86:
without changing the overall number in the DNA. Indels can also be contrasted with Tandem Base
Mutations (TBM), which may result from fundamentally different mechanisms. A TBM is defined as a substitution at adjacent nucleotides (primarily substitutions at two adjacent nucleotides, but substitutions
105:
in a different frame. Indels that are not multiples of 3 are particularly uncommon in coding regions but relatively common in non-coding regions. There are approximately 192-280 frameshifting indels in each person. Indels are likely to represent between 16% and 25% of all sequence polymorphisms in
149:
Using passenger-immunoglobulin mouse models, a study found that the most prevalent indel events are the activation-induced cytidine deaminase (AID)-dependent ±1-base pair (bp) indels, which can lead to deleterious outcomes, whereas longer in-frame indels were rare outcomes.
129:. In systematics, researchers could find differences between sequences, such as from two different species. But it was impossible to infer if one species lost the sequence or the other species gained it. For example, species
878:
Hao, Qian; Zhan, Chuanzong; Lian, Chaoyang; Luo, Simin; Cao, Wenyi; Wang, Binbin; Xie, Xia; Ye, Xiaofei; Gui, Tuantuan; Voena, Claudia; Pighi, Chiara; Wang, Yanyan; Tian, Ying; Wang, Xin; Dai, Pengfei (2023-03-31).
141:
has 5 G's at the same locus. If the mode of selection is unknown, one can not tell if species A lost one G (a "deletion" event") or species B gained one G (an "insertion" event). When one cannot infer the
353:
Buettner VL, Hill KA, Halangoda A, Sommer SS (1999). "Tandem-base mutations occur in mouse liver and adipose tissue preferentially as G:C to T:A transversions and accumulate with age".
649:"Identifying the genome-wide sequence variations and developing new molecular markers for genetics research by re-sequencing a Landrace cultivar of foxtail millet"
318:
Hill KA, Wang J, Farwell KD, Sommer SS (January 2003). "Spontaneous tandem-base mutations (TBM) show dramatic tissue, age, pattern and spectrum specificity".
555:
Nakamura H, Muro T, Imamura S, Yuasa I (March 2009). "Forensic species identification based on size variation of mitochondrial DNA hypervariable regions".
283:
Kaneko T, Tahara S, Matsuo M (May 1996). "Non-linear accumulation of 8-hydroxy-2'-deoxyguanosine, a marker of oxidized DNA damage, during aging".
449:"Whole-gene positive selection, elevated synonymous substitution rates, duplication, and indel evolution of the chloroplast clpP1 gene"
366:
183:
Mahmoud, Medhat; Gobet, Nastassia; Cruz-Dávalos, Diana Ivette; Mounier, Ninon; Dessimoz, Christophe; Sedlazeck, Fritz J. (2019).
94:
studies. It has been shown that genomic regions with multiple indels can also be used for species-identification procedures.
953:
90:
Indels, being either insertions, or deletions, can be used as genetic markers in natural populations, especially in
78:. An indel inserts or deletes nucleotides from a sequence, while a point mutation is a form of substitution that
107:
125:
for use in the sense described above. This is a change from its original use and meaning, which arose from
881:"DNA repair mechanisms that promote insertion-deletion events during immunoglobulin gene diversification"
106:
humans. In most known genomes, including humans, indel frequency tends to be markedly lower than that of
1138:
1112:
1062:
115:
598:
Taberlet P, Coissac E, Pompanon F, Gielly L, Miquel C, Valentini A, et al. (26 January 2007).
1107:
101:
results in a frameshift during mRNA translation that could lead to an inappropriate (premature)
946:
757:
Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, et al. (October 2010).
17:
814:
Mills RE, Luttig CT, Larkins CE, Beauchamp A, Tsui C, Pittard WS, Devine SE (September 2006).
506:
Pereira F, Carneiro J, Matthiesen R, van Asch B, Pinto N, GusmĂŁo L, Amorim A (December 2010).
1067:
1031:
994:
976:
770:
660:
460:
159:
111:
54:
38:
236:"Haplotype-resolved diverse human genomes and integrated analysis of structural variation"
146:
direction of the sequence change, the sequence change event is referred to as an "indel".
8:
1041:
981:
164:
65:
42:
1102:
1092:
1087:
913:
880:
774:
708:"Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor)"
664:
464:
840:
815:
791:
758:
734:
707:
683:
648:
624:
599:
580:
532:
507:
483:
448:
424:
397:
378:
260:
235:
211:
184:
331:
296:
1133:
1026:
1021:
939:
918:
900:
845:
796:
739:
688:
629:
572:
537:
488:
429:
398:"Insertion-deletion polymorphisms (indels) as genetic markers in natural populations"
370:
335:
300:
265:
216:
600:"Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding"
584:
382:
1097:
1046:
908:
892:
835:
827:
786:
778:
729:
719:
678:
668:
619:
611:
564:
527:
519:
478:
468:
419:
409:
362:
327:
292:
255:
247:
206:
196:
64:
of the genome, unless the length of an indel is a multiple of 3, it will produce a
1036:
673:
473:
816:"An initial map of insertion and deletion (INDEL) variation in the human genome"
1013:
896:
724:
74:
69:
706:
Zheng LY, Guo XS, He B, Sun LJ, Peng Y, Dong SS, et al. (November 2011).
568:
508:"Identification of species by multiplex analysis of variable-length sequences"
201:
1127:
904:
61:
251:
989:
922:
849:
800:
743:
692:
633:
576:
541:
492:
433:
374:
339:
269:
220:
91:
414:
304:
615:
523:
126:
83:
782:
68:. For example, a common microindel which results in a frameshift causes
831:
102:
46:
72:
in the Jewish or
Japanese population. Indels can be contrasted with a
367:
10.1002/(SICI)1098-2280(1999)33:4<320::AID-EM9>3.0.CO;2-S
143:
122:
962:
759:"A map of human genome variation from population-scale sequencing"
505:
134:
647:
Bai H, Cao Y, Quan J, Dong L, Li Z, Zhu Y, et al. (2013).
395:
182:
97:
An indel change of a single base pair in the coding part of an
50:
396:
Väli U, Brandström M, Johansson M, Ellegren H (January 2008).
233:
53:
of an organism. Indels ≥ 50 bases in length are classified as
597:
121:
The term "indel" has been co-opted in recent years by genome
756:
931:
813:
699:
352:
98:
185:"Structural variant calling: the long and the short of it"
554:
16:
For the rural locality in
Murmansk Oblast, Russia, see
317:
447:
Erixon P, Oxelman B (January 2008). Volff JN (ed.).
640:
110:, except near highly repetitive regions, including
87:at three adjacent nucleotides have been observed).
282:
1125:
867:(9th ed.). W. H. Freeman. pp. 726–892.
877:
646:
947:
705:
446:
311:
954:
940:
276:
37:etion) is a molecular biology term for an
912:
839:
790:
733:
723:
682:
672:
623:
531:
482:
472:
440:
423:
413:
259:
210:
200:
1081:Mutation with respect to overall fitness
557:International Journal of Legal Medicine
389:
355:Environmental and Molecular Mutagenesis
1126:
862:
935:
807:
108:single nucleotide polymorphisms (SNP)
23:Insertions and deletions in a genome
137:nucleotides at a locus and species
13:
1006:Mutation with respect to structure
234:Ebert, Peter; et al. (2021).
14:
1150:
871:
856:
750:
591:
548:
499:
346:
227:
176:
1:
332:10.1016/S1383-5718(02)00277-2
297:10.1016/S0921-8734(96)90010-7
170:
961:
674:10.1371/journal.pone.0073514
474:10.1371/journal.pone.0001386
7:
153:
10:
1155:
1063:Chromosomal translocations
897:10.1126/sciimmunol.ade1167
725:10.1186/gb-2011-12-11-r114
15:
1080:
1055:
1012:
1005:
969:
569:10.1007/s00414-008-0306-7
202:10.1186/s13059-019-1828-7
1103:Nearly neutral mutation
252:10.1126/science.abf7117
1113:Nonsynonymous mutation
1068:Chromosomal inversions
970:Mechanisms of mutation
865:Molecular Cell Biology
604:Nucleic Acids Research
512:Nucleic Acids Research
18:Indel (rural locality)
1093:Advantageous mutation
1032:Conservative mutation
415:10.1186/1471-2156-9-8
1088:Deleterious mutation
1056:Large-scale mutation
160:Insertion (genetics)
1108:Synonymous mutation
1042:Frameshift mutation
783:10.1038/nature09534
775:2010Natur.467.1061T
769:(7319): 1061–1073.
665:2013PLoSO...873514B
465:2008PLoSO...3.1386E
165:Deletion (genetics)
66:frameshift mutation
55:structural variants
885:Science Immunology
863:Lodish, H (2021).
832:10.1101/gr.4565806
616:10.1093/nar/gkl938
524:10.1093/nar/gkq865
246:(6537): eabf7117.
1139:Molecular biology
1121:
1120:
1076:
1075:
1027:Missense mutation
1022:Nonsense mutation
320:Mutation Research
285:Mutation Research
1146:
1098:Neutral mutation
1047:Dynamic mutation
1010:
1009:
956:
949:
942:
933:
932:
927:
926:
916:
891:(81): eade1167.
875:
869:
868:
860:
854:
853:
843:
826:(9): 1182–1190.
811:
805:
804:
794:
754:
748:
747:
737:
727:
703:
697:
696:
686:
676:
644:
638:
637:
627:
595:
589:
588:
552:
546:
545:
535:
503:
497:
496:
486:
476:
444:
438:
437:
427:
417:
393:
387:
386:
350:
344:
343:
326:(1–2): 173–186.
315:
309:
308:
291:(5–6): 277–285.
280:
274:
273:
263:
231:
225:
224:
214:
204:
180:
1154:
1153:
1149:
1148:
1147:
1145:
1144:
1143:
1124:
1123:
1122:
1117:
1072:
1051:
1037:Silent mutation
1001:
965:
960:
930:
876:
872:
861:
857:
820:Genome Research
812:
808:
755:
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704:
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641:
596:
592:
553:
549:
504:
500:
445:
441:
394:
390:
351:
347:
316:
312:
281:
277:
232:
228:
181:
177:
173:
156:
133:has a run of 4
116:microsatellites
24:
21:
12:
11:
5:
1152:
1142:
1141:
1136:
1119:
1118:
1116:
1115:
1110:
1105:
1100:
1095:
1090:
1084:
1082:
1078:
1077:
1074:
1073:
1071:
1070:
1065:
1059:
1057:
1053:
1052:
1050:
1049:
1044:
1039:
1034:
1029:
1024:
1018:
1016:
1014:Point mutation
1007:
1003:
1002:
1000:
999:
998:
997:
992:
984:
979:
973:
971:
967:
966:
959:
958:
951:
944:
936:
929:
928:
870:
855:
806:
749:
712:Genome Biology
698:
639:
590:
563:(2): 177–184.
547:
498:
439:
388:
361:(4): 320–324.
345:
310:
275:
226:
189:Genome Biology
174:
172:
169:
168:
167:
162:
155:
152:
75:point mutation
70:Bloom syndrome
62:coding regions
22:
9:
6:
4:
3:
2:
1151:
1140:
1137:
1135:
1132:
1131:
1129:
1114:
1111:
1109:
1106:
1104:
1101:
1099:
1096:
1094:
1091:
1089:
1086:
1085:
1083:
1079:
1069:
1066:
1064:
1061:
1060:
1058:
1054:
1048:
1045:
1043:
1040:
1038:
1035:
1033:
1030:
1028:
1025:
1023:
1020:
1019:
1017:
1015:
1011:
1008:
1004:
996:
993:
991:
988:
987:
986:Substitution
985:
983:
980:
978:
975:
974:
972:
968:
964:
957:
952:
950:
945:
943:
938:
937:
934:
924:
920:
915:
910:
906:
902:
898:
894:
890:
886:
882:
874:
866:
859:
851:
847:
842:
837:
833:
829:
825:
821:
817:
810:
802:
798:
793:
788:
784:
780:
776:
772:
768:
764:
760:
753:
745:
741:
736:
731:
726:
721:
717:
713:
709:
702:
694:
690:
685:
680:
675:
670:
666:
662:
659:(9): e73514.
658:
654:
650:
643:
635:
631:
626:
621:
617:
613:
609:
605:
601:
594:
586:
582:
578:
574:
570:
566:
562:
558:
551:
543:
539:
534:
529:
525:
521:
517:
513:
509:
502:
494:
490:
485:
480:
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470:
466:
462:
458:
454:
450:
443:
435:
431:
426:
421:
416:
411:
407:
403:
399:
392:
384:
380:
376:
372:
368:
364:
360:
356:
349:
341:
337:
333:
329:
325:
321:
314:
306:
302:
298:
294:
290:
286:
279:
271:
267:
262:
257:
253:
249:
245:
241:
237:
230:
222:
218:
213:
208:
203:
198:
194:
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186:
179:
175:
166:
163:
161:
158:
157:
151:
147:
145:
140:
136:
132:
128:
124:
119:
117:
113:
109:
104:
100:
95:
93:
88:
85:
81:
77:
76:
71:
67:
63:
58:
56:
52:
48:
44:
40:
36:
32:
28:
19:
990:Transversion
888:
884:
873:
864:
858:
823:
819:
809:
766:
762:
752:
718:(11): R114.
715:
711:
701:
656:
652:
642:
607:
603:
593:
560:
556:
550:
518:(22): e203.
515:
511:
501:
459:(1): e1386.
456:
452:
442:
405:
402:BMC Genetics
401:
391:
358:
354:
348:
323:
319:
313:
288:
284:
278:
243:
239:
229:
192:
188:
178:
148:
144:phylogenetic
138:
130:
120:
112:homopolymers
96:
92:phylogenetic
89:
79:
73:
59:
34:
30:
26:
25:
127:systematics
84:nucleotides
82:one of the
1128:Categories
995:Transition
610:(3): e14.
195:(1): 246.
171:References
123:scientists
103:stop codon
977:Insertion
905:2470-9468
39:insertion
1134:Mutation
982:Deletion
963:Mutation
923:36961908
914:10351598
850:16902084
801:20981092
744:22104744
693:24039970
653:PLOS ONE
634:17169982
585:10531572
577:19052767
542:20923781
493:18167545
453:PLOS ONE
434:18211670
383:37019230
375:10398380
340:12504766
270:33632895
221:31747936
154:See also
80:replaces
43:deletion
33:sertion-
841:1557762
792:3042601
771:Bibcode
735:3334600
684:3769310
661:Bibcode
625:1807943
533:3001097
484:2148103
461:Bibcode
425:2266919
305:8649461
261:8026704
240:Science
212:6868818
49:in the
921:
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903:
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338:
303:
268:
258:
219:
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51:genome
581:S2CID
408:: 8.
379:S2CID
47:bases
27:Indel
919:PMID
901:ISSN
846:PMID
797:PMID
740:PMID
689:PMID
630:PMID
573:PMID
538:PMID
489:PMID
430:PMID
371:PMID
336:PMID
301:PMID
266:PMID
217:PMID
114:and
99:mRNA
909:PMC
893:doi
836:PMC
828:doi
787:PMC
779:doi
767:467
730:PMC
720:doi
679:PMC
669:doi
620:PMC
612:doi
565:doi
561:123
528:PMC
520:doi
479:PMC
469:doi
420:PMC
410:doi
363:doi
328:doi
324:534
293:doi
289:316
256:PMC
248:doi
244:372
207:PMC
197:doi
60:In
45:of
41:or
35:del
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907:.
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738:.
728:.
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606:.
602:.
579:.
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516:38
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510:.
487:.
477:.
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418:.
404:.
400:.
377:.
369:.
359:33
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287:.
264:.
254:.
242:.
238:.
215:.
205:.
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191:.
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830::
803:.
781::
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671::
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412::
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365::
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330::
307:.
295::
272:.
250::
223:.
199::
139:B
135:G
131:A
29:(
20:.
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