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

 

Trichodesmium_erythraeum_IMS101
     
 

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_008312 Click to view the full size in a separate window.

List of recently active Insertion Sequence Annotations for Trichodesmium_erythraeum_IMS101

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ID RefSeq ID Region Annotation Copy no Terminal Inverted Repeats Covering genes
0 NC_008312 7022101-7023050 (-) ISRso1 3 No TIRs detected. 113477951, 113477952, (all)
1 NC_008312 6103907-6104941 (-) ISTcSa 14 details 113477387, (all)
2 NC_008312 1492-2337 (-) ISTcSa 15 No TIRs detected. 113473944, (all)
3 NC_008312 5613890-5614885 (+) ISTcSa 9 No TIRs detected. 113477130, 113477131, (all)
4 NC_008312 7443218-7444174 (+) ISTcSa 15 No TIRs detected. 113478200, (all)
5 NC_008312 2124058-2124730 (-) ISTcSa 12 details 113475107, (all)
6 NC_008312 4849313-4850155 (+) ISTcSa 8 No TIRs detected. 113476714, (all)
7 NC_008312 7459567-7460486 (-) ISTcSa 11 No TIRs detected.  
8 NC_008312 6252809-6253718 (-) ISTcSa 8 No TIRs detected.  
9 NC_008312 1941754-1942710 (-) ISTcSa 6 No TIRs detected. 113475011, (all)
10 NC_008312 1363961-1364856 (-) ISTcSa 12 No TIRs detected. 113474680, (all)
11 NC_008312 5557620-5558529 (-) ISTcSa 14 No TIRs detected.  
12 NC_008312 5060064-5061002 (+) ISTcSa 16 No TIRs detected.  
13 NC_008312 6043529-6044479 (-) ISTcSa 6 No TIRs detected. 113477355, (all)
14 NC_008312 1458416-1459351 (+) IS630-Spn1 9 No TIRs detected. 113474734, (all)
15 NC_008312 42974-43687 (+) IS630-Spn1 11 details  
16 NC_008312 924118-925069 (-) IS630-Spn1 7 No TIRs detected. 113474431, (all)
17 NC_008312 2106285-2107151 (-) IS630-Spn1 6 No TIRs detected.  
18 NC_008312 7506626-7507557 (+) IS630-Spn1 4 details 113478256, 113478257, (all)
19 NC_008312 7446046-7447166 (+) IS630-Spn1 4 No TIRs detected. 113478204, 113478205, (all)
20 NC_008312 7018228-7019453 (-) IS630-Spn1 4 details 113477944, 113477945, (all)
21 NC_008312 4746011-4746952 (-) IS630-Spn1 4 details 113476642, (all)
22 NC_008312 5549039-5549976 (+) IS630-Spn1 14 No TIRs detected.  
23 NC_008312 2610066-2611094 (-) IS1515 4 details 113475393, (all)
24 NC_008312 4723630-4724542 (-) ISRm2011-2 6 details 113476621, (all)
25 NC_008312 7453661-7454698 (-) ISRm2011-2 7 details  
26 NC_008312 7503145-7504181 (-) ISRm10 7 details  
27 NC_008312 4676555-4677588 (+) ISRm10 7 details  
28 NC_008312 4751268-4752301 (+) ISRm10 7 details 113476646, (all)
29 NC_008312 4739239-4740272 (-) ISRm10 7 details  
30 NC_008312 6566510-6567546 (+) ISRm10 7 details  
31 NC_008312 4744980-4746013 (+) ISRm10 7 details 113476640, 113476641, (all)
32 NC_008312 7495969-7497556 (+) IS8402 8 details 113478245, 113478246, (all)
33 NC_008312 7432935-7434707 (-) IS8402 3 details  
34 NC_008312 7511351-7513072 (+) IS8402 8 details 113478260, 113478261, (all)
35 NC_008312 7009370-7010593 (-) IS8402 6 No TIRs detected. 113477937, 113477938, (all)
36 NC_008312 143301-144924 (+) IS8402 8 details  
37 NC_008312 1952708-1954312 (-) IS8402 9 details  
38 NC_008312 1883869-1885493 (-) IS8402 7 details 113474978, (all)
39 NC_008312 2241470-2243100 (+) IS8402 8 details 113475178, 113475179, (all)
40 NC_008312 2511561-2513093 (+) IS8402 8 details 113475333, 113475334, (all)
41 NC_008312 90120-91720 (-) IS8402 3 details 113473986, (all)
42 NC_008312 4634922-4635790 (+) ISJp4 4 No TIRs detected.  
43 NC_008312 5541540-5542443 (-) ISJp4 3 No TIRs detected.  
44 NC_008312 1639893-1640711 (+) ISJp4 3 No TIRs detected.  
45 NC_008312 2316878-2317851 (+) ISMae1 10 details 113475221, (all)
46 NC_008312 1703849-1704889 (+) ISVa2 4 details  
47 NC_008312 3143534-3144840 (-) ISVa2 3 details 113475675, 113475676, (all)
48 NC_008312 7470401-7471514 (-) ISVa2 11 details 113478227, 113478228, (all)
49 NC_008312 4496446-4497255 (+) ISMae3 4 details 113476470, (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.