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

 

Anabaena_variabilis_ATCC_29413
     
 

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_007413 Click to view the full size in a separate window.
   NC_007410 Click to view the full size in a separate window.
   NC_007411 Click to view the full size in a separate window.
   NC_007412 Click to view the full size in a separate window.

List of recently active Insertion Sequence Annotations for Anabaena_variabilis_ATCC_29413

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ID RefSeq ID Region Annotation Copy no Terminal Inverted Repeats Covering genes
0 NC_007413 3082234-3083132 (-) IS5Sa 10 details 75908700, 75908701, (all)
1 NC_007413 1782648-1783546 (+) IS5Sa 10 details 75907662, 75907663, (all)
2 NC_007410 86811-87710 (+) IS5Sa 10 details 75812357, (all)
3 NC_007412 221956-223504 (+) ISGka4 9 details 75812845, (all)
4 NC_007410 320825-322371 (+) ISGka4 9 details 75812581, (all)
5 NC_007410 281624-283170 (+) ISGka4 9 details 75812532, (all)
6 NC_007410 139802-141348 (+) ISGka4 9 details 75812406, (all)
7 NC_007413 5719237-5720783 (+) ISGka4 9 details 75910762, (all)
8 NC_007413 5140139-5141685 (+) ISGka4 9 details 75910324, (all)
9 NC_007413 1702724-1704270 (-) ISGka4 9 details 75907604, (all)
10 NC_007413 3692987-3694535 (+) ISGka4 9 details 75909186, (all)
11 NC_007413 2590796-2592342 (+) ISGka4 9 details 75908319, (all)
12 NC_007413 172129-173361 (-) ISC1048 13 details 75906354, (all)
13 NC_007413 595719-596888 (-) ISC1048 13 No TIRs detected. 75906695, (all)
14 NC_007413 3961815-3963053 (-) ISC1048 13 details 75909396, (all)
15 NC_007413 1982986-1984155 (+) ISC1048 13 No TIRs detected. 75907827, (all)
16 NC_007413 1485858-1487027 (+) ISC1048 13 No TIRs detected. 75907428, (all)
17 NC_007413 1442033-1443202 (+) ISC1048 13 No TIRs detected. 75907396, (all)
18 NC_007413 5769476-5770645 (-) ISC1048 13 No TIRs detected. 75910809, (all)
19 NC_007413 2697761-2698930 (-) ISC1048 13 No TIRs detected. 75908400, (all)
20 NC_007413 3156726-3157895 (-) ISC1048 13 No TIRs detected. 75908770, (all)
21 NC_007410 50626-52234 (-) ISC1048 13 details 75812322, (all)
22 NC_007410 249239-250408 (+) ISC1048 13 No TIRs detected. 75812503, (all)
23 NC_007410 174103-175272 (-) ISC1048 13 No TIRs detected. 75812439, (all)
24 NC_007410 283813-285441 (-) ISC1048 13 details 75812535, (all)
25 NC_007413 1680414-1681312 (-) ISMac15 10 details 75907586, 75907587, (all)
26 NC_007413 4141140-4142038 (+) ISMac15 10 details 75909523, 75909524, (all)
27 NC_007413 1228891-1229789 (+) ISMac15 10 details 75907241, 75907242, (all)
28 NC_007413 981565-982463 (+) ISMac15 10 details 75907023, 75907024, (all)
29 NC_007413 4735332-4736230 (+) ISMac15 10 details 75910004, 75910005, (all)
30 NC_007413 3269123-3270021 (+) ISMac15 10 details 75908854, 75908855, (all)
31 NC_007412 107761-108659 (-) ISMac15 10 details 75812740, 75812741, (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.