>IDB60543-6241-8037-splicePos-70 [const] 9.60000001-61000000 68-139 217133-217193 FF 100% The above two are involved in a conserved alternating exon event. >>IDB61367-256-52578-splicePos-56 [const] Un.18000001-19000000 57-126 440746-440677 RF 100% 13.44000001-45000000 1-56 544809-544754 RF 100% No related splice junctions. >>IDB61558-107864-110519-splicePos-66 [const] 10.20000001-21000000 70-125 22065-22120 FF 100% >>IDB61588-2417-3538-splicePos-61 [alt] 17.47000001-48000000 61-131 454516-454586 FF 100% >>IDB61673-5959-10008-splicePos-70 [const] 13.79000001-80000000 1-70 933291-933208 RF 100% Un.132000001-133000000 71-140 511864-511933 FF 100% No related splice junctions. >>IDB61784-16071-20741-splicePos-70 [const] 15.85000001-86000000 1-70 113741-113810 FF 100% >>IDB62747-726-1571-splicePos-70 [const] X.18000001-19000000 71-140 61295-61364 FF 88% No related splice junctions. >>IDB62829-989-1158-splicePos-69 [const] 9.108000001-109000000 78-133 403369-403424 FF 100% >>IDB62868-104-206-splicePos-70 [const] 10.80000001-81000000 7-62 632255-632310 FF 100% No related splice junctions. >>IDB62998-17024-21847-splicePos-68 [const] 17.23000001-24000000 66-138 804390-804318 RF 100% No related splice junctions. >>IDB63128-142-1461-splicePos-69 [const] 19.6000001-7000000 69-139 813441-813511 FF 92% No related splice junctions. >>IDB63246-2539-18824-splicePos-69 [alt] 2.168000001-169000000 69-139 601984-601914 RF 100% >>IDB63299-3747-4223-splicePos-70 [const] 15.80000001-81000000 2-70 806587-806519 RF 88% >>IDB63319-472-996-splicePos-69 [const] 14.66000001-67000000 77-132 772969-773024 FF 100% >>IDB64065-1208-1635-splicePos-70 [const] 6.7000001-8000000 1-72 304003-304074 FF 98% 115-132 304687-304704 FF 100% intron lengths - human , mouse == 426, 569 >>IDB64065-1681-2213-splicePos-48 [alt] 6.7000001-8000000 48-73 304687-304712 FF 100% The above two splice junctions are involved in a conserved cassette exon event. >>IDB64121-9235-11161-splicePos-70 [alt] 6.39000001-40000000 69-140 342171-342100 RF 100% >>IDB64217-18711-22474-splicePos-70 [const] 6.4000001-5000000 14-71 989620-989676 RF 100% >>IDB64473-1111-29687-splicePos-70 [const] 19.32000001-33000000 71-140 560587-560656 FF 100% No related splice junctions. >>IDB65089-6453-9724-splicePos-70 [const] 12.107000001-108000000 70-140 214700-214631 RF 100% >>IDB66052-12112-12824-splicePos-70 [const] 15.83000001-84000000 1-72 926731-926660 RF 100% >>IDB66052-12912-15087-splicePos-70 [const] 15.83000001-84000000 68-140 923864-923792 RF 100% The above two are involved in a conserved cassette exon event. III. Showing as a long-contiguous match (6 constitutive entries). >>IDB60886-1764-1853-splicePos-70 [const] (Related introns exist and is a clear case of intron-loss). >>IDB60886-2387-2478-splicePos-70 [const] (Related introns exist and is a clear case of intron-loss). >>IDB64313-6758-6840-splicePos-69 [const] (Related introns present in the data set and it looks like a clear intron-loss case). >>IDB64487-119-465-splicePos-70 [const] >>IDB64487-552-792-splicePos-70 [const] (These two introns map to the same chr region; no related splice junctions that match in this region. The human gene maps to a region on 6.8500000. and these two constructs show contigs to this. Though we can call these two cases as intron-loss, we are not sure. There is no ) >>IDB61248-3804-3884-splicePos-70 [const] (No related splice junctions in the data set. The human gene maps to a region 17.33000001-34000000. This construct maps to this region as a long contig. ) None of these above is involved in conserved alt splice event. IV. Showing a weak hit or no hit or difficult to resolve (7 constitutive entries). >>IDB60580-408-538-splicePos-70 [const] no related intron >>IDB60580-611-1205-splicePos-70 [const] no related intron >>IDB62868-314-395-splicePos-69 [const] no related intron >>IDB63141-6019-7861-splicePos-70 [const] Related intron exists; but it is difficult to resolve the matches - positional compatability etc >>IDB62690-413-940-splicePos-70 [const] no related intron >>IDB62983-7828-8011-splicePos-70 [const] no related intron >>IDB64762-40-1830-splicePos-70 [const] no related intron 7 entries. None of the above is involved in conserved alt splice event. ============================================================================================