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

 

Methanosarcina_mazei
     
 

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_003901 Click to view the full size in a separate window.

List of recently active Insertion Sequence Annotations for Methanosarcina_mazei

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ID RefSeq ID Region Annotation Copy no Terminal Inverted Repeats Covering genes
0 NC_003901 2600089-2601757 (+) ISMac20 3 details 21228294, (all)
1 NC_003901 1556507-1558178 (+) ISMac20 3 No TIRs detected. 21227410, (all)
2 NC_003901 2802185-2803854 (+) ISMac20 3 No TIRs detected. 21228447, (all)
3 NC_003901 3213425-3215222 (+) ISMma14 15 details 21228791, 21228792, (all)
4 NC_003901 886044-887653 (-) ISMma14 15 details 21226841, 21226842, (all)
5 NC_003901 2899257-2900055 (+) ISMma14 15 details 21228531, 21228532, (all)
6 NC_003901 2183178-2183976 (+) ISMma14 15 details 21227933, 21227934, (all)
7 NC_003901 1935836-1936634 (+) ISMma14 15 details 21227725, 21227726, (all)
8 NC_003901 1495448-1496872 (+) ISMma14 15 details 21227361, 21227362, (all)
9 NC_003901 3078387-3079185 (-) ISMma14 15 details 21228690, 21228691, (all)
10 NC_003901 3842844-3843642 (-) ISMma14 15 details 21229262, 21229263, (all)
11 NC_003901 3944998-3945796 (-) ISMma14 15 details 21229347, 21229348, (all)
12 NC_003901 461962-462687 (-) ISMma21 9 No TIRs detected. 21226457, (all)
13 NC_003901 3358911-3359698 (+) ISMma21 9 No TIRs detected. 21228901, (all)
14 NC_003901 2912650-2913437 (+) ISMma21 9 No TIRs detected. 21228541, (all)
15 NC_003901 2757213-2758000 (+) ISMma21 9 No TIRs detected. 21228406, (all)
16 NC_003901 2237557-2238282 (-) ISMma21 9 No TIRs detected. 21227986, (all)
17 NC_003901 3488866-3489589 (-) ISMma21 9 No TIRs detected. 21229008, (all)
18 NC_003901 2110641-2111428 (+) ISMma21 9 No TIRs detected. 21227871, (all)
19 NC_003901 3533679-3534404 (-) ISMma21 9 No TIRs detected. 21229038, (all)
20 NC_003901 3106891-3107722 (+) ISMma21 9 No TIRs detected.  
21 NC_003901 2568648-2570105 (+) ISMac19 6 details 21228269, (all)
22 NC_003901 1423632-1425173 (-) ISMma11 6 No TIRs detected. 21227300, (all)
23 NC_003901 3161599-3163140 (-) ISMma11 6 No TIRs detected. 21228749, (all)
24 NC_003901 2170012-2171554 (+) ISMma11 6 No TIRs detected. 21227921, (all)
25 NC_003901 1039888-1041433 (-) ISMma11 6 No TIRs detected. 21226983, (all)
26 NC_003901 1873516-1875062 (+) ISMma11 6 No TIRs detected. 21227675, (all)
27 NC_003901 3849885-3851524 (+) ISMma20 3 No TIRs detected. 21229269, (all)
28 NC_003901 920599-922193 (-) ISMma20 3 No TIRs detected. 21226873, (all)
29 NC_003901 856614-858249 (+) ISMma20 3 No TIRs detected. 21226813, (all)
30 NC_003901 343246-344745 (+) ISMma1 5 details 21226360, (all)
31 NC_003901 2989912-2991408 (+) ISMma1 5 details 21228609, (all)
32 NC_003901 2992132-2993628 (-) ISMma1 5 details 21228611, (all)
33 NC_003901 3966786-3968283 (-) ISMma1 5 details 21229367, (all)
34 NC_003901 3687507-3689006 (-) ISMma1 5 details 21229149, (all)
35 NC_003901 508762-510297 (-) ISMma13 15 details 21226498, 21226499, (all)
36 NC_003901 2134250-2135787 (+) ISMma13 15 details 21227888, 21227889, (all)
37 NC_003901 2909167-2910700 (-) ISMma13 15 details 21228538, 21228539, (all)
38 NC_003901 3484980-3486244 (+) ISMac18 5 No TIRs detected. 21229003, 21229004, (all)
39 NC_003901 3487352-3488565 (-) ISMac18 5 details 21229006, 21229007, (all)
40 NC_003901 4071688-4072951 (+) ISMac18 5 No TIRs detected. 21229445, 21229446, (all)
41 NC_003901 1219115-1220380 (+) ISMac18 5 No TIRs detected. 21227145, 21227146, (all)
42 NC_003901 3925395-3926685 (-) ISMac18 5 details 21229330, 21229331, (all)
43 NC_003901 2295427-2296952 (-) ISMba7 8 No TIRs detected. 21228032, (all)
44 NC_003901 3068654-3070178 (-) ISMba7 8 No TIRs detected. 21228681, (all)
45 NC_003901 650262-651787 (+) ISMba7 8 No TIRs detected. 21226624, (all)
46 NC_003901 69327-70852 (-) ISMba7 8 No TIRs detected. 21226154, 21226155, (all)
47 NC_003901 2016392-2017917 (-) ISMba7 8 No TIRs detected. 21227781, (all)
48 NC_003901 3402749-3404274 (-) ISMba7 8 No TIRs detected. 21228939, (all)
49 NC_003901 124361-125908 (+) ISMba7 8 No TIRs detected. 21226198, (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.