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Internal Transposable Elements | |
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Internal Repeats | |
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| Name: TnXc4 (Synonyms: Tn7210) |
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| Family: Tn3 Group: Tn3 |
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| Evidence of Transposition: no |
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| Host |
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| Host Organism: | Xanthomonas citri subsp. citri strain AW16 | Molecular Source: | plasmid pXCAW58 |
| Place of Origin: | Florida, U.S.A. | Date of Isolation: | 2015 |
| | Other Geographic Information: | citrus infected tissue citrus spp. 2005 |
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| Map |
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| Terminal Inverted Repeats (IR) |
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| IRL (Length: 38 bp) |  | GGGGTTCGGGGAGCAATGGAACAGGGAAGTCAGTTAAG |
| IRR (Length: 38 bp) | | GGGGTTCGGGGAGCAATGGAACAGGGAAGTCAGTTAAG |
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| Sequence |
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--------10 --------20 --------30 --------40 --------50 --------60 --------70 --------80 --------90 -------100
GGGGTTCGGG GAGCAATGGA ACAGGGAAGT CAGTTAAGCC TTCACCAGTG CCGGTCTGTA CCTTCCATGC GGGCGTGGCT CTCTGAGAAA CAGTGGCGGT 100
CATCCGCACC GCAGGCGATG TCGGTTAGCA AATCGTTCAC GGCTTCATCC AGCTCTTCAT CCGTGTCATA GGGCACCTTC AGTTCATATT CCCCGTTCGG 200
CCGCCGCGTG GCATCGTATT GGGCAAGATC AAAAAACTCG ACATGCTCGA TCGAGCGCTT CTTTCCGCGC ACGAACTTGC TATTGTTCTC GATGCGCAAG 300
GTCAGCAGGA TGGTGGCGAC CTTCGGCTGG TCAGCGTTTC CGCTCTCGAC CACGGAGACG TTTATCGGCG ACTGCGCCGA TTGTTTGTAC GGGCCGATCT 400
CTACGCCGCG ATGCCGCAGG TAGCTGTACA GCGTGCTCTT GGACAAGTGC AGTTTCTGCG CAATGGCAGC GACCGACAGC TTGCGCTCGC GGTATAGGGT 500
CTCGGCCGCC AGCGCTGTCG CTTCGGCCTG CGGCGACAGG CCCTTGGGTC GCCCACCGAC CCTGCCACGC GCCCGCGCGG CCGTCAGCCC GGCCTGGGTG 600
CGCTCGCGAA TTAGCTCGCG CTCGAACTCG GCCAGCGTGG CGAACAGGTT GAACACGAAC CGCCCTTGGG CGCTGGTGGT GTCGATGGGG TCATTCAGGC 700
TGAGCAGCCC GACCTTGCGT TCCATCAGGC TACCCACCAA CTCAACCAGG TGCTTGAGTG AGCGTCCCAT GCGGTCGAGT TTCCAGATCA CCAGCACGTC 800
GCCGCCACGC AACTGGCCCA GCAGTTCATC GAGCGCTGGG CGCGCGGTCT TCGCGCCGCT CGCAACGTCC TGATAAATGC GCTCGCAGCC GGCCGCCTTG 900
AGGGAGTCCA CCTGCAAGGC TGGGTTCTGT TCGCGCGTGG ATACGCGCGC ATAGCCGATT TTCATCGTAA TATTTTGCTT TACTCGTTAA TTTTTAATAA 1000
TATCAAACTT TGATTGTACA AACCACTATT ACAGACTGCT TGTTGGCTTA CGGACACCTC GCGCCGATCG CCCCATCAGA GTTCATAAAA ACGATCGTTT 1100
TATTGAACCG TTGCAAAAAA AAACCGCTTA AAGAGTGTAT AAACACCGAT GTGCATAAAC TCTGATTGGA GAGAGCTTCA TGAATACCGT GCGCTGGAAC 1200
ATCGCCGTAT CGCCGGACGT GGATCAGTCC GTCCGCATGT TCATCGCCGC GCAAGGCGGC GGTCGCAAGG GCGACCTGTC ACGCTTCATC GAGGATGCGG 1300
TGCGCGCCTA CCTCTTCGAG CGGGCTGTGG AACAAGCCAA AGCCGCTACG GTGGGTATGG GTGAGACAGA ACTGAACGAC CTCATTGATG AGGCGGTGCA 1400
ATGGGCGCGT GAGCATTAAT GCGGGTCGTC CTCGACACCA ACGTATTGCT GGCCGCGCTG ATCTCGTCGC ACAGCCCACC CGACATCATC TATCGCGGTT 1500
GGCTTGCAGC ACGCTTTGAA CTGGTGACAG GGACGGCGCA GCTTGATGAA CTGCGCCGCG TGAGCCGTTA CCCGAAGATC AAGGCAATCC TGCCCGCGCA 1600
TCGCGTCGGC ACGATGATCA ACAACATGCA GCGCGCCGTT GTGCTGCATG TATTGCCGCC TCTGCCTGAT CGCATCGAGG TCAATGATCC GAACGATGCG 1700
TTCCTGCTGG CGATGGCACT GGCCAGCGAG GCCGATTACC TTGTGACTGG CGACCGCCGC GCTGGGCTGC TGCAACGCGG TAGCATTGGC CGCACGCGCA 1800
TCGTCACGCC AGTCACCTTC TGCGCCGAGG CGCTTTGACG CCATGCCGGT CAGCTTCCTG TCCACCACAC AACGGGAACG CTACGGCCGC TATCCAGACA 1900
CGCTTTCCAG CGAAGAGCTG GCGCGCTATT TCCACCTGGA CGACGATGAC CGCGAGTGGA TCGCCACCAA GCGACGCGAC AGCAGTCGCC TCGGTTATGC 2000
GCTGCAACTG ACCACGGCGC GGTTTCTCGG CACCTTTCTG GAAGACCCTA CCGCCGTGCC AAGCCCGGTG CTGCATACGC TGTCGTCGCA ACTTGGCATC 2100
GCCGACCCTT CCGATTGCGT CATTGACTAC CGGACAACTC GGCAGCGCTG GCAGCACACG AGCGAGATTC GCACCCGCTA TGGCTACCGC GAGTTCACGG 2200
GTACCGGCGT CCAGTTCCGC CTTGGCCGCT GGTTGTGCGC GTTGTGCTGG ACGGGCACTG ACCGCCCGAG TGCGCTGTTC GACTACGCCA ACGGCTGGCT 2300
GGTCGGCCAC AAGGTGCTGC TACCCGGCGT CACCTTGCTG GAGCGCTTTA TCGCCGAGAT ACGCTCACGC ATGGAGTCGC GTCTGTGGCG ACTACTGGTG 2400
CACGGCGTGA CACCCGAGCA GCGACAACGC CTCGATGACT TGCTCAAGCT TGTCGAAGGC AGCCGGCAGT CTTGGCTGGA TCGATTGCGC AAGGGGCCGG 2500
TACGCGTCAG CGCTCCGGCG CTCGTTGCGG CCTTGCTGCG AATCGAAACC GTGCGTGGCT TGGGCATTAA GCTGCCAGGC ACCCATGTGC CGCCGAGCCG 2600
CATCGCAGCG CTGGCCCGCT TCGCCAGTAC TGCCAAGGTA TCCGCCGTGG CTCGATTGCC GGAGGTGCGA CGCATCGCCA CGCTAGTGGC CTTCGTCCAC 2700
TGCCTGGAAG CCAGCGCGCA AGACGATGCC ATCGATGTGC TCGACCTGCT GCTGCGCGAG CTGTTCACCA AGGCTGAGAA AGAAGATCGT AAGGTCAGGC 2800
AGCGCTCCCT CAAGGATCTG GATCGGGCCG CCTCGACGCT GGCCGAGGCA TGCCGGATGC TGCTCGATCC GGCCCTGCCG GACGGCGAAC TGCGCGAGCG 2900
CGTCTATGCC GCCATCGGCC ACGATGAACT GGCCCAGGCG CTCAATGAAG TGCGCGGTCT GGTGCGCCCG CCCAACGATG TGTTCTACAC CGAACTGGAA 3000
GCCCGCAAGG CCACCGTCTC GCGCTTCCTG CCGGCGTTGC TGCGCGTCAT CCGCTTTGAC GCCAATCCGG CCGCGCAACC TTTGGCGCAG GCGTTGCAAT 3100
GGCTGCATGA GAAGCCCGAC CATGATCCGC CCACGGCCAT CGTCGGCAAG GCGTGGCAAC GCCATGTCGT TCAGGATGAT GGCCGCATCA ATGCCACAGC 3200
CTATTCGTTC TGCGCGCTCG ACAAGCTGCG CAGTGCGATT CGCCGCCGCG ACGTGTTCAT CAGCCCGAGT TGGCGCTACG CCGATCCACG CGCCGGGCTG 3300
CTGGCCGGAG CTGAATGGGA GGCCTCGCGG CCTATCGTCT GCCGCTCGCT GAGCCTGTCG GCGCAGCCCG AGGCCACGTT GTCCGAGCTG ACGCGCGAGC 3400
TGGACGAAAC CTACCGCCGC GTCGCCGCGC GCCTGCCCCA GAACGACGCA GTGCGCTTCG AGAACGTTGG CGACAAGACG GAACTGGTGC TCAGTCCGCT 3500
TGAAGCATTG GAGGAGCCGC CTTCATTGAT CGCGCTGCGC AACGAAATCA AGGCGCGCAT GCCGCGCGTC GATCTTCCGG AAATCCTGCT GGAAGTCGCC 3600
GGTCGTACTG GCTGCATGGA AGCGTTCACG CACCTGACTG AACGCACCGC GCGCGCGGCC GACCTGACCA CCAGCCTGTG CGCGGTGCTG ATGGCCGAAG 3700
CCTGCAACAC CGGCCCGGAA CCACTGGTGC GGCCAGACAC TCCGGCGCTC AAGCGCGACC GGCTGATGTG GGTCGATCAG AACTATGTGC GTGACGACAC 3800
GCTGACAGCC TGCAATGCCG TGCTGGTGGC CGCGCAAAGT CGTATCGCAC TGGCGCGAAC CTGGGGAGGT GGCGATGTGG CTTCGGCCGA CGGCATGCGA 3900
TTCGTGGTGC CGGTGCGCAC GATCCACGCT GGACCGAACC CAAAGTATTT CAATCGCGGG CGCGGCGTCA CTTGGTACAA CTTGCTTTCC GATCAGCGCA 4000
CCGGACTGAA CGCGATCACT GTGCCTGGCA CGCTGCGCGA CAGTTTGATT TTGCTAGCGG TTGTGCTGGA GCAGCAAACG GAGTTGCAGC CGACCCAGAT 4100
CATGACCGAC ACCGGCGCGT ACAGCGATTT GGTGTTCGGT TTGTTCCGCC TCTCCAACTA TCGATTCTGC CCGCGCCTGG CCGATGTTGG CGGTACCCGT 4200
TTCTGGCGCG TCGATCCCGA CGCCGACTAT GGCGACCTCA ATGCGCTGGC CCGGCAGCGT GTGAATCTCG ACCGTATCAC CCCGCATTGG GATGATGTGC 4300
TGCGTCTGGT CGGCTCGCTC AAGCTCGGTC TGGTTCCGGC GATGGGCATC ATGCGCACCT TACAGGTCGA TGAACGGCCC ACCAGCCTGG CGCAAGCCAT 4400
CGCCGAAATC GGCCGTATCG ACAAGACCAT CCACACGTTG AATTTCATCG ACGACGAAGC CCGCCGTCGC GCCACGCTGC TGCAACTGAA TCTCGGTGAA 4500
GGCCGCCACA GCCTGGCGCG CGAGGTTTTC CACGGCAAGC GCGGCGAGCT GTTCCAGCGC TACCGCGAAG GGCAGGAAGA CCAGTTGAGC GCGCTCGGCC 4600
TGGTCGTGAA CATGATCGTG CTTTGGAACA CGCTGTACAT GGATGCGGTG CTGACGCAGT TGCGCAGCGA AGGCTACCCC GTGAAGCCAG AAGACGAGGC 4700
ACGGCTGTCG CCGTTCGGCC ACGAGCACAT CAACATGCTC GGACGCTATT CGTTCTCGGT GCCGGAAGCT GTCGCGCGCG GCGAGCTGAG ACCGTTGACC 4800
AAACCGAATG ATCCTTAAAA ACCTTGGAAA TTCACCATGC AACAAATGAC GCAACAACCG TTGAACGATG CCCAGCTTGA TCGGCTGGGC GACTTTCTCG 4900
AAGGAGTCGG CGCACCTGCA ATGAATCTCG AAATGCTCGA TGGGTTCTTT GCCGCACTCA TTTGTGGTCC AGAAACGGTT TTGCCCAGCG AATACTTGCC 5000
ACAAGTATTC GGGGAAGACC ATTGCTTCGA CAGCAATGAC CAAGCCGCCG AAATTCTTGG CTTGGTCATG CGGCACTGGA ACACGATTGC ATCAGAATTG 5100
TTCCGCACTC TGGAGAAAGA CGATGTCTAC CTTCCCGTGC TACTCGAAGA TGCGGATGGG GCCGTACACG GTAACGACTG GGCACGTGGT TTCATGCGCG 5200
GCATTCAATT ACGGCCCAAT AGTTGGCAAG AGTTGATCGG CAGCGAAGAA TTTGGCGGGC CCATGCTGCC AATCATGATC TTGACCCATG AACATGATCC 5300
TGATCCCGCC ATGCGCCCGC CAGAGATTGC GCCGGACAAA CGCGATGAGT TGCTTCAGTC CCTGGTTGCC GGACTGACGC ACATCTATCG CTACTTTGCC 5400
TCACATCGCC AATTGGCAAC CCAAGGGCCT TTACGCAGAC AAGGTCCTAA GATTGGGAGA AATGATCAGT GCCCATGTGG CAGTGGGCGG AAGTACAAGC 5500
ATTGCTGTGC TACCAGCGCT CCGACATTTC ATTGATACCG GCTTAACTGA CTTCCCTGTT CCATTGCTCC CCGAACCCC
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| Recombination Sites |
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| Name |
Coordinates |
Gene |
Sequence |
| res |
973-1112 |
140 |
TTTTGCTTTA CTCGTTAATT TTTAATAATA TCAAACTTTG ATTGTACAAA CCACTATTAC
AGACTGCTTG TTGGCTTACG GACACCTCGC GCCGATCGCC CCATCAGAGT TCATAAAAAC
GATCGTTTTA TTGAACCGTT |
| res_site_III |
973-1001 |
29 |
TTTTGCTTTA CTCGTTAATT TTTAATAAT |
| res_site_II |
1005-1040 |
36 |
AAACTTTGAT TGTACAAACC ACTATTACAG ACTGCT |
| res_site_I |
1080-1112 |
33 |
AGTTCATAAA AACGATCGTT TTATTGAACC GTT |
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| ORFs |
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| Gene Name |
Associated TE |
Coordinates |
Class |
Sub Class |
Orientation |
| tnpR |
TnXc4 |
42-965 |
Accessory Gene |
Resolvase |
- |
| RHH_6 |
TnXc4 |
1180-1419 |
Passenger Gene |
Antitoxin |
+ |
| PIN_3 |
TnXc4 |
1419-1838 |
Passenger Gene |
Toxin |
+ |
| tnpA |
TnXc4 |
1843-4818 |
Transposase |
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+ |
| secC |
TnXc4 |
4837-5535 |
Passenger Gene |
Plant Pathogenicity |
+ |
| Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
| tnpR |
TnpR |
TnXc4 |
924 |
42-965 |
- |
| Class: | Accessory Gene |
| Sub Class: | Resolvase |
| Transpoase Chemistry: | Serine |
| Sequence Family: | Serine Site-Specific Recombinase |
Protein Sequence:
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MKIGYARVST REQNPALQVD SLKAAGCERI YQDVASGAKT ARPALDELLG QLRGGDVLVI WKLDRMGRSL KHLVELVGSL MERKVGLLSL NDPIDTTSAQ
GRFVFNLFAT LAEFERELIR ERTQAGLTAA RARGRVGGRP KGLSPQAEAT ALAAETLYRE RKLSVAAIAQ KLHLSKSTLY SYLRHRGVEI GPYKQSAQSP
INVSVVESGN ADQPKVATIL LTLRIENNSK FVRGKKRSIE HVEFFDLAQY DATRRPNGEY ELKVPYDTDE ELDEAVNDLL TDIACGADDR HCFSESHARM
EGTDRHW
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| Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
| RHH_6 |
RHH_6 |
TnXc4 |
240 |
1180-1419 |
+ |
| Class: | Passenger Gene |
| Sub Class: | Antitoxin |
| Sequence Family: | RHH_6 (Pfam:PF16762) |
Protein Sequence:
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MNTVRWNIAV SPDVDQSVRM FIAAQGGGRK GDLSRFIEDA VRAYLFERAV EQAKAATVGM GETELNDLID EAVQWAREH
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| Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
| PIN_3 |
PIN_3 |
TnXc4 |
420 |
1419-1838 |
+ |
| Class: | Passenger Gene |
| Sub Class: | Toxin |
| Target: | single stranded RNA |
| Sequence Family: | PIN_3 (Pfam:PF13470) |
| Comment: | tRNA(fMet)-specific endonuclease |
Protein Sequence:
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MRVVLDTNVL LAALISSHSP PDIIYRGWLA ARFELVTGTA QLDELRRVSR YPKIKAILPA HRVGTMINNM QRAVVLHVLP PLPDRIEVND PNDAFLLAMA
LASEADYLVT GDRRAGLLQR GSIGRTRIVT PVTFCAEAL
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| Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
| tnpA |
TnpA |
TnXc4 |
2976 |
1843-4818 |
+ |
| Class: | Transposase |
| Transpoase Chemistry: | DDE |
Protein Sequence:
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MPVSFLSTTQ RERYGRYPDT LSSEELARYF HLDDDDREWI ATKRRDSSRL GYALQLTTAR FLGTFLEDPT AVPSPVLHTL SSQLGIADPS DCVIDYRTTR
QRWQHTSEIR TRYGYREFTG TGVQFRLGRW LCALCWTGTD RPSALFDYAN GWLVGHKVLL PGVTLLERFI AEIRSRMESR LWRLLVHGVT PEQRQRLDDL
LKLVEGSRQS WLDRLRKGPV RVSAPALVAA LLRIETVRGL GIKLPGTHVP PSRIAALARF ASTAKVSAVA RLPEVRRIAT LVAFVHCLEA SAQDDAIDVL
DLLLRELFTK AEKEDRKVRQ RSLKDLDRAA STLAEACRML LDPALPDGEL RERVYAAIGH DELAQALNEV RGLVRPPNDV FYTELEARKA TVSRFLPALL
RVIRFDANPA AQPLAQALQW LHEKPDHDPP TAIVGKAWQR HVVQDDGRIN ATAYSFCALD KLRSAIRRRD VFISPSWRYA DPRAGLLAGA EWEASRPIVC
RSLSLSAQPE ATLSELTREL DETYRRVAAR LPQNDAVRFE NVGDKTELVL SPLEALEEPP SLIALRNEIK ARMPRVDLPE ILLEVAGRTG CMEAFTHLTE
RTARAADLTT SLCAVLMAEA CNTGPEPLVR PDTPALKRDR LMWVDQNYVR DDTLTACNAV LVAAQSRIAL ARTWGGGDVA SADGMRFVVP VRTIHAGPNP
KYFNRGRGVT WYNLLSDQRT GLNAITVPGT LRDSLILLAV VLEQQTELQP TQIMTDTGAY SDLVFGLFRL SNYRFCPRLA DVGGTRFWRV DPDADYGDLN
ALARQRVNLD RITPHWDDVL RLVGSLKLGL VPAMGIMRTL QVDERPTSLA QAIAEIGRID KTIHTLNFID DEARRRATLL QLNLGEGRHS LAREVFHGKR
GELFQRYREG QEDQLSALGL VVNMIVLWNT LYMDAVLTQL RSEGYPVKPE DEARLSPFGH EHINMLGRYS FSVPEAVARG ELRPLTKPND P
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| Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
| secC |
SecC |
TnXc4 |
699 |
4837-5535 |
+ |
| Class: | Passenger Gene |
| Sub Class: | Plant Pathogenicity |
| Comment: | contains 2 target sites for ISXac1 insertions |
Protein Sequence:
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MQQMTQQPLN DAQLDRLGDF LEGVGAPAMN LEMLDGFFAA LICGPETVLP SEYLPQVFGE DHCFDSNDQA AEILGLVMRH WNTIASELFR TLEKDDVYLP
VLLEDADGAV HGNDWARGFM RGIQLRPNSW QELIGSEEFG GPMLPIMILT HEHDPDPAMR PPEIAPDKRD ELLQSLVAGL THIYRYFASH RQLATQGPLR
RQGPKIGRND QCPCGSGRKY KHCCATSAPT FH
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| References |
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Zhang Y, Jalan N, Zhou X, Goss E, Jones JB, Setubal JC, Deng X, Wang N. Positive selection is the main driving force for evolution of citrus canker-causing Xanthomonas. ISME J. 2015 Oct;9(10):2128-38. doi: 10.1038/ismej.2015.15. Epub 2015 Feb 17. PubMed ID: 25689023
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