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Fragments of introns

Incompletely sequenced introns

Format of information for incompletely sequenced introns

Intron fragment in Eubacteria

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)

 


 

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