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

 

Methanospirillum_hungatei_JF-1
     
 

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_007796 Click to view the full size in a separate window.

List of recently active Insertion Sequence Annotations for Methanospirillum_hungatei_JF-1

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ID RefSeq ID Region Annotation Copy no Terminal Inverted Repeats Covering genes
0 NC_007796 1351425-1353146 (-) ISMhu5 5 No TIRs detected. 88602477, (all)
1 NC_007796 2983644-2985360 (-) ISMhu5 5 No TIRs detected. 88603947, (all)
2 NC_007796 3048177-3050425 (-) ISMhu5 5 details 88604016, (all)
3 NC_007796 3390003-3391696 (-) ISMhu5 5 No TIRs detected. 88604344, (all)
4 NC_007796 3438308-3440085 (-) ISMhu5 5 details  
5 NC_007796 3388368-3390117 (+) ISMac20 7 details 88604343, (all)
6 NC_007796 164323-166066 (-) ISMac20 7 details 88601462, (all)
7 NC_007796 462992-464733 (-) ISMac20 7 details 88601721, (all)
8 NC_007796 1338615-1340356 (+) ISMac20 7 details 88602465, (all)
9 NC_007796 3064339-3066082 (-) ISMac20 7 details 88604027, (all)
10 NC_007796 91392-93154 (-) ISMac20 18 No TIRs detected. 88601391, (all)
11 NC_007796 203677-205439 (-) ISMac20 18 No TIRs detected. 88601498, (all)
12 NC_007796 297983-299777 (-) ISMac20 18 details 88601581, (all)
13 NC_007796 394799-396561 (-) ISMac20 18 No TIRs detected. 88601661, (all)
14 NC_007796 426421-428073 (-) ISMac20 18 details 88601693, (all)
15 NC_007796 510922-512684 (-) ISMac20 18 No TIRs detected. 88601742, (all)
16 NC_007796 2916691-2918451 (+) ISMac20 18 No TIRs detected. 88603881, (all)
17 NC_007796 806973-808735 (-) ISMac20 18 No TIRs detected. 88601991, (all)
18 NC_007796 2283247-2285009 (+) ISMac20 18 No TIRs detected. 88603275, (all)
19 NC_007796 1766881-1768641 (+) ISMac20 18 No TIRs detected. 88602808, (all)
20 NC_007796 1972667-1974428 (-) ISMac20 18 No TIRs detected. 88603011, (all)
21 NC_007796 725728-727534 (+) ISMac20 18 details 88601925, (all)
22 NC_007796 674784-676545 (+) ISMac20 18 No TIRs detected. 88601890, (all)
23 NC_007796 559132-560894 (+) ISMac20 18 No TIRs detected. 88601787, (all)
24 NC_007796 457115-458877 (+) ISMac20 18 No TIRs detected. 88601718, (all)
25 NC_007796 3399809-3402222 (-) ISMac20 18 details 88604352, (all)
26 NC_007796 13307-15067 (+) ISMac20 18 No TIRs detected. 88601331, (all)
27 NC_007796 302838-304501 (-) ISMac20 18 No TIRs detected. 88601585, (all)
28 NC_007796 2412667-2414410 (+) ISMac20 7 details  
29 NC_007796 304391-306192 (-) ISMhu4 6 details 88601586, (all)
30 NC_007796 642682-644483 (-) ISMhu4 6 details 88601856, (all)
31 NC_007796 2818139-2819940 (+) ISMhu4 6 details 88603779, (all)
32 NC_007796 765529-767330 (-) ISMhu4 6 details 88601959, (all)
33 NC_007796 1206143-1207944 (+) ISMhu4 6 details 88602361, (all)
34 NC_007796 3419196-3420997 (-) ISMhu4 6 details 88604360, (all)
35 NC_007796 251523-253661 (+) ISMhu6 5 details 88601539, (all)
36 NC_007796 824030-825677 (-) ISMhu6 5 No TIRs detected. 88602013, (all)
37 NC_007796 2154612-2156263 (-) ISMhu6 5 No TIRs detected. 88603161, (all)
38 NC_007796 3094999-3096783 (-) ISMhu6 5 details 88604054, (all)
39 NC_007796 3435263-3437048 (+) ISMhu6 5 details  
40 NC_007796 1394371-1395486 (-) ISPlu15 5 No TIRs detected. 88602510, (all)
41 NC_007796 1396629-1397723 (-) ISPlu15 6 No TIRs detected. 88602512, (all)
42 NC_007796 1397768-1398867 (-) ISPlu15 6 No TIRs detected. 88602513, (all)
43 NC_007796 266442-267529 (+) ISMhu9 7 details 88601553, (all)
44 NC_007796 2570854-2571951 (+) ISMhu9 7 details 88603559, (all)
45 NC_007796 3396916-3397999 (-) ISMhu9 7 details 88604350, (all)
46 NC_007796 2415493-2416577 (+) ISMhu9 7 details 88603385, (all)
47 NC_007796 552710-553807 (+) ISMhu9 7 details 88601781, (all)
48 NC_007796 1750349-1751433 (-) ISMhu9 7 details 88602795, (all)
49 NC_007796 2092013-2093097 (+) ISMhu9 7 details 88603112, 88603113, (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.