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 Eubacteria
Intron fragments in Archaebacteria

Intron fragments in Eubacteria

NameSpeciesIntron RNA domainsIntron ORF domainsSizeClosest relativeLocusNotesGenbank
A.sp.F1Anabaena sp.423750, 4-7, X, En1869 bpB.a.I1 (30% over 302 aa)Tas transpos-able elementInternal deletion of RT domains 1-3; RNA structure matches B2 classU13767 (3012-4881)
B.c.F1Bacillus cereus4249676 bpB.c.I2 (82% over 67 bp)ChromosomeNC_004722 (2621273-2621348)
B.h.F1Bacillus halodurans1126 bpB.h.I1 (90% over 126 bp)ChromosomeA putative terminator is directly upstreamAP001513 (82798-82923)
B.h.F2Bacillus halodurans42373398 bpB.h.I1 (88% over 398 bp)ChromosomeA putative terminator is directly upstream; a transposase is downstreamAP001509 (236458-236855)
B.h.F3Bacillus halodurans5, 673 bpB.h.I1 (89% over 68 bp)ChromosomeA transposase is upstreamAP001518 (279207-279280)
B.j.F1Bradyrhizobium japonicum5, 60-7491 aaS.ma.I1 (53% over 491 aa)ChromosomeProved to be full-length intron, see info of B.j.I2 in full-length intron tableAF322013 (11219-12768)
B.j.F2Bradyrhizobium japonicum42373161 aaC.a.I1 (47% over 151 aa)ChromosomeAF322013 (61716-62201)
B.j.F3Bradyrhizobium japonicum4-7, X306 aaB.a.I1 (27 % over 218 aa)ChromosomeAF322013 (64129-65049)
B.j.F4Bradyrhizobium japonicum0-4240 aaS.ma.I1 (52% over 240 aa)ChromosomeAF322012 (109786-110508)
B.j.F5Bradyrhizobium japonicum4-7, X237 aaS.ma.I1 (50% over 173 aa)ChromosomeAF322012 (~112711-113404)
B.the.F1Bacteroides thetaiotaomicron1-5,(6)0-7, X1782 bpB.t.I3 (52% over 411 aa)ChromosomeRNA domain 6 was inserted by another intron, similar situation found in B.t.I3 and B.t.I4AE016936 (56021-57802)
B.t.F1Bacillus thuringiensis4249687 bpB.me.I1 (88% over 87 bp)UnknownAF547282 (134-220)
B.c.F2Bacillus thuringiensis4249692 bpChromosomeNC_005957 (2284679-2284770)
C.g.F1Corynebacterium glutamicum4249686 bpE.f.I3 (84% over 83 bp)ChromosomeAP005279 (216855-216940)
C.t.F1Clostridium tetani E8842371315 bpC.a.I1 (85% over 313 bp)ChromosomeAE015940 (57392-57706)
E.f.F1Enterococcus faecium5, 67, X195 aaB.h.I1 (40% over 187 aa)ChromosomeIS1542 is upstream and on the opposite strandAF242872 (5457-~6118)
E.c.F1Escherichia coli5, 67-X121 aaS.me.I1 (31% over 118 aa)IS3 is upstreamX60106 (205-727)
E.c.F2Escherichia coil0-7322 aaS.f.I1 (98% over 310 aa)3' end is truncated by IS5; 5' exon is IS911D37919 (1-1122)
E.c.F3Escherichia coli5, 60-7, X448 aaS.f.I1 (99% over 366 aa)3' exon is IS629D37918 (154-1590)
E.c.F4Escherichia coli-1193 bpE.c.I1 (99% over 193 bp)RshEAF044501 (1631-1823)
E.c.F5Escherichia coli 0157:H7-1193 bpE.c.I1 (98% over 193 bp)ChromosomeAE005360 (2258-2450)
E.c.F6Escherichia coli 0157:H7-1193 bpE.c.I1 (98% over 193 bp)ChromosomeAP002557 (72163-72355)
E.c.F7Escherichia coli-1159 bpE.c.I1 (99% over 159 bp)UnknownAF044503 (8964-9122)
E.c.F8Escherichia coli CFT073-197 bpE.c.I1 (97% over 97 bp)UnknownAE016771 (291635-291731)
E.c.F9Escherichia coli 0157423730-21104 bpE.c.I5 (99% over 1104 bp)UnknownY16016 (83-1186)
Ma.sp.F2Magnetococcus sp. MC-1424967,X534 bpMa.sp.I1 (98% over 543 bp)ChromosomeTransposase at 5' endNZ_AAAN01000054 (6215-6748)
Ma.sp.F3Magnetococcus sp. MC-1423730,1,3,41597 bpMa.sp.I1 (99% over 1597 bp)ChromosomeTwo 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.F4Magnetococcus sp. MC-1-1162 bpMa.sp.I1 (100% over 162 bp)ChromosomeNZ_AAAN01000039 (3099-3260)
Ma.sp.F5Magnetococcus sp. MC-1 (Ma.sp.F5)423730-7320 aaP.a.I1 (58% over 311 aa)ChromosomeStop codon and frame shift in ORF, after terminatorNZ_AAAN01000139 (22445-23847)
Ma.sp.F6Magnetococcus sp. MC-14249642407341 aaB.j.I1 (50% over 332 aa)ChromosomeHas overlap with Ma.sp.F6. Very possible the Ma.sp.F1 and F6 are the same intronNZ_AAAN01000041 (1963-3050)
M.lo.F1Mesorhizobium loti423730780 bpP.p.I2 (82% over 589 bp)ChromosomeAP003008 (75689-76468)
M.b.F1Methanosarcina barkeri1,2,5-6M.a.I1-1ChromosomeInternal deletion of intron ORF and some RNA domainsNZ_AAAR01001642 (2313-2979)
M.le.F1Mycobacterium leprae42373C.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.lepraeAL583918 (25817-26960)
M.le.F2Mycobacterium leprae42374S..me.I2 (33% over 267 aa)ChromosomeFrame shifts between RT domains 2a and 3, 3 and 4; four pseudogenes upstream and two pseudogenes downstreamAL583918 (~200511-~201270)
M.t.F1Mycobaterium tuberculosis0-2S.me.I2 (47% over 157 aa)Chromosome5 X 9 bp repeat upstream of domain 0AE006920 (~407-1042)
P.al.F1Pseudomonas alcaligenes1, 5-6682 bpP.a.I1 (93% over 351 bp)ChromosomeInternal deletion of ORF and RNA domains (1),2-4AF323438 (1952-2634)
P.l.F1Photorhabdus luminescens1-7,X404 aaB.j.I2 (48% over 404 aa)ChromosomeIntron was truncated at both ends by IS elementsBX571862BX571862 (231958-235010)
P.p.F3Pseudomonas putida5, 6 ?4-7, X267 aaS.ma.I1 (50% over 230 aa)pDK1Frameshifts after RT domain 5 and X; RNA domains 5, 6 are degenerateAF134348 (~720-1494)
P.p.F4Pseudomonas putida3-7, X~226 aaS.ma.I1 (55% over 223 aa)pRE4Stop codon in RT domain 6AF006691 (~19530-20220)
P.p.F5Pseudomonas putida KT2440424961-7, X1173 bpA.v.I5 (89% over 1081 bp)ChromosomeAE016790 (208013-209185)
P.p.F6Pseudomonas putida pDK1424967, X675 bpA.v.I5 (88% over 583 bp)pDK1plasmidAF134348 (825-1494)
P.p.F7Pseudomonas putida(1),5-6302 bpA.v.I5 (93% over 298 bp)OCT plasmidInternal deletion of intron ORFAJ245436 (17048-17349)
P.sp.F1Pseudomonas sp.5, 6(X)185 bpP.p.I1 (88 % over 185 bp)Tn5041Surrounded by transposon ORFs, downstream is an inverted repeatX98999 (4224-4418)
P.st.F1Pseuodmonas stutzeri-1216 bpA.v.I3 (84% over 257 bp)unknownAF039534 (682-936)
R.e.F1Rhizobium etli423720-2856 bpS.me.I1 (91 % over 856 bp)Pa plasmidFrame shift in domain 0AF176227 (9216-10069)
R.e.F2Rhizobium etli423760-5865 bpS.me.I1 (90 % over 956 bp)Plasmid P42dU80928 (223116-224119)
R.e.F3Rhizobium etli-16-7,X387 bpS.me.I1 (90 % over 429 bp)Plasmid P42dInternal deletionU80928 (101332-101767)
R.sp.F1Rhizobium sp. NGR2340-2133 aaS.me.I2 (40% over 117 aa)pNGR234aAE000069 (5461-6042)
S.a.F1Streptomyces avermitilis424960-7, X, En588 aaB.a.I1 (39% over 570 aa)Chromosome5' of the intron is truncated by transposaseAP005021 (264494-266317)
S.f.F1Shigella flexneri42434~161 aaS.f.I1 (75% over 129 aa)pMYSH6000Stop codon between RT domains 3, 4D26468 (3211-3612)
S.f.F2Shigella flexneri(1), 2-60-7, X405 aaS.me.I1 (46% over 387 aa)pWR501Continuous deletion of 522 bp of upstream exon (IS-like ORF31) and 34 bp of 5' intron. 3' exon is ORF31; an IS629 copy is upstreamAF348706 (29835-31623)
S.f.F3Shigella flexneri5, 60-7, X360 aaS.me.I1 (50% over 360 aa)pWR501Frameshifts, stop codons in ORF; domain 6 degenerated; 3' exon is ORF31; IS600 is upstreamAF348706 (151605-153082)
S.me.F1Sinorhizobium meliloti(1-2), 3-60-7, X453 aaS.me.I3 (98% over 1522 bp)pSymBA terminator is directly upstream of the fragment; probable internal truncation within RNA domains 1 and 2AL603645 (28607-30146)
S.o.F1Shewanella oneidensis MR-142371559 bpA.g.I1 (90% over 440 bp)ChromosomeAE015645 (2404-2930)
S.p.F1Streptococcus pneumoniae(X) 5, 6187 bpS.p.I1 (99% over 181 bp)ChromosomeAE007346 (102-289)
S.p.F2Streptococcus pneumoniae(1, 2)328 bpS.p.I1 (95% over 266 bp)ChromosomeAE007409 (11094-) to AE007410 (-89)
S.p.F3Streptococcus pneumoniae5, 6(X)181 bpS.p.I1 (99% over 181 bp)ChromosomeAE007372 (5515-5697)
S.p.F4Streptococcus pneumoniae5, 6(X)454 bpS.p.I1 (99% over 353 bp)ChromosomeIn the middle of the fragment is a RUPA-28 insertion (107 bp repeated extragenetic element)AE007369 (7460-7914)
S.p.F5Streptococcus pneumoniae(1), 5, 6(X)489 bpS.p.I1 (98% over 381 bp)ChromosomeInternal deletion of RNA domain 2-4 and most RT domains. Contains RUP element (107 bp) in the middle of the fragmentAE008434 (1474-1963)
S.p.F6Streptococcus pneumoniae1306 bpS.p.I1 (86% over 157 bp)ChromosomeAfter terminator structureAE008536 (21-327)
S.p.F7Streptococcus pneumoniae1, 2345 bpS.p.I1 (80% over 250 bp)ChromosomeAfter terminator structureAE008467 (9532-9877)
S.p.F8Streptococcus pneumoniae376 bpS.p.I1 (94% over 76 bp)ChromosomeAE007478 (241-316)
S.p.F9Streptococcus pneumoniae(1), 2327 bpS.p.I1 (97% over 268 bp)ChromosomeUpstream is RUP elementAE008471 (9510-9837)
S.c.F1Streptomyces coelicolor0-2145 aaS.f.I1 (37% over 100 aa)ChromosomeAL049661 (11519-11956)
Th.e.F1Thermosynechococcus elongatus BP-14249694 bpTh.e.I1 (90% over 94 bp)ChromosomeAP005374 (215166-215259)
Th.e.F2Thermosynechococcus elongatus BP-1(1),5-6409 bpTh.e.I1 (87% over 370 bp)Chromosomeinternal deletionAP005374 (216672-217080)
Tr.e.F1Trichodesmium erythraeumIMS101423750,X,En2094 bpT.sp.I1 (84% over 916 bp)Chromosomeinternal deletion of intron ORFNZ_AAAU01000017 (18413-20506)
Tr.2.F2Trichodesmium erythraeumIMS10142375En1331 bpTr.e.I2 (87% over 1231 bp)Chromosomeinternal deletion of intron ORFNZ_AAAU01000002 (9475-10805)
Tr.e.F3Trichodesmium erythraeumIMS101423751258 bpTr.e.I4 (87% over 720 bp)Chromosomeinternal deletion of intron ORFNZ_AAAU01000059 (16240-17497)
Tr.e.F4Trichodesmium erythraeumIMS10142375En1407 bpT.sp.I1 (84% over 855 bp)Chromosomeinternal deletion of intron ORFNZ_AAAU01000021 (53554-54961)
Tr.e.F5Trichodesmium erythraeumIMS101423751128 bpT.sp.I1 (88% over 567 bp)Chromosomeinternal deletion of intron ORFNZ_AAAU01000021 (55017-56144)
Tr.e.F6Trichodesmium erythraeumIMS101 (Tr.e.F6)42375X,En1835 bpTh.e.I1 (88% over 872 bp)Chromosomeinternal deletion of intron ORFNZ_AAAU01000021 (56303-58137)
Tr.e.F7Trichodesmium erythraeumIMS101 (Tr.e.F7)42375979 bpTh.e.I1 (87% over 670 bp)Chromosomeinternal deletion of intron ORFNZ_AAAU01000021 (58441-59419)
Tr.e.F11Trichodesmium erythraeumIMS101423730951 bpTh.e.I2 (90% over 951 bp)Chromosome3' end truncationNZ_AAAU01000039 (19166-20116)
Y.e.F1Yersinia enterocolitica5, 67, X611 bpS.f.I1 (94% over 611 bp)pYVe8081Domain 5 contains mispairsAF336309 (40186-40488)
Y.p.F1Yersinia pestis423731, 21127 bpS.f.I1 (93% over 1088 bp)pMT-1An IS600 remnant is upstreamAF074611 (54417-55543)

Intron fragments in Archaebacteria

NameSpeciesIntron RNA domainsIntron ORF domainsSizeClosest relativeLocusNotesGenbank
M.a.I1-F1Methanosarcina acetivorans423720-41278 bpM.a.I1-1 (88% over 525 bp)ChromosomeTruncated by M.a.I1-3AE011130(6248-7525)
M.a.I1-F2Methanosarcina acetivorans42496(7),X629 bpM.a.I1-1 (96% over 75 bp)ChromosomeTruncated by M.a.I1-F2AE010979(6611-7239)
M.a.I2-F1Methanosarcina acetivorans423720-41877 bpM.a.I1-1 (62% over 525 bp)ChromosomeTruncated by M.a.I1-F1AE011130(7526-9438)
M.a.I3-F1Methanosarcina acetivorans423720-41482 bpM.a.I1-1 (61% over 525 bp)ChromosomeTruncated by M.a.I1-2AE011185(5745-7226)
M.a.I6-F1Methanosarcina acetivorans42406306 bpM.a.I6-1 (82% over 306 bp)ChromosomeAE010902(10030-10335)
M.a.F1Methanosarcina acetivorans42496(4-7),X1214 bpM.a.I1-1 (55% over 75 bp)Chromosome5' end truncated by putative transposaseAE010964(6933-8146)
M.a.F2Methanosarcina acetivorans4249683 bpM.a.I1-1 (55% over 75 bp)ChromosomeDegenerated intronAE010848(4041-4124)
M.a.F3Methanosarcina acetivorans0-4313 aaM.a.I1-2 (55% over 233 aa)ChromosomeAE011134(6345-7286)
M.a.F4Methanosarcina acetivorans42496(4-7),X2724 bpM.a.I1-1 (71% over 75 bp)ChromosomeInterrupted by M.a.I1-2AE010979(3887-6610)
M.b.F1Methanosarcina barkeri1,5-6667 bpM.a.I3-F1 (92% over 590 bp)ChromosomeInternal deletion of intron ORFNZ_AAAR01001642 (2313-2979)
M.b.F2Methanosarcina barkeri423720-41310 bpM.a.I3-F1 (87% over 1159 bp)Chromosome3' end truncationNZ_AAAR01001590 (749-2058)
M.b.F3Methanosarcina barkeri42372327 bpM.a.I3-F1 (88% over 327 bp)Chromosome3' end truncationNZ_AAAR01001948 (294-620)