Fragments of introns
Incompletely sequenced introns
Format of information for incompletely sequenced introns
Intron fragment in Archaebacteria
Intron fragments in Eubacteria
Format of information for intron fragments
| Species | Intron RNA domains | Intron ORF domains | Size |
Closest relative | Locus | Notes | DNA Accession Number |
| Anabaena sp. (A.sp F1) | 1-6 | 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) |
| Bacillus cereus (B.c.F1) | 5-6 | 76 bp | B.c.I2 (82% over 67 bp) | Chromosome | NC_004722 (2621273-2621348) | ||
| Bacillus halodurans (B.h.F1) | 1 | 126 bp | B.h.I1 (90% over 126 bp) | Chromosome | A putative terminator is directly upstream | AP001513 (82798-82923) | |
| Bacillus halodurans (B.h.F2) | 1-4 | 398 bp | B.h.I1 (88% over 398 bp) | Chromosome | A putative terminator is directly upstream; a transposase is downstream | AP001509 (236458-236855) | |
| Bacillus halodurans (B.h.F3) | 5, 6 | 73 bp | B.h.I1 (89% over 68 bp) | Chromosome | A transposase is upstream | AP001518 (279207-279280) | |
| Bradyrhizobium japonicum (B.j.F1) | 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) |
| Bradyrhizobium japonicum (B.j.F2) | 1-4 | 161 aa | C.a.I1 (47% over 151 aa) | Chromosome | AF322013 (61716-62201) | ||
| Bradyrhizobium japonicum (B.j.F3) | 4-7, X | 306 aa | B.a.I1 (27 % over 218 aa) | Chromosome | AF322013 (64129-65049) | ||
| Bradyrhizobium japonicum (B.j.F4) | 0-4 | 240 aa | S.ma.I1 (52% over 240 aa) | Chromosome | AF322012 (109786-110508) | ||
| Bradyrhizobium japonicum (B.j.F5) | 4-7, X | 237 aa | S.ma.I1 (50% over 173 aa) | Chromosome | AF322012 (~112711-113404) | ||
| Bacteroides thetaiotaomicron (B.the.F1) | 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) |
| Bacillus thuringiensis (B.t.F1) | 5-6 | 87 bp | B.me.I1 (88% over 87 bp) | Unknown | AF547282 (134-220) | ||
| Bacillus thuringiensis (B.t.F2) | 5-6 | 92 bp | Chromosome | NC_005957 (2284679-2284770) | |||
| Corynebacterium glutamicum (C.g.F1) | 5-6 | 86 bp | E.f.I3 (84% over 83 bp) | Chromosome | AP005279 (216855-216940) | ||
| Clostridium tetani E88 (C.t.F1) | 1-2 | 315 bp | C.a.I1 (85% over 313 bp) | Chromosome | AE015940 (57392-57706) | ||
| Enterococcus faecium (E.f.F1) | 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) |
| Escherichia coli (E.c.F1) | 5, 6 | 7-X | 121 aa | S.me.I1 (31% over 118 aa) | IS3 is upstream | X60106 (205-727) | |
| Escherichia coil (E.c.F2) | 0-7 | 322 aa | S.f.I1 (98% over 310 aa) | 3’ end is truncated by IS5; 5' exon is IS911 | D37919 (1-1122) | ||
| Escherichia coli (E.c.F3) | 5, 6 | 0-7, X | 448 aa | S.f.I1 (99% over 366 aa) | 3' exon is IS629 | D37918 (154-1590) | |
| Escherichia coli (E.c.F4) | (1) | 193 bp | E.c.I1 (99% over 193 bp) | RshE | AF044501 (1631-1823) | ||
| Escherichia coli 0157:H7(E.c.F5) | (1) | 193 bp | E.c.I1 (98% over 193 bp) | Chromosome | AE005360 (2258-2450) | ||
| Escherichia coli 0157:H7(E.c.F6) | (1) | 193 bp | E.c.I1 (98% over 193 bp) | Chromosome | AP002557 (72163-72355) | ||
| Escherichia coli (E.c.F7) | (1) | 159 bp | E.c.I1 (99% over 159 bp) | Unknown | AF044503 (8964-9122) | ||
| Escherichia coli CFT073 (E.c.F8) | (1) | 97 bp | E.c.I1 (97% over 97 bp) | Unknown | AE016771 (291635-291731) | ||
| Escherichia coli 0157 (E.c.F9) | 1-4 | 0-2 | 1104 bp | E.c.I5 (99% over 1104 bp) | Unknown | Y16016 (83-1186) | |
| Magnetococcus sp. MC-1 (Ma.sp.F2) | 5-6 | 7,X | 534 bp | Ma.sp.I1 (98% over 543 bp) | Chromosome | Transposase at 5' end | NZ_AAAN01000054 (6215-6748) |
| Magnetococcus sp. MC-1 (Ma.sp.F3) | 1-4 | 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) |
| Magnetococcus sp. MC-1 (Ma.sp.F4) | (1) | 162 bp | Ma.sp.I1 (100% over 162 bp) | Chromosome | NZ_AAAN01000039 (3099-3260) | ||
| Magnetococcus sp. MC-1 (Ma.sp.F5) | 1-4 | 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) |
| Magnetococcus sp. MC-1 (Ma.sp.F6) | 5-6 | 2-7 | 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) |
| Mesorhizobium loti (M.lo.F1) | 1-4 | 0 | 780 bp | P.p.I2 (82% over 589 bp) | Chromosome | AP003008 (75689-76468) | |
| Methanosarcina barkeri (M.b.F1) | 1,2,5-6 | M.a.I1-1 | Chromosome | Internal deletion of intron ORF and some RNA domains | NZ_AAAR01001642 (2313-2979) | ||
| Mycobacterium leprae (M.le.F1) | 1-4 | 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)g | |||
| Mycobacterium leprae (M.le.F2) | 1-5 | 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) | ||
| Mycobaterium tuberculosis (M.t.F1) | 0-2 | S.me.I2 (47% over 157 aa) | Chromosome | 5 X 9 bp repeat upstream of domain 0 | AE006920 (~407-1042) | ||
| Pseudomonas alcaligenes (P.al.F1) | 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) | |
| Photorhabdus luminescens (P.l.F1) | 1-7,X | 404 aa | B.j.I2 (48% over 404 aa) | Chromosome | Intron was truncated at both ends by IS elements | BX571862 (231958-235010) | |
| Pseudomonas putida (P.p.F3) | 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) |
| Pseudomonas putida (P.p.F4) | 3-7, X | ~226 aa | S.ma.I1 (55% over 223 aa) | pRE4 | Stop codon in RT domain 6 | AF006691 (~19530-20220) | |
| Pseudomonas putida KT2440 (P.p.F5) | 5-6 | 1-7, X | 1173 bp | A.v.I5 (89% over 1081 bp) | Chromosome | AE016790 (208013-209185) | |
| Pseudomonas putida pDK1 (P.p.F6) | 5-6 | 7, X | 675 bp | A.v.I5 (88% over 583 bp) | pDK1plasmid | AF134348 (825-1494) | |
| Pseudomonas putida (P.p.F7) | (1),5-6 | 302 bp | A.v.I5 (93% over 298 bp) | OCT plasmid | Internal deletion of intron ORF | AJ245436 (17048-17349) | |
| Pseudomonas sp. (P.sp.F1) | 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) |
| Pseuodmonas stutzeri (P.st.F1) | (1) | 216 bp | A.v.I3 (84% over 257 bp) | unknown | AF039534 (682-936) | ||
| Rhizobium etli (R.e.F1) | 1-3 | 0-2 | 856 bp | S.me.I1 (91 % over 856 bp) | Pa plasmid | Frame shift in domain 0 | AF176227 (9216-10069) |
| Rhizobium etli (R.e.F2) | 1-7 | 0-5 | 865 bp | S.me.I1 (90 % over 956 bp) | Plasmid P42d | U80928 (223116-224119) | |
| Rhizobium etli (R.e.F3) | (1) | 6-7,X | 387 bp | S.me.I1 (90 % over 429 bp) | Plasmid P42d | Internal deletion | U80928 (101332-101767) |
| Rhizobium sp. NGR234 (R.sp.F1) | 0-2 | 133 aa | S.me.I2 (40% over 117 aa) | pNGR234a | AE000069 (5461-6042) | ||
| Streptomyces avermitilis (S.a.F1) | 5-6 | 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) |
| Shigella flexneri (S.f.F1) | 3-5 | ~161 aa | S.f.I1 (75% over 129 aa) | pMYSH6000 | Stop codon between RT domains 3, 4 | D26468 (3211-3612) | |
| Shigella flexneri (S.f.F2) | (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) |
| Shigella flexneri (S.f.F3) | 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) |
| Sinorhizobium meliloti (S.me.F1) | (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) |
| Shewanella oneidensis MR-1 (S.o.F1) | 1-2 | 559 bp | A.g.I1 (90% over 440 bp) | Chromosome | AE015645 (2404-2930) | ||
| Streptococcus pneumoniae (S.p.F1) | (X) 5, 6 | 187 bp | S.p.I1 (99% over 181 bp) | Chromosome | AE007346 (102-289) | ||
| Streptococcus pneumoniae (S.p.F2) | (1, 2) | 328 bp | S.p.I1 (95% over 266 bp) | Chromosome | AE007409 (11094-) to AE007410 (-89) | ||
| Streptococcus pneumoniae (S.p.F3) | 5, 6 | (X) | 181 bp | S.p.I1 (99% over 181 bp) | Chromosome | AE007372 (5515-5697) | |
| Streptococcus pneumoniae (S.p.F4) | 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) |
| Streptococcus pneumoniae (S.p.F5) | (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) |
| Streptococcus pneumoniae (S.p.F6) | 1 | 306 bp | S.p.I1 (86% over 157 bp) | Chromosome | After terminator structure | AE008536 (21-327) | |
| Streptococcus pneumoniae (S.p.F7) | 1, 2 | 345 bp | S.p.I1 (80% over 250 bp) | Chromosome | After terminator structure | AE008467 (9532-9877) | |
| Streptococcus pneumoniae (S.p.F8) | 3 | 76 bp | S.p.I1 (94% over 76 bp) | Chromosome | AE007478 (241-316) | ||
| Streptococcus pneumoniae (S.p.F9) | (1), 2 | 327 bp | S.p.I1 (97% over 268 bp) | Chromosome | Upstream is RUP element | AE008471 (9510-9837) | |
| Streptomyces coelicolor (S.c.F1) | 0-2 | 145 aa | S.f.I1 (37% over 100 aa) | Chromosome | AL049661 (11519-11956) | ||
| Thermosynechococcus elongatus BP-1 (Th.e.F1) | 5-6 | 94 bp | Th.e.I1 (90% over 94 bp) | Chromosome | AP005374 (215166-215259) | ||
| Thermosynechococcus elongatus BP-1 (Th.e.F2) | (1),5-6 | 409 bp | Th.e.I1 (87% over 370 bp) | Chromosome | internal deletion | AP005374 (216672-217080) | |
| Trichodesmium erythraeum IMS101 (Tr.e.F1) | 1-6 | 0,X,En | 2094 bp | T.sp.I1 (84% over 916 bp) | Chromosome | internal deletion of intron ORF | NZ_AAAU01000017 (18413-20506) |
| Trichodesmium erythraeum IMS101 (Tr.e.F2) | 1-6 | En | 1331 bp | Tr.e.I2 (87% over 1231 bp) | Chromosome | internal deletion of intron ORF | NZ_AAAU01000002 (9475-10805) |
| Trichodesmium erythraeum IMS101 (Tr.e.F3) | 1-6 | 1258 bp | Tr.e.I4 (87% over 720 bp) | Chromosome | internal deletion of intron ORF | NZ_AAAU01000059 (16240-17497) | |
| Trichodesmium erythraeum IMS101 (Tr.e.F4) | 1-6 | En | 1407 bp | T.sp.I1 (84% over 855 bp) | Chromosome | internal deletion of intron ORF | NZ_AAAU01000021 (53554-54961) |
| Trichodesmium erythraeum IMS101 (Tr.e.F5) | 1-6 | 1128 bp | T.sp.I1 (88% over 567 bp) | Chromosome | internal deletion of intron ORF | NZ_AAAU01000021 (55017-56144) | |
| Trichodesmium erythraeum IMS101 (Tr.e.F6) | 1-6 | X,En | 1835 bp | Th.e.I1 (88% over 872 bp) | Chromosome | internal deletion of intron ORF | NZ_AAAU01000021 (56303-58137) |
| Trichodesmium erythraeum IMS101 (Tr.e.F7) | 1-6 | 979 bp | Th.e.I1 (87% over 670 bp) | Chromosome | internal deletion of intron ORF | NZ_AAAU01000021 (58441-59419) | |
| Trichodesmium erythraeum IMS101 (Tr.e.F11) | 1-4 | 0 | 951 bp | Th.e.I2 (90% over 951 bp) | Chromosome | 3' end truncation | NZ_AAAU01000039 (19166-20116) |
| Yersinia enterocolitica (Y.e.F1) | 5, 6 | 7, X | 611 bp | S.f.I1 (94% over 611 bp) | pYVe8081 | Domain 5 contains mispairs | AF336309 (40186-40488) |
| Yersinia pestis (Y.p.F1) | 1-4 | 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
| Species | Intron RNA domains | Intron ORF domains | Size |
Closest relative | Locus | Notes | DNA Accession Number |
| Methanosarcina acetivorans (M.a.I1-F1) | 1-3 | 0-4 | 1278 bp | M.a.I1-1 (88% over 525 bp) | Chromosome | Truncated by M.a.I1-3 | AE011130(6248-7525) |
| Methanosarcina acetivorans (M.a.I1-F2) | 5-6 | (7),X | 629 bp | M.a.I1-1 (96% over 75 bp) | Chromosome | Truncated by M.a.I1-F2 | AE010979(6611-7239) |
| Methanosarcina acetivorans (M.a.I2-F1) | 1-3 | 0-4 | 1877 bp | M.a.I1-1 (62% over 525 bp) | Chromosome | Truncated by M.a.I1-F1 | AE011130(7526-9438) |
| Methanosarcina acetivorans (M.a.I3-F1) | 1-3 | 0-4 | 1482 bp | M.a.I1-1 (61% over 525 bp) | Chromosome | Truncated by M.a.I1-2 | AE011185(5745-7226) |
| Methanosarcina acetivorans (M.a.I6-F1) | 2-6 | 306 bp | M.a.I6-1 (82% over 306 bp) | Chromosome | AE010902(10030-10335) | ||
| Methanosarcina acetivorans (M.a.F1) | 5-6 | (4-7),X | 1214 bp | M.a.I1-1 (55% over 75 bp) | Chromosome | 5' end truncated by putative transposase | AE010964(6933-8146) |
| Methanosarcina acetivorans (M.a.F2) | 5-6 | 83 bp | M.a.I1-1 (55% over 75 bp) | Chromosome | Degenerated intron | AE010848(4041-4124) | |
| Methanosarcina acetivorans (M.a.F3) | 0-4 | 313 aa | M.a.I1-2 (55% over 233 aa) | Chromosome | AE011134(6345-7286) | ||
| Methanosarcina acetivorans (M.a.F4) | 5-6 | (4-7),X | 2724 bp | M.a.I1-1 (71% over 75 bp) | Chromosome | Interrupted by M.a.I1-2 | AE010979(3887-6610) |
| Methanosarcina barkeri (M.b.F1) | 1,5-6 | 667 bp | M.a.I3-F1 (92% over 590 bp) | Chromosome | Internal deletion of intron ORF | NZ_AAAR01001642 (2313-2979) | |
| Methanosarcina barkeri (M.b.F2) | 1-3 | 0-4 | 1310 bp | M.a.I3-F1 (87% over 1159 bp) | Chromosome | 3' end truncation | NZ_AAAR01001590 (749-2058) |
| Methanosarcina barkeri (M.b.F3) | 1-3 | 327 bp | M.a.I3-F1 (88% over 327 bp) | Chromosome | 3' end truncation | NZ_AAAR01001948 (294-620) |
| Introduction | Intron secondary structure | Intron ORF structure | Introns listed by organism | Bacterial intron fragments | Alignment of insertion sequence |
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