Fragments of introns
Below is a sampling of truncated intron sequences found in bacterial genomes. This website does not list all truncated introns found in GenBank. In bacteria, there are more truncated introns than full length. In mitochondria and chloroplasts, most introns are full length and functional.
We no longer attempt to catalog all truncated and inactivated intron sequences in bacterial genomes, as there is a huge number that exceeds the number of full-length introns. Below is a representative sampling of intron fragments in bacterial genomes.
Intron fragments in EubacteriaIntron fragments in Archaebacteria
Intron fragments in Eubacteria
| Name | Species | Intron RNA domains | Intron ORF domains | Size | Closest relative | Locus | Notes | Genbank |
|---|---|---|---|---|---|---|---|---|
| A.sp.F1 | Anabaena sp. | 42375 | 0, 4-7, X, En | 1869 bp | B.a.I1 (30% over 302 aa) | Tas transpos-able element | Internal deletion of RT domains 1-3; RNA structure matches B2 class | U13767 (3012-4881) |
| B.c.F1 | Bacillus cereus | 42496 | 76 bp | B.c.I2 (82% over 67 bp) | Chromosome | NC_004722 (2621273-2621348) | ||
| B.h.F1 | Bacillus halodurans | 1 | 126 bp | B.h.I1 (90% over 126 bp) | Chromosome | A putative terminator is directly upstream | AP001513 (82798-82923) | |
| B.h.F2 | Bacillus halodurans | 42373 | 398 bp | B.h.I1 (88% over 398 bp) | Chromosome | A putative terminator is directly upstream; a transposase is downstream | AP001509 (236458-236855) | |
| B.h.F3 | Bacillus halodurans | 5, 6 | 73 bp | B.h.I1 (89% over 68 bp) | Chromosome | A transposase is upstream | AP001518 (279207-279280) | |
| B.j.F1 | Bradyrhizobium japonicum | 5, 6 | 0-7 | 491 aa | S.ma.I1 (53% over 491 aa) | Chromosome | Proved to be full-length intron, see info of B.j.I2 in full-length intron table | AF322013 (11219-12768) |
| B.j.F2 | Bradyrhizobium japonicum | 42373 | 161 aa | C.a.I1 (47% over 151 aa) | Chromosome | AF322013 (61716-62201) | ||
| B.j.F3 | Bradyrhizobium japonicum | 4-7, X | 306 aa | B.a.I1 (27 % over 218 aa) | Chromosome | AF322013 (64129-65049) | ||
| B.j.F4 | Bradyrhizobium japonicum | 0-4 | 240 aa | S.ma.I1 (52% over 240 aa) | Chromosome | AF322012 (109786-110508) | ||
| B.j.F5 | Bradyrhizobium japonicum | 4-7, X | 237 aa | S.ma.I1 (50% over 173 aa) | Chromosome | AF322012 (~112711-113404) | ||
| B.the.F1 | Bacteroides thetaiotaomicron | 1-5,(6) | 0-7, X | 1782 bp | B.t.I3 (52% over 411 aa) | Chromosome | RNA domain 6 was inserted by another intron, similar situation found in B.t.I3 and B.t.I4 | AE016936 (56021-57802) |
| B.t.F1 | Bacillus thuringiensis | 42496 | 87 bp | B.me.I1 (88% over 87 bp) | Unknown | AF547282 (134-220) | ||
| B.c.F2 | Bacillus thuringiensis | 42496 | 92 bp | Chromosome | NC_005957 (2284679-2284770) | |||
| C.g.F1 | Corynebacterium glutamicum | 42496 | 86 bp | E.f.I3 (84% over 83 bp) | Chromosome | AP005279 (216855-216940) | ||
| C.t.F1 | Clostridium tetani E88 | 42371 | 315 bp | C.a.I1 (85% over 313 bp) | Chromosome | AE015940 (57392-57706) | ||
| E.f.F1 | Enterococcus faecium | 5, 6 | 7, X | 195 aa | B.h.I1 (40% over 187 aa) | Chromosome | IS1542 is upstream and on the opposite strand | AF242872 (5457-~6118) |
| E.c.F1 | Escherichia coli | 5, 6 | 7-X | 121 aa | S.me.I1 (31% over 118 aa) | IS3 is upstream | X60106 (205-727) | |
| E.c.F2 | Escherichia coil | 0-7 | 322 aa | S.f.I1 (98% over 310 aa) | 3' end is truncated by IS5; 5' exon is IS911 | D37919 (1-1122) | ||
| E.c.F3 | Escherichia coli | 5, 6 | 0-7, X | 448 aa | S.f.I1 (99% over 366 aa) | 3' exon is IS629 | D37918 (154-1590) | |
| E.c.F4 | Escherichia coli | -1 | 193 bp | E.c.I1 (99% over 193 bp) | RshE | AF044501 (1631-1823) | ||
| E.c.F5 | Escherichia coli 0157:H7 | -1 | 193 bp | E.c.I1 (98% over 193 bp) | Chromosome | AE005360 (2258-2450) | ||
| E.c.F6 | Escherichia coli 0157:H7 | -1 | 193 bp | E.c.I1 (98% over 193 bp) | Chromosome | AP002557 (72163-72355) | ||
| E.c.F7 | Escherichia coli | -1 | 159 bp | E.c.I1 (99% over 159 bp) | Unknown | AF044503 (8964-9122) | ||
| E.c.F8 | Escherichia coli CFT073 | -1 | 97 bp | E.c.I1 (97% over 97 bp) | Unknown | AE016771 (291635-291731) | ||
| E.c.F9 | Escherichia coli 0157 | 42373 | 0-2 | 1104 bp | E.c.I5 (99% over 1104 bp) | Unknown | Y16016 (83-1186) | |
| Ma.sp.F2 | Magnetococcus sp. MC-1 | 42496 | 7,X | 534 bp | Ma.sp.I1 (98% over 543 bp) | Chromosome | Transposase at 5' end | NZ_AAAN01000054 (6215-6748) |
| Ma.sp.F3 | Magnetococcus sp. MC-1 | 42373 | 0,1,3,4 | 1597 bp | Ma.sp.I1 (99% over 1597 bp) | Chromosome | Two intron pieces are next to each other but in the wrong order. Not clear they are two tandem copies or flipped by artificial effect. | NZ_AAAN01000014 (13-1609) |
| Ma.sp.F4 | Magnetococcus sp. MC-1 | -1 | 162 bp | Ma.sp.I1 (100% over 162 bp) | Chromosome | NZ_AAAN01000039 (3099-3260) | ||
| Ma.sp.F5 | Magnetococcus sp. MC-1 (Ma.sp.F5) | 42373 | 0-7 | 320 aa | P.a.I1 (58% over 311 aa) | Chromosome | Stop codon and frame shift in ORF, after terminator | NZ_AAAN01000139 (22445-23847) |
| Ma.sp.F6 | Magnetococcus sp. MC-1 | 42496 | 42407 | 341 aa | B.j.I1 (50% over 332 aa) | Chromosome | Has overlap with Ma.sp.F6. Very possible the Ma.sp.F1 and F6 are the same intron | NZ_AAAN01000041 (1963-3050) |
| M.lo.F1 | Mesorhizobium loti | 42373 | 0 | 780 bp | P.p.I2 (82% over 589 bp) | Chromosome | AP003008 (75689-76468) | |
| M.b.F1 | Methanosarcina barkeri | 1,2,5-6 | M.a.I1-1 | Chromosome | Internal deletion of intron ORF and some RNA domains | NZ_AAAR01001642 (2313-2979) | ||
| M.le.F1 | Mycobacterium leprae | 42373 | C.sp.I1 (32% over 155 aa) | Stop codon between RT domains 1 and 2; a 23 bp stem loop is located after domain 4; a transposase fragment is downstream. Ten identical repeats are present in the genome of Mycobacterium.leprae | AL583918 (25817-26960) | |||
| M.le.F2 | Mycobacterium leprae | 42374 | S..me.I2 (33% over 267 aa) | Chromosome | Frame shifts between RT domains 2a and 3, 3 and 4; four pseudogenes upstream and two pseudogenes downstream | AL583918 (~200511-~201270) | ||
| M.t.F1 | Mycobaterium tuberculosis | 0-2 | S.me.I2 (47% over 157 aa) | Chromosome | 5 X 9 bp repeat upstream of domain 0 | AE006920 (~407-1042) | ||
| P.al.F1 | Pseudomonas alcaligenes | 1, 5-6 | 682 bp | P.a.I1 (93% over 351 bp) | Chromosome | Internal deletion of ORF and RNA domains (1),2-4 | AF323438 (1952-2634) | |
| P.l.F1 | Photorhabdus luminescens | 1-7,X | 404 aa | B.j.I2 (48% over 404 aa) | Chromosome | Intron was truncated at both ends by IS elements | BX571862BX571862 (231958-235010) | |
| P.p.F3 | Pseudomonas putida | 5, 6 ? | 4-7, X | 267 aa | S.ma.I1 (50% over 230 aa) | pDK1 | Frameshifts after RT domain 5 and X; RNA domains 5, 6 are degenerate | AF134348 (~720-1494) |
| P.p.F4 | Pseudomonas putida | 3-7, X | ~226 aa | S.ma.I1 (55% over 223 aa) | pRE4 | Stop codon in RT domain 6 | AF006691 (~19530-20220) | |
| P.p.F5 | Pseudomonas putida KT2440 | 42496 | 1-7, X | 1173 bp | A.v.I5 (89% over 1081 bp) | Chromosome | AE016790 (208013-209185) | |
| P.p.F6 | Pseudomonas putida pDK1 | 42496 | 7, X | 675 bp | A.v.I5 (88% over 583 bp) | pDK1plasmid | AF134348 (825-1494) | |
| P.p.F7 | Pseudomonas putida | (1),5-6 | 302 bp | A.v.I5 (93% over 298 bp) | OCT plasmid | Internal deletion of intron ORF | AJ245436 (17048-17349) | |
| P.sp.F1 | Pseudomonas sp. | 5, 6 | (X) | 185 bp | P.p.I1 (88 % over 185 bp) | Tn5041 | Surrounded by transposon ORFs, downstream is an inverted repeat | X98999 (4224-4418) |
| P.st.F1 | Pseuodmonas stutzeri | -1 | 216 bp | A.v.I3 (84% over 257 bp) | unknown | AF039534 (682-936) | ||
| R.e.F1 | Rhizobium etli | 42372 | 0-2 | 856 bp | S.me.I1 (91 % over 856 bp) | Pa plasmid | Frame shift in domain 0 | AF176227 (9216-10069) |
| R.e.F2 | Rhizobium etli | 42376 | 0-5 | 865 bp | S.me.I1 (90 % over 956 bp) | Plasmid P42d | U80928 (223116-224119) | |
| R.e.F3 | Rhizobium etli | -1 | 6-7,X | 387 bp | S.me.I1 (90 % over 429 bp) | Plasmid P42d | Internal deletion | U80928 (101332-101767) |
| R.sp.F1 | Rhizobium sp. NGR234 | 0-2 | 133 aa | S.me.I2 (40% over 117 aa) | pNGR234a | AE000069 (5461-6042) | ||
| S.a.F1 | Streptomyces avermitilis | 42496 | 0-7, X, En | 588 aa | B.a.I1 (39% over 570 aa) | Chromosome | 5' of the intron is truncated by transposase | AP005021 (264494-266317) |
| S.f.F1 | Shigella flexneri | 42434 | ~161 aa | S.f.I1 (75% over 129 aa) | pMYSH6000 | Stop codon between RT domains 3, 4 | D26468 (3211-3612) | |
| S.f.F2 | Shigella flexneri | (1), 2-6 | 0-7, X | 405 aa | S.me.I1 (46% over 387 aa) | pWR501 | Continuous deletion of 522 bp of upstream exon (IS-like ORF31) and 34 bp of 5' intron. 3' exon is ORF31; an IS629 copy is upstream | AF348706 (29835-31623) |
| S.f.F3 | Shigella flexneri | 5, 6 | 0-7, X | 360 aa | S.me.I1 (50% over 360 aa) | pWR501 | Frameshifts, stop codons in ORF; domain 6 degenerated; 3' exon is ORF31; IS600 is upstream | AF348706 (151605-153082) |
| S.me.F1 | Sinorhizobium meliloti | (1-2), 3-6 | 0-7, X | 453 aa | S.me.I3 (98% over 1522 bp) | pSymB | A terminator is directly upstream of the fragment; probable internal truncation within RNA domains 1 and 2 | AL603645 (28607-30146) |
| S.o.F1 | Shewanella oneidensis MR-1 | 42371 | 559 bp | A.g.I1 (90% over 440 bp) | Chromosome | AE015645 (2404-2930) | ||
| S.p.F1 | Streptococcus pneumoniae | (X) 5, 6 | 187 bp | S.p.I1 (99% over 181 bp) | Chromosome | AE007346 (102-289) | ||
| S.p.F2 | Streptococcus pneumoniae | (1, 2) | 328 bp | S.p.I1 (95% over 266 bp) | Chromosome | AE007409 (11094-) to AE007410 (-89) | ||
| S.p.F3 | Streptococcus pneumoniae | 5, 6 | (X) | 181 bp | S.p.I1 (99% over 181 bp) | Chromosome | AE007372 (5515-5697) | |
| S.p.F4 | Streptococcus pneumoniae | 5, 6 | (X) | 454 bp | S.p.I1 (99% over 353 bp) | Chromosome | In the middle of the fragment is a RUPA-28 insertion (107 bp repeated extragenetic element) | AE007369 (7460-7914) |
| S.p.F5 | Streptococcus pneumoniae | (1), 5, 6 | (X) | 489 bp | S.p.I1 (98% over 381 bp) | Chromosome | Internal deletion of RNA domain 2-4 and most RT domains. Contains RUP element (107 bp) in the middle of the fragment | AE008434 (1474-1963) |
| S.p.F6 | Streptococcus pneumoniae | 1 | 306 bp | S.p.I1 (86% over 157 bp) | Chromosome | After terminator structure | AE008536 (21-327) | |
| S.p.F7 | Streptococcus pneumoniae | 1, 2 | 345 bp | S.p.I1 (80% over 250 bp) | Chromosome | After terminator structure | AE008467 (9532-9877) | |
| S.p.F8 | Streptococcus pneumoniae | 3 | 76 bp | S.p.I1 (94% over 76 bp) | Chromosome | AE007478 (241-316) | ||
| S.p.F9 | Streptococcus pneumoniae | (1), 2 | 327 bp | S.p.I1 (97% over 268 bp) | Chromosome | Upstream is RUP element | AE008471 (9510-9837) | |
| S.c.F1 | Streptomyces coelicolor | 0-2 | 145 aa | S.f.I1 (37% over 100 aa) | Chromosome | AL049661 (11519-11956) | ||
| Th.e.F1 | Thermosynechococcus elongatus BP-1 | 42496 | 94 bp | Th.e.I1 (90% over 94 bp) | Chromosome | AP005374 (215166-215259) | ||
| Th.e.F2 | Thermosynechococcus elongatus BP-1 | (1),5-6 | 409 bp | Th.e.I1 (87% over 370 bp) | Chromosome | internal deletion | AP005374 (216672-217080) | |
| Tr.e.F1 | Trichodesmium erythraeumIMS101 | 42375 | 0,X,En | 2094 bp | T.sp.I1 (84% over 916 bp) | Chromosome | internal deletion of intron ORF | NZ_AAAU01000017 (18413-20506) |
| Tr.2.F2 | Trichodesmium erythraeumIMS101 | 42375 | En | 1331 bp | Tr.e.I2 (87% over 1231 bp) | Chromosome | internal deletion of intron ORF | NZ_AAAU01000002 (9475-10805) |
| Tr.e.F3 | Trichodesmium erythraeumIMS101 | 42375 | 1258 bp | Tr.e.I4 (87% over 720 bp) | Chromosome | internal deletion of intron ORF | NZ_AAAU01000059 (16240-17497) | |
| Tr.e.F4 | Trichodesmium erythraeumIMS101 | 42375 | En | 1407 bp | T.sp.I1 (84% over 855 bp) | Chromosome | internal deletion of intron ORF | NZ_AAAU01000021 (53554-54961) |
| Tr.e.F5 | Trichodesmium erythraeumIMS101 | 42375 | 1128 bp | T.sp.I1 (88% over 567 bp) | Chromosome | internal deletion of intron ORF | NZ_AAAU01000021 (55017-56144) | |
| Tr.e.F6 | Trichodesmium erythraeumIMS101 (Tr.e.F6) | 42375 | X,En | 1835 bp | Th.e.I1 (88% over 872 bp) | Chromosome | internal deletion of intron ORF | NZ_AAAU01000021 (56303-58137) |
| Tr.e.F7 | Trichodesmium erythraeumIMS101 (Tr.e.F7) | 42375 | 979 bp | Th.e.I1 (87% over 670 bp) | Chromosome | internal deletion of intron ORF | NZ_AAAU01000021 (58441-59419) | |
| Tr.e.F11 | Trichodesmium erythraeumIMS101 | 42373 | 0 | 951 bp | Th.e.I2 (90% over 951 bp) | Chromosome | 3' end truncation | NZ_AAAU01000039 (19166-20116) |
| Y.e.F1 | Yersinia enterocolitica | 5, 6 | 7, X | 611 bp | S.f.I1 (94% over 611 bp) | pYVe8081 | Domain 5 contains mispairs | AF336309 (40186-40488) |
| Y.p.F1 | Yersinia pestis | 42373 | 1, 2 | 1127 bp | S.f.I1 (93% over 1088 bp) | pMT-1 | An IS600 remnant is upstream | AF074611 (54417-55543) |
Intron fragments in Archaebacteria
| Name | Species | Intron RNA domains | Intron ORF domains | Size | Closest relative | Locus | Notes | Genbank |
|---|---|---|---|---|---|---|---|---|
| M.a.I1-F1 | Methanosarcina acetivorans | 42372 | 0-4 | 1278 bp | M.a.I1-1 (88% over 525 bp) | Chromosome | Truncated by M.a.I1-3 | AE011130(6248-7525) |
| M.a.I1-F2 | Methanosarcina acetivorans | 42496 | (7),X | 629 bp | M.a.I1-1 (96% over 75 bp) | Chromosome | Truncated by M.a.I1-F2 | AE010979(6611-7239) |
| M.a.I2-F1 | Methanosarcina acetivorans | 42372 | 0-4 | 1877 bp | M.a.I1-1 (62% over 525 bp) | Chromosome | Truncated by M.a.I1-F1 | AE011130(7526-9438) |
| M.a.I3-F1 | Methanosarcina acetivorans | 42372 | 0-4 | 1482 bp | M.a.I1-1 (61% over 525 bp) | Chromosome | Truncated by M.a.I1-2 | AE011185(5745-7226) |
| M.a.I6-F1 | Methanosarcina acetivorans | 42406 | 306 bp | M.a.I6-1 (82% over 306 bp) | Chromosome | AE010902(10030-10335) | ||
| M.a.F1 | Methanosarcina acetivorans | 42496 | (4-7),X | 1214 bp | M.a.I1-1 (55% over 75 bp) | Chromosome | 5' end truncated by putative transposase | AE010964(6933-8146) |
| M.a.F2 | Methanosarcina acetivorans | 42496 | 83 bp | M.a.I1-1 (55% over 75 bp) | Chromosome | Degenerated intron | AE010848(4041-4124) | |
| M.a.F3 | Methanosarcina acetivorans | 0-4 | 313 aa | M.a.I1-2 (55% over 233 aa) | Chromosome | AE011134(6345-7286) | ||
| M.a.F4 | Methanosarcina acetivorans | 42496 | (4-7),X | 2724 bp | M.a.I1-1 (71% over 75 bp) | Chromosome | Interrupted by M.a.I1-2 | AE010979(3887-6610) |
| M.b.F1 | Methanosarcina barkeri | 1,5-6 | 667 bp | M.a.I3-F1 (92% over 590 bp) | Chromosome | Internal deletion of intron ORF | NZ_AAAR01001642 (2313-2979) | |
| M.b.F2 | Methanosarcina barkeri | 42372 | 0-4 | 1310 bp | M.a.I3-F1 (87% over 1159 bp) | Chromosome | 3' end truncation | NZ_AAAR01001590 (749-2058) |
| M.b.F3 | Methanosarcina barkeri | 42372 | 327 bp | M.a.I3-F1 (88% over 327 bp) | Chromosome | 3' end truncation | NZ_AAAR01001948 (294-620) |