Insertion Sequence Annotation (ISA) System - Browser

Insertion Sequences show diverse recent activities in Cyanobacteria and Archaea.
Fengfeng Zhou, Victor Olman and Ying Xu.
BMC Genomics 2008, 9:36.


It is worth mentioning that a single-copy IS element might also be active in the host genome. For example, a recently invaded IS element in a genome might not have enough time to accumulate more than one copy. But it's difficult to identify the complete structures of these IS elements. This work defines a recently active IS element as those with two other highly conserved copies in the same genome, and identifies the complete structures of the IS elements with recent activities by comparing the multiple copies of the same element.

Cyano_genomes
Anabaena variabilis ATCC 29413 Gloeobacter violaceus PCC 7421 Nostoc sp. PCC 7120
Prochlorococcus marinus str. MIT 9312 Prochlorococcus marinus str. MIT 9313 Prochlorococcus marinus str. NATL2A
Prochlorococcus marinus subsp. marinus str. CCMP1375 Prochlorococcus marinus subsp. pastoris str. CCMP1986 Synechococcus elongatus PCC 6301
Synechococcus elongatus PCC 7942 Synechococcus sp. CC9311 Synechococcus sp. CC9605
Synechococcus sp. CC9902 Synechococcus sp. JA-2-3B'a(2-13) Synechococcus sp. JA-3-3Ab
Synechococcus sp. WH 8102 Synechocystis sp. PCC 6803 Thermosynechococcus elongatus BP-1
Trichodesmium erythraeum IMS101

Archaea_genomes
Aeropyrum pernix K1 Archaeoglobus fulgidus DSM 4304 Haloarcula marismortui ATCC 43049
Halobacterium sp. NRC-1 Haloquadratum walsbyi DSM 16790 Methanocaldococcus jannaschii DSM 2661
Methanococcoides burtonii DSM 6242 Methanococcus maripaludis S2 Methanopyrus kandleri AV19
Methanosaeta thermophila PT Methanosarcina acetivorans C2A Methanosarcina barkeri str. Fusaro
Methanosarcina mazei Go1 Methanosphaera stadtmanae DSM 3091 Methanospirillum hungatei JF-1
Methanothermobacter thermautotrophicus str. Delta H Nanoarchaeum equitans Kin4-M Natronomonas pharaonis DSM 2160
Picrophilus torridus DSM 9790 Pyrobaculum aerophilum str. IM2 Pyrobaculum islandicum DSM 4184
Pyrococcus abyssi GE5 Pyrococcus furiosus DSM 3638 Pyrococcus horikoshii OT3
Sulfolobus acidocaldarius DSM 639 Sulfolobus solfataricus P2 Sulfolobus tokodaii str. 7
Thermococcus kodakarensis KOD1 Thermofilum pendens Hrk 5 Thermoplasma acidophilum DSM 1728
Thermoplasma volcanium GSS1

 

Sulfolobus_solfataricus
     
 

Distribution of recently active Insertion Sequence elements (raIS) and A+T contents (window size: 1,000 bp) of each chromosomes and plasmids:

raIS elements annotated with different colors based on the IS families and groups they belong to. The information could be found details .
1 A+T contents ranging in [0%, 100%]
2 Positions of annotated raIS
3 A+T content of the chromosome or plasmid
 


   NC_002754 Click to view the full size in a separate window.

List of recently active Insertion Sequence Annotations for Sulfolobus_solfataricus

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ID RefSeq ID Region Annotation Copy no Terminal Inverted Repeats Covering genes
0 NC_002754 1903177-1904272 (+) ISC1078 8 details 15898874, (all)
1 NC_002754 1711151-1712234 (-) ISC1078 8 details 15898692, (all)
2 NC_002754 1959047-1960124 (-) ISC1078 8 details 15898916, (all)
3 NC_002754 2734628-2735710 (+) ISC1078 8 details 15899703, 15899704, (all)
4 NC_002754 1088785-1089865 (-) ISC1078 8 details 15898106, 15898107, (all)
5 NC_002754 35309-36391 (+) ISC1078 8 details 15897010, 15897011, (all)
6 NC_002754 1224733-1225813 (+) ISC1078 8 details 15898223, 15898224, (all)
7 NC_002754 1584544-1585627 (-) ISC1078 8 details 15898550, 15898551, (all)
8 NC_002754 2174885-2176109 (-) ISC1225 7 details 15899141, (all)
9 NC_002754 2774099-2775323 (-) ISC1225 7 details 15899733, (all)
10 NC_002754 1362899-1364123 (-) ISC1225 7 details 15898336, (all)
11 NC_002754 1244062-1245286 (+) ISC1225 7 details 15898236, (all)
12 NC_002754 2641556-2642797 (+) ISC1225 7 details 15899600, 15899601, 15899602, (all)
13 NC_002754 1747365-1748550 (+) ISSto5 10 No TIRs detected. 15898727, (all)
14 NC_002754 1070464-1071652 (-) ISSto4 4 No TIRs detected. 15898085, 15898086, (all)
15 NC_002754 1561284-1563005 (+) ISSto4 3 No TIRs detected. 15898527, 15898528, (all)
16 NC_002754 2853436-2854876 (+) ISC1439B 6 details 15899810, (all)
17 NC_002754 2670130-2671568 (+) ISC1439B 6 details 15899635, (all)
18 NC_002754 1531155-1532599 (-) ISC1439B 6 details 15898492, (all)
19 NC_002754 1609993-1611430 (-) ISC1439B 6 details 15898576, (all)
20 NC_002754 1397547-1398764 (+) ISC1439B 6 No TIRs detected. 15898369, (all)
21 NC_002754 445742-447108 (+) ISC1359 9 details 15897439, (all)
22 NC_002754 1300527-1301887 (-) ISC1359 9 details 15898284, (all)
23 NC_002754 1607602-1608968 (+) ISC1359 9 details 15898574, (all)
24 NC_002754 1075227-1076593 (+) ISC1359 9 details 15898093, (all)
25 NC_002754 2884745-2886192 (-) ISC1359 8 details 15899839, (all)
26 NC_002754 1652431-1653667 (-) ISC1359 8 No TIRs detected. 15898624, (all)
27 NC_002754 1572131-1573493 (-) ISC1359 9 details 15898537, (all)
28 NC_002754 1041397-1042301 (-) ISC1048 10 details 15898053, 15898054, (all)
29 NC_002754 1071068-1072803 (+) ISC1048 10 details 15898087, (all)
30 NC_002754 1553088-1554141 (+) ISC1048 10 No TIRs detected. 15898516, 15898517, (all)
31 NC_002754 1625548-1626601 (-) ISC1048 10 No TIRs detected. 15898591, 15898592, (all)
32 NC_002754 2692912-2693982 (-) ISC1048 10 No TIRs detected. 15899655, 15899656, (all)
33 NC_002754 1560478-1561532 (-) ISC1048 10 No TIRs detected. 15898525, 15898526, (all)
34 NC_002754 1198203-1199258 (+) ISC1048 10 No TIRs detected. 15898202, 15898203, (all)
35 NC_002754 2675532-2676721 (+) ISC1048 10 details 15899641, 15899642, (all)
36 NC_002754 2673057-2674111 (-) ISC1048 10 No TIRs detected. 15899637, 15899638, (all)
37 NC_002754 1370581-1371818 (-) ISC1048 10 details 15898343, 15898344, 15898345, (all)
38 NC_002754 1173055-1174959 (+) ISC1904 9 No TIRs detected. 15898178, 15898179, (all)
39 NC_002754 1657998-1659882 (-) ISC1904 9 No TIRs detected. 15898630, 15898631, (all)
40 NC_002754 2918782-2920672 (+) ISC1904 9 No TIRs detected. 15899875, 15899876, (all)
41 NC_002754 1023917-1025818 (+) ISC1904 9 No TIRs detected. 15898035, 15898036, (all)
42 NC_002754 1055187-1057008 (-) ISC1904 8 No TIRs detected. 15898068, 15898069, (all)
43 NC_002754 1512757-1514596 (+) ISC1904 10 No TIRs detected. 15898477, 15898478, (all)
44 NC_002754 2689539-2691406 (+) ISC1904 9 No TIRs detected. 15899652, 15899653, (all)
45 NC_002754 2905555-2907449 (-) ISC1904 9 No TIRs detected. 15899859, 15899860, (all)
46 NC_002754 929410-931267 (-) ISC1904 10 No TIRs detected. 15897939, 15897940, (all)
47 NC_002754 670422-671862 (-) ISC1439A 25 details 15897690, (all)
48 NC_002754 1325405-1326843 (-) ISC1439A 25 details 15898299, (all)
49 NC_002754 1972474-1973912 (+) ISC1439A 25 details 15898928, (all)
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Disclaimer:
The dataset and this website is freely available to academic users. Commercial users should contact the CSBL lab.

Website created by Fengfeng Zhou © 2007

Last updated: Oct-26-2007.