 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Internal Transposable Elements | |
|
|
Internal Repeats | |
|
|
References | |
|
|
|
|
|
|
|
|
|
| Name: TnXc4.1 (Synonyms: Tn7211) |
|
| Family: Tn3 Group: Tn3 |
|
| Evidence of Transposition: no |
|
|
|
| Host |
 |
|
| Host Organism: | Xanthomonas oryzae pv. oryzicola strain CFBP7331 | Molecular Source: | chromosome |
| Place of Origin: | Niono, Mali | Date of Isolation: | 2015 |
| | Other Geographic Information: | strain MAI10 |
|
| Map |
|
| Terminal Inverted Repeats (IR) |
|
|
| | |
| IRL (Length: 38 bp) |  | GGGGTTCGGGGAGCAATGGAACAGGGAAGTCAGTTAAG |
| IRR (Length: 38 bp) | | GGGGTCCGGGGAGCAATGGAACAGGGAAGTCAGTTAAG |
|
| Sequence |
|
|
|
|
--------10 --------20 --------30 --------40 --------50 --------60 --------70 --------80 --------90 -------100
GGGGTTCGGG GAGCAATGGA ACAGGGAAGT CAGTTAAGCC TTCACCAGTG CCGGTCGGTG CCCTCCATGC GCGCGTCGCT CTCCGAGAAG CAGTGCCGGT 100
CGTCCGCACC GCTGGCGATG TCGGTCAGCA ATTCGTTCAC AGCTTCATCC AGTTCTTCGT CGGTGTCATA GGGCACCTTC AGCTCATATT CGCCGTTCGG 200
CCGTCGCGTG GCGTCGTATT GGTCGAGGTA AAAGCTCTCG ACGTGCTCAA TCGTGCGCTT CTTGCCGCGC ACGAACTTGC TGTTGTTCTC GATGCGCAGC 300
GTCAGCAGGA TGGTGGCGAC TTTCGGCGGG GCGTCATTGC CGCTTTCAAG GGCCGACATG CTTGATGGTT GCTGCTCCGT TTTCTTGTAC GGACCGATCT 400
CTACACCGCG ATGTCGCAGG TAGCTGTACA GCGTGCTCTT GGACAGGTGC AGCTTCTGTG CGATGGCGGC GACCGACAGT TTCCGCTCGC GGTACAGGGT 500
CTCTGCCGCC AGCGCCGTCG CTTCGGCCTG CGGCGACAGT CCTGTGGGTC GCCCGCCGAC CCGACCGCGT GCCCGCGCGG CCGTCAGCCC GGCCTGGGTG 600
CGTTCGCGGA TCAGTTCGCG CTCGAACTCG GCCAGCGTAG CGAACAGGTT GAACACAAAC CGCCCCTGGG CGCTGGTGGT GTCGATGGGA TCGTTCAGAC 700
TGAGGAGTCC AACCTTGCGC TCCATCAGGT TGCCGACCAG CTCGACCAGG TGCTTGAGCG AGCGCCCCAT GCGGTCGAGC TTCCAGATCA CCAGCACGTC 800
GCCGGCGCGC AACTGACCCA GTAGCTCATC GAGCGCCGGA CGTGCGGTCT TCGCGCCGCT CGCCACATCA TGATAGATGC GCTCGCAACC GGCCGCCTTG 900
AGAGCGTCCA CCTGCAAGGC CGGGTTCTGT TCTCGCGTGG AGACGCGAGC GTAGCCGATT TTCATCCGAA AATTCCGTTT TACTCGTTGA TTAAGACAAT 1000
ATCAAACTTT GATTATGCAA ACCACTTTTA TAGACTGCTT GTTGGCCTGC GGGCATGTCA TGCCCGTTGC TTCGTTGTAG TTCAGATAAA CGATCGTTTT 1100
ATCGAACCAT TGCGCATGTA ACGAGTAAAG TGTATAAACA CCTATGTGCA CAAACACTGT TCTGGAGGGC ATCATGAATA CCGTGCGTTG GAACATCGCC 1200
GTGTCGCCGG ACGTGGATCA GTCCGTGCGC ATGTTCATTG CCGCCCAAGG CGGCGGCCGC AAGGGCGACC TGTCGCGCTT CATTGAGGAG GCGGTGCGCG 1300
CCTATCTTTT TGAACGGGCG GTCGAGCAAG CCAAGGCCGC GACGGCAGGT ATGGGCGAGG CAGAATTGAA CGACCTCATC GACGAGGCGG TGCAGTGGGC 1400
GCGTGAGCAC TGATGCGGGT CGTCCTTGAC ACCAACGTGC TGCTGGCCGC GCTGATCTCG TCGCACAGCC CTCCCGACAT CATCTATCGC GCCTGGCTTG 1500
CTGGACGTTT TGACCTGGTG ACAGGGGCGG AACAGCTCGA CGAACTGCGC CGCGTGAGCC GTTACCCAAA GATCAGGGCC ATTTTGCCCG CACATCGCAT 1600
CGGCACCATG ATTAACAACA TACAGCGCGC CGTCGTGCTG AACACACTGC CGCCGCTGCC GAACGGCATC GATGCCAACG ATCCGAATGA TGCCTTCCTG 1700
CTGGCGATGT CACTGGCCGG TGAGGCTGAT TACCTCGTCA CTGGCGACCG TCGCGCGGGG CTGCTGCAAC GCGGCAGTAT TGGCCGCACG CGTATCGTCA 1800
CCCCGGCCAC CTTTTGCGCC GAGGCGCTTT GACGCCATGC CGGTCAGCTT CCTGTCCACC ACGCAACGGG AACGCTATGG CCGCTATCCA GAGGCGCTTT 1900
CCAGCGAGGA ACTGGGGCGT TACTTCCACC TGGACGACGA CGACCGCGAG TTGATCGCCA CCAAGCGGCG CGACAGCAGC CGCCTCGGTT ACGCACTGCA 2000
ACTGACGACG GCGCGGTTTC TCGGCACCTT TCTGGAAGAC CCTACCGCCG TGCCAAGCCC GGTGCTGCAT ACGCTGTCGT CGCAACTTGG CATCGCCGAC 2100
CCTTCCGATT GTGTTATCGA CTACCGGACG ACCCGGCAGC GCTGGCAGCA CACGACCGAG ATTCGCGCTC GCTACGGCTA CCGCGAATTC GCCGAACGTG 2200
GCGTGCAGTT CCGCCTTGGC CGCTGGCTGT GCGCGCTGTG CTGGACGGGC ACCGACCGTC CGAGTGCGCT GTTCGACTAC GCCAACGGTT GGCTGGTCGG 2300
CCACAAGGTA CTGCTGCCCG GCGTCACGGT GCTGGAACGC TTTATCGCCG ATATACGCTC GCGCATGGAG TCGCGCCTGT GGCGTTTGCT GGTGCGCGGC 2400
GTGACGGTCG CACAGCGGCA GCGTCTCGAA GACTTGCTCA AGCCTGCCGA AGGCAGCCGC CAGTCCTGGC TGGATCGGCT GCGCAAGGGG CCGGTGCGCG 2500
TCAGCGCTCC GGCGCTTGTG ATGGCCTTGC TGCGCATCGA AACCGTGCGG GATCTGGGCA TCAAACTGCC CGGCACCCAT GTGCCACCAA GCCGGATCGC 2600
GGCACTCGCC CGCTTTGCCA GTACGGTCAA GGTATCCGCC GTGGCCAGGC TGCCGGAGGC GCGGCGCATC GCCACGCTGG TCGCCTTCGT GCATTGCCTG 2700
GAAGCCAGCG CTCAGGACGA TGCCCTTGAT GTGCTCGACC TGCTGCTGCG CGAACTGTTC ACCAAGGCTG AGAAGGAAGA CCGCAAGTTC AGGCAGCGCT 2800
CCCTCAAAGA TCTGGATCGG GCTGCCTCGA CGCTGGCTGA GGCGTGCCGG ATGCTGCTCG ATCCCGGTTT GCCGGACGGC GAACTACGCG AGCGTGTCTA 2900
TGCCGCCATC GGCCGCGATG AACTGGCCCA GGCGCTCAAC GAAGTTCGCG GCCTGGTGCG CCCGCCCAAC GATGTGTTCT ACACCGAACT GGAAGCCAGG 3000
AAGGCCACCG TCTCGCGCTT CCTGCCGACA TTGCTGCGCG TCATCCGCTT CGACGCCAAT CCAGCCGCGC AGCCTTTGGC GCAGGCGTTG AAATGGCTGC 3100
ATGAGAAGCC CGACCATGAT CCGCCCACGG CCATCGTCGG CAAAGCGTGG CAACGCCATG TCGTGCAGGA GGACGGCCGG ATCAATGCCA CGGCCTATTC 3200
TTTCTGCGCG CTCGACAAGC TGCGCAGCGC GATCCGCCGC CGCGACATGT TCATCAGCCC GAGCTGGCGT TACGCCGATC CGCGTGCCGG ACTGCTGGCA 3300
GGAGCCGAGT GGGAGGCCGC ACGGCCCATC GTCTGCCGCT CGCTGAGCCT GACGGCGCAA CCGGAAGCAA CGCTGGCGAC ACTCACGCGC GAACTGGACA 3400
AAACCTACCG GCGCGTCGCG GCTCGCCTGC CCGAGAACGA CGCGGTGCGC TTCGAGACGG TCGGCGACAA GACCGAACTG GTGCTCAGCC CCTTGGAAGC 3500
GTTGGAAGAA CCAACTTCGC TGATCGCGCT GCGCAACGAA ATCAAGGCGC GCATGCCGCG CGTCGATCTG CCGGAAATCC TGCTGGAAGT CGCCGCGCGT 3600
ACTGGCTGCA TGGATGCCTT CACGCACCTG ACCGAGCGCA CGGCGCGTGC GGCCGACCTG ACCACCAGCT TGTGCGCGGT GCTGATGGCT GAAGCCTGCA 3700
ACACCGGCCC GGAACCGCTG GTGCGGCAGG ACACCCCGGC GCTCAAACGC GACCGGCTGA TGTGGGTCGA TCAGAACTAT GTGCGTGATG ACACGCTGGT 3800
TGCCTGCAAC GCCGTGCTGG TGGCGGCGCA AAACCGCATC GCATTGGCGC GCACCTGGGG CGGCGGTGAC GTGGCCTCCG CCGACGGCAT GCGCTTTGTG 3900
GTGCCGGTAC GGACCATCCA CGCCGCGCCG AACCCGAAAT ACTTCAATCG CGGGCGTGGC GTCACCTGGT ACAACCTGCT GTCCGATCAA TGTACTGGGC 4000
TGAACACGAT CACCGTGCCC GGCACGCTGC GCGACAGCCT GGTCTTGCTG GCGGTCGTGC TGGAGCAGCA GACCGAGTTG CAGCCGACAC AGATCATGAC 4100
CGACACCGGT GCGTACAGCG ATTTGGTGTT TGGCCTGTTC AGGCTCTCCA ACTACCGCTT CTGCCCGCGC CTGGCCGATG TCGGCGGCAC ACGCTTCTGG 4200
CGTGTCGATC CCGACGCTGA CTATGGCGAG CTCAACGCGC TCGCCCGGCA GCGTGTGAAC CTCGACCGCA TCACGCCGCA TTGGGATGAC GTGCTGCGCC 4300
TGGTCGGCTC GCTCAAGCTC GGCCTGGTAC CGGCGATGAG CATCATGCGC ACCTTGCAGG TCGATGAACG GCCGACCAGC CTAGCGCAGG CCATCGCCGA 4400
AATCGGTCGC ATCGACAAGA CCATCCACAC GCTGAACTTC ATCGACGACG AGGCCCGCCG CCGCGCCACG CTTCTGCAAT TGAACCTCGG CGAAGGCCGC 4500
CACAGTTTGG CGCGCGAGGT TTTTCACGGC AAGCGCGGCG AACTGTTCCA GCGCTACCGC GAAGGACAGG AAGACCAGTT GAGCGCGCTC GGCCTGGTTG 4600
TGAACATGAT CGTGCTGTGG AACACGCTGT ACATGGACGC GGTACTGGCG CAGTTGCGCA GCGAGGGCTA CCCGATCCGC CCCGAAGACG AGGCGCGGTT 4700
GTCGGCGTTC GTCCACGAGC ACATCAATAT GCTCGGACGC TACTCGTTCT CGGTGCCTGA AGCAGTCGCG CGTGGCGAAC TGAGACCGTT GACCAAACAA 4800
AATGAACCTT AAAAACCATG GAAATTCACT ATGCAACAGA TGACGCAACA ATCCTTGAAC GATGCCGAAC TTGATCGGTT GGGCGACTTT CTCGAAGGAG 4900
TCGGCGCACC TGCAATGAAT CTCGAAATGC TCGATGGGTT CTTTGCCGCA CTCATTTGCG GCCCTGAAAC GGTATTGCCC AGCGAATACT TGCCACAGGT 5000
ACTTGGGGAA GGCCATTGCT TCGACAGCAA TGACCAAGCC GCGGAGATTC TTGGCTTGGT CATGCGGCAT TGGAACACGA TTGCATCAGA ACTGTTCCGC 5100
ACTCTGGAGA AAGACGATGT CTACCTCCCC GTGCTGCTCG AAGATGCGGA TGGGGCCGTA CACGGCAATG ACTGGGCACG TGGTTTCATG CGCGGCATTC 5200
AATTACGGCC CAATAGTTGG CAAGAGCTGA TCGGCAGCGA CGAGTTTGGC GGGCCAATGC TGCCAATTAT GATTTTGACC TATGAACATG ATCCTGATCC 5300
CGCCATGCGC CCGCCAGAGA TTGCGCCGGA CAAACGCGAT GAGTTGCTTC AGTCCCTGAT TGCCGGACTT ACACACATCT ATCGCTACTT CGCGTCACAT 5400
CGCCAATTGG CAACCCACGT GCCTTTACGC AGGCAAGGCC CTAAAGTTGG GAGAAACGAT CAATGTCCAT GTGGCAGTGG GCGGAAGTAC AAGCATTGCT 5500
GTGCTACCGG CGGGCCAATA TTTCATTGAT ATCGGCTTAA CTGACTTCCC TGTTCCATTG CTCCCCGGAC CCC
|
|
|
|
| Recombination Sites |
|
|
| Name |
Coordinates |
Gene |
Sequence |
| res |
972-1107 |
136 |
ATTCCGTTTT ACTCGTTGAT TAAGACAATA TCAAACTTTG ATTATGCAAA CCACTTTTAT
AGACTGCTTG TTGGCCTGCG GGCATGTCAT GCCCGTTGCT TCGTTGTAGT TCAGATAAAC
GATCGTTTTA TCGAAC |
| res_site_III |
972-1000 |
29 |
ATTCCGTTTT ACTCGTTGAT TAAGACAAT |
| res_site_II |
1004-1036 |
33 |
AAACTTTGAT TATGCAAACC ACTTTTATAG ACT |
| res_site_I |
1079-1111 |
33 |
AGTTCAGATA AACGATCGTT TTATCGAACC ATT |
|
| ORFs |
|
|
| Gene Name |
Associated TE |
Coordinates |
Class |
Sub Class |
Orientation |
| tnpR |
TnXc4.1 |
42-965 |
Accessory Gene |
Resolvase |
- |
| RHH_6 |
TnXc4.1 |
1174-1413 |
Passenger Gene |
Antitoxin |
+ |
| PIN_3 |
TnXc4.1 |
1413-1832 |
Passenger Gene |
Toxin |
+ |
| tnpA |
TnXc4.1 |
1837-4812 |
Transposase |
|
+ |
| secA |
TnXc4.1 |
4831-5529 |
Passenger Gene |
Plant Pathogenicity |
+ |
| Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
| tnpR |
TnpR |
TnXc4.1 |
924 |
42-965 |
- |
| Class: | Accessory Gene |
| Sub Class: | Resolvase |
| Transpoase Chemistry: | Serine |
| Sequence Family: | Serine Site-Specific Recombinase |
Protein Sequence:
|
MKIGYARVST REQNPALQVD ALKAAGCERI YHDVASGAKT ARPALDELLG QLRAGDVLVI WKLDRMGRSL KHLVELVGNL MERKVGLLSL NDPIDTTSAQ
GRFVFNLFAT LAEFERELIR ERTQAGLTAA RARGRVGGRP TGLSPQAEAT ALAAETLYRE RKLSVAAIAQ KLHLSKSTLY SYLRHRGVEI GPYKKTEQQP
SSMSALESGN DAPPKVATIL LTLRIENNSK FVRGKKRTIE HVESFYLDQY DATRRPNGEY ELKVPYDTDE ELDEAVNELL TDIASGADDR HCFSESDARM
EGTDRHW
|
| Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
| RHH_6 |
RHH_6 |
TnXc4.1 |
240 |
1174-1413 |
+ |
| Class: | Passenger Gene |
| Sub Class: | Antitoxin |
| Sequence Family: | RHH_6 (Pfam:PF16762) |
Protein Sequence:
|
MNTVRWNIAV SPDVDQSVRM FIAAQGGGRK GDLSRFIEEA VRAYLFERAV EQAKAATAGM GEAELNDLID EAVQWAREH
|
| Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
| PIN_3 |
PIN_3 |
TnXc4.1 |
420 |
1413-1832 |
+ |
| Class: | Passenger Gene |
| Sub Class: | Toxin |
| Target: | single stranded RNA |
| Sequence Family: | PIN_3 (Pfam:PF13470) |
| Comment: | tRNA(fMet)-specific endonuclease |
Protein Sequence:
|
MRVVLDTNVL LAALISSHSP PDIIYRAWLA GRFDLVTGAE QLDELRRVSR YPKIRAILPA HRIGTMINNI QRAVVLNTLP PLPNGIDAND PNDAFLLAMS
LAGEADYLVT GDRRAGLLQR GSIGRTRIVT PATFCAEAL
|
| Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
| tnpA |
TnpA |
TnXc4.1 |
2976 |
1837-4812 |
+ |
| Class: | Transposase |
| Transpoase Chemistry: | DDE |
Protein Sequence:
|
MPVSFLSTTQ RERYGRYPEA LSSEELGRYF HLDDDDRELI ATKRRDSSRL GYALQLTTAR FLGTFLEDPT AVPSPVLHTL SSQLGIADPS DCVIDYRTTR
QRWQHTTEIR ARYGYREFAE RGVQFRLGRW LCALCWTGTD RPSALFDYAN GWLVGHKVLL PGVTVLERFI ADIRSRMESR LWRLLVRGVT VAQRQRLEDL
LKPAEGSRQS WLDRLRKGPV RVSAPALVMA LLRIETVRDL GIKLPGTHVP PSRIAALARF ASTVKVSAVA RLPEARRIAT LVAFVHCLEA SAQDDALDVL
DLLLRELFTK AEKEDRKFRQ RSLKDLDRAA STLAEACRML LDPGLPDGEL RERVYAAIGR DELAQALNEV RGLVRPPNDV FYTELEARKA TVSRFLPTLL
RVIRFDANPA AQPLAQALKW LHEKPDHDPP TAIVGKAWQR HVVQEDGRIN ATAYSFCALD KLRSAIRRRD MFISPSWRYA DPRAGLLAGA EWEAARPIVC
RSLSLTAQPE ATLATLTREL DKTYRRVAAR LPENDAVRFE TVGDKTELVL SPLEALEEPT SLIALRNEIK ARMPRVDLPE ILLEVAARTG CMDAFTHLTE
RTARAADLTT SLCAVLMAEA CNTGPEPLVR QDTPALKRDR LMWVDQNYVR DDTLVACNAV LVAAQNRIAL ARTWGGGDVA SADGMRFVVP VRTIHAAPNP
KYFNRGRGVT WYNLLSDQCT GLNTITVPGT LRDSLVLLAV VLEQQTELQP TQIMTDTGAY SDLVFGLFRL SNYRFCPRLA DVGGTRFWRV DPDADYGELN
ALARQRVNLD RITPHWDDVL RLVGSLKLGL VPAMSIMRTL QVDERPTSLA QAIAEIGRID KTIHTLNFID DEARRRATLL QLNLGEGRHS LAREVFHGKR
GELFQRYREG QEDQLSALGL VVNMIVLWNT LYMDAVLAQL RSEGYPIRPE DEARLSAFVH EHINMLGRYS FSVPEAVARG ELRPLTKQNE P
|
| Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
| secA |
SecA |
TnXc4.1 |
699 |
4831-5529 |
+ |
| Class: | Passenger Gene |
| Sub Class: | Plant Pathogenicity |
| Comment: | contains 2 target sites for ISXac1 insertions |
Protein Sequence:
|
MQQMTQQSLN DAELDRLGDF LEGVGAPAMN LEMLDGFFAA LICGPETVLP SEYLPQVLGE GHCFDSNDQA AEILGLVMRH WNTIASELFR TLEKDDVYLP
VLLEDADGAV HGNDWARGFM RGIQLRPNSW QELIGSDEFG GPMLPIMILT YEHDPDPAMR PPEIAPDKRD ELLQSLIAGL THIYRYFASH RQLATHVPLR
RQGPKVGRND QCPCGSGRKY KHCCATGGPI FH
|
|
|
