Table S3. List of mapped common carp transcripts overlapping intronic, intergenic and non-zebrafish ESTs/cDNA regions

zebrafish
chromosome		 chromosome position zebrafish annotation common carp clusterID
or GenBank ID
2 36192769:36192991 intergenic DW722755
3 29265136:29265597 intergenic DW723876
20 30066449:30066578 intergenic DW724082
13 31275715:31276095 intergenic DW724248
22 33277352:33277792 intergenic DW721291
19 53710552:53710738 intergenic AU240324
23 55343449:55344008 intergenic DW723242
9 15621335:15621611 intergenic CA968995
19 31778487:31779030 intergenic DW721686
2 38731507:38731992 intergenic DW721395
7 25403156:25403676 intergenic CA969817
21 32618084:32623723 intergenic CA969518
1 37227841:37227994 intergenic CA967977
12 24542528:24542959 Prediction CA969665
10 21114165:21114473 Prediction CA968054
12 29941450:29941945 Prediction DW724156
9 17989309:17989842 Prediction CA965048
6 24239704:24239829 Prediction DW722097
7 55560525:55561302 Prediction CF661460
13 13669323:13669523 Prediction CA965770
16 29315215:29315857 Prediction 448
10 29354711:29355210 Prediction 34
23 42394671:42394824 Prediction CA969538
13 5197985:5214289 Prediction DW721345
16 35772064:35772586 Prediction CF662901
11 32902954:32903414 Prediction CA968791
12 28042268:28042592 Prediction CA964575
24 16631125:16631347 Prediction DW720892
18 13002698:13002860 Prediction DW722920
6 19417741:19418114 Prediction DW724184
11 32201832:32202183 Prediction CA969769
10 29336396:29337021 Prediction DW721433
6 1992175:1992418 Prediction DW724287
22 35266569:35266906 Prediction CA968932
10 6293156:6293304 Prediction DW722763
19 32344740:32345200 zebrafish gene: intron 1195
6 31010225:31010593 zebrafish gene: intron CF661933
6 13791526:13792001 zebrafish gene: intron CA969336
17 13420948:13421073 zebrafish gene: intron AU183368
24 7925119:7925523 zebrafish gene: intron CA969876
14 25694308:25695110 zebrafish gene: intron CF661031
15 31640728:31641094 zebrafish gene: intron CF661577
20 22840761:22841412 zebrafish gene: intron CA966816
22 22358872:22359160 zebrafish gene: intron DW719961
3 7550027:7550488 zebrafish gene: intron DW722928
2 39860289:39860895 zebrafish gene: intron DW722848
1 27503602:27506336 zebrafish gene: intron DW721285
18 13386453:13387080 zebrafish gene: intron CA969955
5 49943918:49944122 zebrafish gene: intron CA968239
10 11444113:11444354 zebrafish gene: intron DW721565
6 26339782:26342584 zebrafish gene: intron CF661379
23 45882331:45905810 zebrafish gene: intron CF662690
17 39292068:39292176 zebrafish gene: intron DW721679
7 34463759:34463866 zebrafish gene: intron CA970303
19 51447464:51447803 zebrafish gene: intron DW722551
13 10360841:10361419 zebrafish gene: intron DW720871
15 7327499:7327693 zebrafish gene: intron CA965670
8 36962988:36963064 zebrafish gene: intron CA969194
3 29602523:29603191 non-zebrafish: intron 409
14 64794372:64797309 non-zebrafish: intron 112
5 42105454:42106003 non-zebrafish: intron 788
12 22982576:22983128 non-zebrafish: intron CA967413
18 28048179:28048888 non-zebrafish: intron DW723349
24 6197416:6197891 non-zebrafish: intron 297
12 26466017:26466106 non-zebrafish: intron CA966466
13 5431809:5432219 non-zebrafish: intron DW724065
1 50713559:50713935 non-zebrafish: intron CA969200
12 18980749:18981292 non-zebrafish: intron CA969572
14 19057890:19058036 non-zebrafish: intron CF661917
1 11787546:11788033 non-zebrafish: exon 908
5 56497549:56498229 non-zebrafish: exon 1077
15 40385331:40385910 non-zebrafish: exon DW722641
21 29856966:29857823 non-zebrafish: exon CF660862
21 16142328:16147144 non-zebrafish: exon CA970399
19 26365278:26365433 non-zebrafish: exon CA964595
21 37053439:37056429 non-zebrafish: exon CF660617
17 25571503:25571599 non-zebrafish: exon DW719915
24 30295615:30309748 non-zebrafish: exon CF662750
2 7554455:7565675 non-zebrafish: exon CA964681
1 41248343:41248651 non-zebrafish: exon CA966405
20 12702354:12706940 non-zebrafish: exon CF662562
15 8213686:8217842 non-zebrafish: exon DW723943
16 51276175:51277771 non-zebrafish: exon CA969090
21 22827572:22828629 non-zebrafish: exon CA966451
22 35925053:35929545 non-zebrafish: exon CA966071
21 27009198:27021859 non-zebrafish: exon C88398
2 40395902:40406055 non-zebrafish: exon DW721296
16 20578438:20580986 non-zebrafish: exon CA964537
12 4483688:4489749 non-zebrafish: exon CA969772
22 28696378:28697081 non-zebrafish: exon CF661329
18 46228840:46239594 non-zebrafish: exon DW723921