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

 

Pyrococcus_furiosus
     
 

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_003413 Click to view the full size in a separate window.

List of recently active Insertion Sequence Annotations for Pyrococcus_furiosus

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ID RefSeq ID Region Annotation Copy no Terminal Inverted Repeats Covering genes
0 NC_003413 552573-553289 (-) ISPfu5 15 details 18976908, (all)
1 NC_003413 870596-871383 (-) ISPfu5 15 details 18977270, (all)
2 NC_003413 977592-978398 (-) ISPfu5 4 details 18977395, (all)
3 NC_003413 771356-772145 (+) ISPfu5 4 details 18977157, (all)
4 NC_003413 12565-13345 (-) ISPfu1 8 details 18976385, (all)
5 NC_003413 1629432-1630212 (+) ISPfu1 8 details 18978124, (all)
6 NC_003413 1612358-1613129 (+) ISPfu1 8 No TIRs detected. 18978108, (all)
7 NC_003413 415413-416193 (-) ISPfu1 8 details 18976780, (all)
8 NC_003413 1161575-1162357 (+) ISPfu1 8 details 18977599, (all)
9 NC_003413 909865-910645 (+) ISPfu1 8 details 18977318, (all)
10 NC_003413 1284309-1285089 (-) ISPfu1 8 details 18977738, (all)
11 NC_003413 579454-580236 (+) ISPfu1 8 details 18976934, (all)
12 NC_003413 558356-559288 (+) ISPfu3 5 details 33359484, 33359485, (all)
13 NC_003413 785081-786008 (+) ISPfu3 5 details 33359512, 18977173, (all)
14 NC_003413 772731-773662 (+) ISPfu3 5 details 33359510, 33359508, (all)
15 NC_003413 627228-628160 (-) ISPfu3 5 details 33359490, 33359491, (all)
16 NC_003413 1182145-1183078 (-) ISPfu3 5 details 33359553, 33359554, (all)
17 NC_003413 72919-73761 (-) ISPfu2 11 details 18976441, (all)
18 NC_003413 361447-362296 (-) ISPfu2 11 details 18976720, (all)
19 NC_003413 463528-464330 (-) ISPfu2 15 details 18976819, (all)
20 NC_003413 797060-797905 (-) ISPfu2 11 details 18977189, (all)
21 NC_003413 767500-768249 (+) ISPfu2 15 details 18977152, (all)
22 NC_003413 752275-753078 (+) ISPfu2 15 details 18977128, (all)
23 NC_003413 397584-398451 (+) ISPfu2 11 details 18976761, (all)
24 NC_003413 284988-285834 (+) ISPfu2 11 details 18976646, (all)
25 NC_003413 1720204-1721093 (-) ISPfu2 11 details 18978236, (all)
26 NC_003413 1877670-1878516 (-) ISPfu2 11 details 18978407, (all)
27 NC_003413 1141976-1142814 (-) ISPfu2 11 details 18977572, (all)
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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.