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

 

Thermosynechococcus_elongatus
     
 

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_004113 Click to view the full size in a separate window.

List of recently active Insertion Sequence Annotations for Thermosynechococcus_elongatus

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ID RefSeq ID Region Annotation Copy no Terminal Inverted Repeats Covering genes
0 NC_004113 2320396-2322077 (-) IS609 10 No TIRs detected. 22299780, 22299781, (all)
1 NC_004113 2411782-2413446 (-) IS609 10 No TIRs detected. 22299864, 22299865, (all)
2 NC_004113 1447267-1448947 (-) IS609 10 No TIRs detected. 22298922, 22298923, (all)
3 NC_004113 397187-398867 (-) IS609 10 No TIRs detected. 22297943, 22297944, (all)
4 NC_004113 241107-242781 (-) IS609 10 No TIRs detected. 22297800, 22297801, (all)
5 NC_004113 2511994-2513675 (-) IS609 10 No TIRs detected. 22299941, 22299942, (all)
6 NC_004113 1211289-1212964 (-) IS606 10 No TIRs detected. 22298718, 22298719, (all)
7 NC_004113 2113575-2115255 (-) IS606 10 No TIRs detected. 22299574, 22299575, (all)
8 NC_004113 1554697-1555911 (+) IS1136A 20 No TIRs detected. 22299032, (all)
9 NC_004113 706540-707815 (-) IS1136A 20 No TIRs detected. 22298229, (all)
10 NC_004113 611383-612658 (-) IS1136A 20 No TIRs detected. 22298147, (all)
11 NC_004113 403529-404817 (+) IS1136A 20 details 22297949, (all)
12 NC_004113 185710-186984 (-) IS1136A 20 No TIRs detected. 22297749, (all)
13 NC_004113 202448-203662 (-) IS1136A 20 No TIRs detected. 22297766, (all)
14 NC_004113 1200410-1201624 (-) IS1136A 20 No TIRs detected. 22298705, (all)
15 NC_004113 1159947-1161393 (+) IS1136A 20 details 22298670, (all)
16 NC_004113 2091779-2092993 (-) IS1136A 20 No TIRs detected. 22299547, (all)
17 NC_004113 2266271-2267485 (+) IS1136A 20 No TIRs detected. 22299725, (all)
18 NC_004113 2263208-2264528 (+) IS1136A 20 No TIRs detected. 22299722, (all)
19 NC_004113 1183828-1185042 (-) IS1136A 20 No TIRs detected. 22298695, (all)
20 NC_004113 1440751-1441995 (-) IS1136A 20 details 22298917, (all)
21 NC_004113 2545420-2546634 (-) IS1136A 20 No TIRs detected. 22299974, (all)
22 NC_004113 2486230-2487550 (+) IS1136A 20 No TIRs detected. 22299919, (all)
23 NC_004113 507903-509812 (-) IS1136A 20 details 22298055, (all)
24 NC_004113 114398-115674 (+) IS1136A 20 No TIRs detected. 22297678, (all)
25 NC_004113 257467-258787 (+) IS1136A 20 No TIRs detected. 22297817, (all)
26 NC_004113 2283085-2284361 (+) IS1136A 20 No TIRs detected. 22299742, (all)
27 NC_004113 987233-988508 (-) IS1136A 20 No TIRs detected. 22298507, (all)
28 NC_004113 1143574-1144879 (+) IS1136A 13 No TIRs detected. 22298657, (all)
29 NC_004113 138787-140091 (-) IS1136A 13 No TIRs detected. 22297699, 22297700, (all)
30 NC_004113 1024566-1025414 (+) ISNeu3 8 No TIRs detected. 22298542, 22298543, (all)
31 NC_004113 467758-469422 (-) ISMba17 10 No TIRs detected. 22298011, 22298012, 22298013, (all)
32 NC_004113 386552-388219 (-) ISMba17 10 No TIRs detected. 22297930, 22297931, 22297932, (all)
33 NC_004113 381498-382600 (-) IS481 14 No TIRs detected. 22297925, (all)
34 NC_004113 563291-564393 (-) IS481 14 No TIRs detected. 22298109, (all)
35 NC_004113 742523-743625 (-) IS481 14 No TIRs detected. 22298263, (all)
36 NC_004113 1642407-1643509 (+) IS481 14 No TIRs detected. 22299123, (all)
37 NC_004113 951829-952931 (-) IS481 14 No TIRs detected. 22298472, (all)
38 NC_004113 1412060-1413165 (+) IS481 14 No TIRs detected. 22298896, (all)
39 NC_004113 1043114-1044216 (+) IS481 14 No TIRs detected. 22298561, (all)
40 NC_004113 1551621-1552723 (-) IS481 14 No TIRs detected. 22299029, (all)
41 NC_004113 1709434-1710535 (-) IS481 14 No TIRs detected. 22299178, (all)
42 NC_004113 2020020-2021121 (-) IS481 14 No TIRs detected. 22299472, (all)
43 NC_004113 2220507-2221612 (-) IS481 14 No TIRs detected. 22299680, (all)
44 NC_004113 197147-198249 (+) IS481 14 No TIRs detected. 22297759, (all)
45 NC_004113 471282-472384 (-) IS481 14 No TIRs detected. 22298018, (all)
46 NC_004113 1145377-1146479 (+) IS481 14 No TIRs detected. 22298659, (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.