Table 2 Alternative start codons for CDS with internal TSS or long 5′ UTRs ≥ 150 nt, as predicted by Prodigal
From: Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315
TSS position | Strand | Gene | Annotated gene position | Alternative gene start | Annotated start codon | Alternative start codon | Alternative gene is |
|---|---|---|---|---|---|---|---|
Replicon 1 | |||||||
108753 | + | BCAL0088 | 108758..109138 | 108842 | GTG | ATG | shorter |
175808 | + | BCAL0151 | 175965..177107 | 175872 | ATG | ATG | longer |
196936 | + | BCAL0175 | 196857..197147 | 196965 | ATG | ATG | shorter |
317647 | + | BCAL0289 | 317651..322474 | 317771 | GTG | ATG | shorter |
566857 | - | BCAL0515 | Complement (565664..566551) | 566617 | ATG | ATG | longer |
700318 | + | BCAL0646 | 700302..701309 | 700341 | GTG | ATG | shorter |
787134 | + | BCAL0722 | 787317..788582 | 787293 | GTG | GTG | longer |
937522 | + | BCAL0865 | 937677..938504 | 937566 | TTG | ATG | longer |
999283 | - | BCAL0916 | Complement (998559..999290) | 999245 | ATG | ATG | shorter |
1041114 | - | BCAL0952 | Complement (1040227..1040955) | 1041075 | ATG | ATG | longer |
1147555 | + | BCAL1059 | 1147734..1148927 | 1147695 | ATG | ATG | longer |
1161150 | - | BCAL1069 | Complement (1159161..1160903) | 1160996 | ATG | ATG | longer |
1207883 | - | BCAL1102 | Complement (1207594..1207914) | 1207848 | GTG | ATG | shorter |
1390938 | - | BCAL1277 | Complement (1388805..1390997) | 1390868 | ATG | ATG | shorter |
1463359 | - | BCAL1335 | Complement (1462753 ..1463376) | 1463334 | ATG | ATG | shorter |
1892553 | + | BCAL1715 | 1892545..1893150 | 1892578 | GTG | GTG | shorter |
1933621 | + | BCAL1753 | 1933609..1934565 | 1933672 | ATG | ATG | shorter |
2041280 | - | BCAL1849 | Complement (2040670..2041326) | 2041221 | ATG | ATG | shorter |
2067405 | - | BCAL1871 | Complement (2065350..2067203) | 2067380 | ATG | ATG | longer |
2120545 | + | BCAL1921 | 2120767..2121222 | 2120662 | GTG | ATG | longer |
2136329 | + | BCAL1937 | 2136797..2138446 | 2136644 | ATG | ATG | longer |
2656999 | - | BCAL2401 | Complement (2656576..2657001) | 2656953 | GTG | ATG | shorter |
2822661 | - | BCAL2559 | Complement (2822212..2822745) | 2822661 | TTG | ATG | shorter |
3011653 | + | BCAL2740 | 3011646..3012689 | 3011679 | ATG | ATG | shorter |
3037852 | - | BCAL2766 | Complement (3037324..3037656) | 3037734 | TTG | ATG | longer |
3093624 | - | BCAL2818 | Complement (3092132..3093673) | 3093598 | GTG | ATG | shorter |
3094006 | + | BCAL2819 | 3093965..3095413 | 3094037 | GTG | ATG | shorter |
3122838 | - | BCAL2841 | Complement (3121514..3122860) | 3122710 | GTG | ATG | shorter |
3257864 | - | BCAL2974 | Complement (3257551..3257931) | 3257820 | ATG | ATG | shorter |
3266225 | + | BCAL2981 | 3266173..3268080 | 3266245 | ATG | ATG | shorter |
3461898 | + | BCAL3168 | 3461889..3462575 | 3461937 | ATG | ATG | shorter |
3533713 | - | BCAL3229 | Complement (3531274..3533205) | 3533499 | GTG | ATG | longer |
3584399 | - | BCAL3275 | Complement (3583374..3584396) | ATG | TTG | shorter | |
3619212 | - | BCAL3302 | Complement (3616817..3619048) | 3619129 | GTG | ATG | longer |
3666930 | + | BCAL3349 | 3666923..3667387 | 3666965 | ATG | ATG | shorter |
3721637 | - | BCAL3395 | Complement (3719319..3721676) | 3721619 | ATG | ATG | shorter |
Replicon 2 | |||||||
14979 | + | BCAM0014 | 15152..15757 | 15110 | ATG | ATG | longer |
184425 | - | BCAM0158 | Complement (182630..184141) | 184234 | ATG | ATG | longer |
570490 | + | BCAM0516 | 570437..570919 | 570545 | TTG | ATG | shorter |
713692 | + | BCAM0645 | 713658..715211 | 713733 | ATG | ATG | shorter |
878428 | + | BCAM0795 | 878392..878856 | 878428 | TTG | ATG | shorter |
904562 | + | BCAM0820 | 904770..905861 | 904728 | ATG | ATG | longer |
1009355 | + | BCAM0918 | 1009947..1011812 | 1009395 | GTG | ATG | longer |
1203868 | + | BCAM1112 | 1204104..1206368 | 1204068 | ATG | ATG | longer |
1405396 | + | BCAM1280 | 1405387..1406880 | 1405435 | ATG | ATG | shorter |
1419414 | + | BCAM1290 | 1419396..1420382 | 1419438 | TTG | ATG | shorter |
1967577 | + | BCAM1756 | 1967535..1969922 | 1967598 | GTG | ATG | shorter |
2032438 | + | BCAM1814 | 2032438..2034045 | 2032462 | ATG | ATG | shorter |
2291422 | - | BCAM2058 | Complement (2290470..2291126) | 2291303 | TTG | ATG | longer |
2291441 | + | BCAM2059 | 2291632..2292495 | 2291587 | ATG | ATG | longer |
2300468 | + | BCAM2066 | 2300462..2301877 | 2300489 | ATG | ATG | shorter |
2471730 | - | BCAM2210 | Complement (2471467..2471733) | 2471658 | ATG | ATG | shorter |
2613643 | + | BCAM2327 | 2613607..2614722 | 2613697 | ATG | ATG | shorter |
2703044 | + | BCAM2401 | 2703049..2703798 | 2703109 | ATG | ATG | shorter |
2703867 | + | BCAM2402 | 2703876..2704169 | 2703900 | GTG | ATG | shorter |
3026129 | + | BCAM2679 | 3026111..3026374 | 3026153 | TTG | ATG | shorter |
3058373 | - | BCAM2703 | Complement (3057460..3058437) | 3058353 | GTG | ATG | shorter |
3077665 | - | BCAM2719 | Complement (3077106..3077669) | 3077606 | ATG | ATG | shorter |
3133147 | + | BCAM2769 | 3133305..3134042 | 3133281 | GTG | ATG | longer |
Replicon 3 | |||||||
69880 | - | BCAS0060 | Complement (68555..69688) | 69709 | ATG | ATG | longer |
80842 | - | BCAS0070 | Complement (79501..80850) | 80742 | TTG | ATG | shorter |
769919 | + | BCAS0706 | 770234..771562 | 770120 | TTG | ATG | longer |
Plasmid | |||||||
2363 | + | pBCA003 | 2363..3220 | 2546 | ATG | ATG | shorter |
79981 | - | pBCA080 | Complement (79541..79750) | 79891 | ATG | ATG | longer |