475:
718:
differ from prokaryotes in distribution of overlap types: while unidirectional (i.e., same-strand) overlaps are most common in prokaryotes, opposite or antiparallel-strand overlaps are more common in eukaryotes. Among the opposite-strand overlaps, convergent orientation is most common. Most studies of eukaryotic gene overlap have found that overlapping genes are extensively subject to genomic reorganization even in closely related species, and thus the presence of an overlap is not always well-conserved. Overlap with older or less taxonomically restricted genes is also a common feature of genes likely to have originated
153:
398:
257:(HBV), whose DNA genome contains numerous overlapping genes, showed the mean number of synonymous nucleotide substitutions per site in overlapping coding regions was significantly lower than that of non-overlapping regions. The same study showed that it was possible for some of these overlapping regions and their proteins to diverge significantly from the original when there's weak selection against amino acid change. The
499:
781:
may be inappropriate for the detection of overlapping genes as they are reliant on already curated genes while overlapping genes are generally overlooked contain atypical sequence composition. Genome annotation standards are also often biased against feature overlaps, such as genes entirely contained
717:
Compared to prokaryotic genomes, eukaryotic genomes are often poorly annotated and thus identifying genuine overlaps is relatively challenging. However, examples of validated gene overlaps have been documented in a variety of eukaryotic organisms, including mammals such as mice and humans. Eukaryotes
130:
regions of the genome. It is believed that most overlapping genes, or genes whose expressible nucleotide sequences partially overlap with each other, evolved in part due to this mechanism, suggesting that each overlap is composed of one ancestral gene and one novel gene. Subsequently, overprinting is
691:
co-regulated. In prokaryotic genomes, unidirectional overlaps are most common, possibly due to the tendency of adjacent prokaryotic genes to share orientation. Among unidirectional overlaps, long overlaps are more commonly read with a one-nucleotide offset in reading frame (i.e., phase 1) and short
550:
longer than the measured length of its genome. Analysis of the fully sequenced 5386 nucleotide genome showed that the virus possessed extensive overlap between coding regions, revealing that some genes (like genes D and E) were translated from the same DNA sequences but in different reading frames.
730:
The precise functions of overlapping genes seems to vary across the domains of life but several experiments have shown that they are important for virus lifecycles through proper protein expression and stoichiometry as well as playing a role in proper protein folding. A version of
139:
organization of viruses, likely to greatly increase the number of potential expressible genes from a small set of viral genetic information. It is likely that overprinting is responsible for the generation of numerous novel proteins by viruses over the course of their
786:
markedly penalizes overlaps between predicted ORFs. However, rapid advancement of genome-scale protein and RNA measurement tools along with increasingly advanced prediction algorithms have revealed an avalanche of overlapping genes and ORFs within numerous genomes.
465:
than older members, but the older members are also more disordered than other proteins, presumably as a way of alleviating the increased evolutionary constraints posed by overlap. Overlaps are more likely to originate in proteins that already have high disorder.
811:
is also used to identify genomic regions containing overlapping transcripts. It has been utilized to identify 180,000 alternate ORFs within previously annotated coding regions found in humans. Newly discovered ORFs such as these are verified using a variety of
768:
to deliver large human genes such as CFTR81. Therefore, it is suggested that overlapping genes evolved as a means to overcome these physical constraints, increasing genetic diversity by utilizing only the existing sequence rather than increasing genome length.
81:, gene overlap is almost always defined as mRNA transcript overlap. Specifically, a gene overlap in eukaryotes is defined when at least one nucleotide is shared between the boundaries of the primary mRNA transcripts of two or more genes, such that a DNA base
630:
and less restrictive genome sizes. The lower mutation rate of DNA viruses facilitates greater genomic novelty and evolutionary exploration within a structurally constrained genome and may be the primary driver of the evolution of overlapping genes.
602:
geometry. However, other studies dispute this conclusion and argue that the distribution of overlaps in viral genomes is more likely to reflect overprinting as the evolutionary origin of overlapping viral genes. Overprinting is a common source of
571:
was shown to express a novel protein that induces lysis of E. coli by inhibiting biosynthesis of its cell wall, suggesting that de novo protein creation through the process of overprinting can be a significant factor in the evolution of
295:
are encoded by overlapping genes that form a 549 nt coding region, and p19 is shown to be under positive selection while p22 is under purifying selection. Additional examples are mentioned in studies involving overlapping genes of the
1389:
Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJ, Staden R, Young IG (April 1981). "Sequence and organization of the human mitochondrial genome".
252:
change is favored. Overlapping genes are reasoned to evolve under strict constraints as a single nucleotide substitution is able to alter the structure and function of the two proteins simultaneously. A study on the
678:
genomes typically find that around one third of bacterial genes are overlapped, though usually only by a few base pairs. Most studies of overlap in bacterial genomes find evidence that overlap serves a function in
244:
Studies on overlapping genes suggest that their evolution can be summarized in two possible models. In one model, the two proteins encoded by their respective overlapping genes evolve under similar
236:
occurs when the shared sequences use different reading frames. This can occur in "phase 1" or "phase 2", depending on whether the reading frames are offset by 1 or 2 nucleotides. Because a
1811:"Sequence analysis of Potato leafroll virus isolates reveals genetic stability, major evolutionary events and differential selection pressure between overlapping reading frame products"
226:
occurs when the shared sequences use the same reading frame. This is also known as "phase 0". Unidirectional genes with phase 0 overlap are not considered distinct genes, but rather as
745:
size limitations. Dramatic viability loss was observed in viruses with genomes engineered to be longer than the wild-type genome. Increasing the single-stranded DNA genome length of
626:
or in separate capsids, are more likely to contain an overlapping sequence than non-segmented viruses. RNA viruses have fewer overlapping genes than DNA viruses which possess lower
46:
partially overlaps with the expressible nucleotide sequence of another gene. In this way, a nucleotide sequence may make a contribution to the function of one or more
1586:
Rogozin IB, Spiridonov AN, Sorokin AV, Wolf YI, Jordan I, Tatusov RL, Koonin EV (May 2002). "Purifying and directional selection in overlapping prokaryotic genes".
583:
622:
contain overlapping coding sequences. Segmented viruses in particular, or viruses with their genome split into separate pieces and packaged either all in the same
179:
end of another gene on the same strand. This arrangement can be symbolized with the notation → → where arrows indicate the reading frame from start to end.
2376:
Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes JC, Hutchison CA, Slocombe PM, Smith M (1977). "Nucleotide sequence of bacteriophage ΦX174 DNA".
437:, who identified a candidate gene that may have arisen by this mechanism. Some de novo genes originating in this way may not remain overlapping, but
478:
Overlapping genes in the bacteriophage ΦX174 genome. There are 11 genes in this genome (A, A*, B-H, J, K). Genes B, K, E overlap with genes A, C, D.
474:
275:
The second model suggests that the two proteins and their respective overlap genes evolve under opposite selection pressures: one frame experiences
2618:"Finally, a Role Befitting A star : Strongly Conserved, Unessential Microvirus A* Proteins Ensure the Product Fidelity of Packaging Reactions"
280:
2186:
1301:
4378:"Viral Proteins Originated De Novo by Overprinting Can Be Identified by Codon Usage: Application to the "Gene Nursery" of Deltaretroviruses"
3231:
Cock PJ, Whitworth DE (19 March 2007). "Evolution of Gene
Overlaps: Relative Reading Frame Bias in Prokaryotic Two-Component System Genes".
2674:
1332:"Viral Proteins Originated De Novo by Overprinting Can Be Identified by Codon Usage: Application to the "Gene Nursery" of Deltaretroviruses"
4197:"Targeted replacement of full-length CFTR in human airway stem cells by CRISPR-Cas9 for pan-mutation correction in the endogenous locus"
272:
compared to the overlap regions that were highly conserved among different HBV strains, which are absolutely essential for the process.
265:
and the pre-S1 region of a surface protein of HBV, for example, had a percentage of conserved amino acids of 30% and 40%, respectively.
4634:
Prensner JR, Enache OM, Luria V, Krug K, Clauser KR, Dempster JM, Karger A, Wang L, Stumbraite K, Wang VM, Botta G (28 January 2021).
3659:"Overlapping genes of Aedes aegypti: evolutionary implications from comparison with orthologs of Anopheles gambiae and other insects"
3382:
Fellner L, Simon S, Scherling C, Witting M, Schober S, Polte C, Schmitt-Kopplin P, Keim DA, Scherer S, Neuhaus K (18 December 2015).
462:
4195:
Vaidyanathan S, Baik R, Chen L, Bravo DT, Suarez CJ, Abazari SM, Salahudeen AA, Dudek AM, Teran CA, Davis TH, Lee CM (March 2021).
2031:
Saha D, Podder S, Panda A, Ghosh TC (May 2016). "Overlapping genes: A significant genomic correlate of prokaryotic growth rates".
4536:"Decision letter: Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins"
4311:"Overlapping genes and the proteins they encode differ significantly in their sequence composition from non-overlapping genes"
85:
at any point of the overlapping region would affect the transcripts of all genes involved. This definition includes 5′ and 3′
308:. This phenomenon of overlapping genes experiencing different selection pressures is suggested to be a consequence of a high
824:. Attempts at proof-by-synthesis are also performed to show beyond doubt the absence of any undiscovered overlapping genes.
1756:"Conserved and non-conserved regions in the Sendai virus genome: Evolution of a gene possessing overlapping reading frames"
389:
of the overlapping genes. Gene overlaps introduce novel evolutionary constraints on the sequences of the overlap regions.
152:
112:
651:
503:
406:
292:
288:
1689:"Positive Selection or Free to Vary? Assessing the Functional Significance of Sequence Change Using Molecular Dynamics"
650:. In some cases overprinted proteins do have well-defined, but novel, three-dimensional structures; one example is the
2204:"Birth of a unique enzyme from an alternative reading frame of the preexisted, internally repetitious coding sequence"
791:
methods have been essential in discovering numerous overlapping genes and include a combination of techniques such as
556:
77:
transcripts, and is defined when these coding sequences share a nucleotide on either the same or opposite strands. In
61:. The current definition of an overlapping gene varies significantly between eukaryotes, prokaryotes, and viruses. In
3038:"Overlapping Genes Produce Proteins with Unusual Sequence Properties and Offer Insight into De Novo Protein Creation"
1544:
Normark S., Bergstrom S., Edlund T., Grundstrom T., Jaurin B., Lindberg F.P., Olsson O. (1983). "Overlapping genes".
3443:"New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation"
3384:"Evidence for the recent origin of a bacterial protein-coding, overlapping orphan gene by evolutionary overprinting"
634:
Studies of overprinted viral genes suggest that their protein products tend to be accessory proteins which are not
761:
413:
associated with blood cancers. This region contains numerous overlapping genes, several of which likely originated
313:
131:
also believed to be a source of novel proteins, as de novo proteins coded by these novel genes usually lack remote
156:
Tandem out-of-phase overlap of the human mitochondrial genes ATP8 (+1 frame, in red) and ATP6 (+3 frame, in blue)
4691:
Cao X, Khitun A, Luo Y, Na Z, Phoodokmai T, Sappakhaw K, Olatunji E, Uttamapinant C, Slavoff SA (5 March 2020).
1858:
Stamenković GG, Ćirković VS, Šiljić MM, Blagojević JV, Knežević AM, Joksić ID, Stanojević MP (24 October 2016).
563:
of the original A protein but possessing a different function It was concluded that other undiscovered sites of
119:
while still preserving the function of the original gene. Overprinting has been hypothesized as a mechanism for
4582:"Faculty Opinions recommendation of Pervasive functional translation of noncanonical human open reading frames"
753:, believed to be the result of the strict physical constraints imposed by the finite capsid volume. Studies on
684:
567:
could be hidden through the genome due to overlapping genes. An identified de novo gene of another overlapping
507:
379:
738:
has also been created where all gene overlaps were removed proving they were not necessary for replication.
765:
317:
754:
688:
383:
227:
1446:
Fukuda Y, Nakayama Y, Tomita M (December 2003). "On dynamics of overlapping genes in bacterial genomes".
610:
The proportion of viruses with overlapping coding sequences within their genomes varies. Double-stranded
4607:
4553:
4507:
4461:
301:
276:
245:
160:
Genes may overlap in a variety of ways and can be classified by their positions relative to each other.
43:
764:
showed that viral packaging is constrained by genetic cargo size limits, requiring the use of multiple
422:
3826:"Genome Modularization Reveals Overlapped Gene Topology Is Necessary for Efficient Viral Reproduction"
312:
of nucleotide substitution with different effects on the two frames; the substitutions may be majorly
4763:
4704:
4389:
4322:
3980:
3729:
3670:
3562:
3395:
3240:
2566:
2503:
2443:
2385:
2215:
2082:
1985:
1871:
1700:
1637:
1399:
1343:
1226:
1167:
792:
564:
438:
99:
refers to a type of overlap in which all or part of the sequence of one gene is read in an alternate
4309:
Pavesi A, Vianelli A, Chirico N, Bao Y, Blinkova O, Belshaw R, Firth A, Karlin D (19 October 2018).
4490:"Faculty Opinions recommendation of The RAST Server: rapid annotations using subsystems technology"
817:
297:
86:
700:. Robustly validated examples of long overlaps in bacterial genomes are rare; in the well-studied
4595:
4234:
4120:
3880:
3861:
3333:"Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions?"
3264:
3151:
2981:"New insights into the evolutionary features of viral overlapping genes by discriminant analysis"
2598:
2535:
2409:
1954:
1791:
1669:
1423:
1104:
Normark S, Bergström S, Edlund T, Grundström T, Jaurin B, Lindberg FP, Olsson O (December 1983).
796:
647:
591:
345:
120:
4636:"Noncanonical open reading frames encode functional proteins essential for cancer cell survival"
429:
by mutations to introduce novel ORFs in alternate reading frames; he described the mechanism as
397:
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4781:
4732:
4673:
4655:
4425:
4407:
4358:
4340:
4291:
4273:
4226:
4177:
4159:
4112:
4104:
4063:
4055:
4016:
3998:
3949:
3941:
3900:
3853:
3845:
3806:
3757:
3698:
3639:
3590:
3526:
3472:
3423:
3364:
3313:
3256:
3210:
3192:
3143:
3102:
3085:
Abroi A (1 December 2015). "A protein domain-based view of the virosphere–host relationship".
3067:
3018:
3000:
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2943:
2902:
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2845:
2827:
2783:
2732:
2655:
2637:
2590:
2582:
2527:
2519:
2469:
2401:
2353:
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2243:
2182:
2159:
2110:
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2013:
1946:
1905:
1887:
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1195:
1133:
1125:
1086:
1068:
1020:
958:
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890:
821:
697:
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are more common for convergent genes; however, putative long overlaps have very high rates of
269:
132:
4789:
4771:
4722:
4714:
4663:
4647:
4585:
4539:
4493:
4447:
4415:
4397:
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4265:
4216:
4208:
4167:
4151:
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4047:
4006:
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3931:
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3747:
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3354:
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3303:
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3200:
3182:
3133:
3094:
3057:
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3008:
2992:
2951:
2933:
2892:
2876:
2835:
2819:
2773:
2763:
2722:
2714:
2645:
2629:
2574:
2511:
2459:
2451:
2393:
2343:
2335:
2287:
2279:
2233:
2223:
2149:
2141:
2100:
2090:
2040:
2003:
1993:
1936:
1895:
1879:
1822:
1767:
1726:
1708:
1645:
1595:
1553:
1513:
1505:
1455:
1407:
1361:
1351:
1289:
1252:
1234:
1185:
1175:
1117:
1076:
1058:
1010:
1002:
948:
932:
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813:
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toward small genome sizes mediated by the physical constraints of packaging the genome in a
568:
539:
531:
442:
356:
104:
3920:"A fully decompressed synthetic bacteriophage øX174 genome assembled and archived in yeast"
4620:
4566:
4520:
4474:
680:
483:
410:
386:
141:
1105:
248:. The proteins and the overlap region are highly conserved when strong selection against
4767:
4693:"Alt-RPL36 downregulates the PI3K-AKT-mTOR signaling pathway by interacting with TMEM24"
4393:
4326:
3984:
3733:
3674:
3566:
3399:
3244:
2570:
2507:
2447:
2389:
2219:
2086:
1989:
1875:
1704:
1641:
1557:
1403:
1347:
1230:
1171:
1121:
328:
Overlapping genes are particularly common in rapidly evolving genomes, such as those of
240:
is three nucleotides long, an offset of three nucleotides is an in-phase, phase 0 frame.
4824:
4794:
4751:
4727:
4692:
4668:
4420:
4377:
4353:
4310:
4286:
4221:
4196:
4172:
3881:"Translational Coupling Controls Expression and Function of the DrrAB Drug Efflux Pump"
3801:
3776:
3752:
3717:
3693:
3658:
3585:
3550:
3521:
3494:
3467:
3442:
3418:
3383:
3359:
3332:
3308:
3283:
3205:
3170:
3062:
3037:
3013:
2956:
2921:
2897:
2840:
2778:
2751:
2727:
2702:
2650:
2464:
2431:
2348:
2323:
2292:
2267:
2154:
2130:"A Simple Method for Estimating the Strength of Natural Selection on Overlapping Genes"
2129:
2105:
2070:
2008:
1973:
1941:
1924:
1900:
1731:
1688:
1366:
1331:
1081:
1046:
953:
920:
885:
856:
800:
788:
778:
701:
635:
363:
305:
127:
108:
51:
17:
4099:
4082:
4011:
3968:
3634:
3609:
3138:
2238:
2203:
1599:
1518:
1493:
1047:"Origin, Evolution and Stability of Overlapping Genes in Viruses: A Systematic Review"
1015:
982:
4818:
4599:
4238:
4051:
3865:
3825:
1257:
1214:
1190:
1155:
758:
732:
639:
627:
547:
535:
515:
450:
309:
216:
100:
74:
70:
4124:
3268:
3155:
1795:
1673:
857:"Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic"
498:
4444:"Supplemental Information 2: NCBI genome database accession information (PDF file)"
2679:
2602:
2539:
2413:
1958:
1427:
741:
The retention and evolution of overlapping genes within viruses may also be due to
659:
595:
454:
337:
207:
ends of the two genes overlap on opposite strands. This can be written as ← →.
193:
ends of the two genes overlap on opposite strands. This can be written as → ←.
47:
4590:
4581:
4035:
3121:
1281:
355:
By extension of an existing ORF upstream into a contiguous gene due to loss of an
107:. The alternative open reading frames (ORF) are thought to be created by critical
4402:
4335:
4253:
3742:
3098:
2980:
2095:
1713:
1356:
1293:
4635:
4452:
4443:
4269:
4212:
3936:
3919:
3284:"Origin and Length Distribution of Unidirectional Prokaryotic Overlapping Genes"
2996:
2675:"Scientists Just Found a Mysteriously Hidden 'Gene Within a Gene' in SARS-CoV-2"
2283:
1827:
1810:
833:
804:
750:
709:, only four gene pairs are well validated as having long, overprinted overlaps.
655:
599:
552:
458:
446:
434:
284:
254:
4718:
4651:
2208:
Proceedings of the
National Academy of Sciences of the United States of America
2044:
1459:
1160:
Proceedings of the
National Academy of Sciences of the United States of America
936:
4709:
3896:
3841:
3408:
3252:
2938:
2768:
1771:
643:
615:
560:
349:
262:
258:
249:
62:
4785:
4659:
4498:
4489:
4411:
4344:
4277:
4163:
4108:
4059:
4002:
3945:
3849:
3683:
3196:
3187:
3004:
2947:
2888:
2831:
2641:
2586:
2523:
2432:"Recognition of small interfering RNA by a viral suppressor of RNA silencing"
1891:
1836:
1779:
1755:
1722:
1657:
1248:
1129:
1072:
944:
692:
overlaps are more commonly read in phase 2. Long overlaps of greater than 60
405:
indicating the likely evolutionary trajectory of the gene-dense pX region in
370:
The use of the same nucleotide sequence to encode multiple genes may provide
4776:
4544:
4535:
4254:"Gene Birth Contributes to Structural Disorder Encoded by Overlapping Genes"
3575:
3511:
3349:
2864:
2339:
2268:"Gene Birth Contributes to Structural Disorder Encoded by Overlapping Genes"
1239:
1180:
1006:
782:
within another gene. Furthermore, some bioinformatics pipelines such as the
746:
693:
619:
614:
have fewer than a quarter that contains them while almost three-quarters of
611:
523:
402:
371:
78:
4803:
4736:
4677:
4429:
4362:
4295:
4230:
4181:
4020:
3993:
3953:
3904:
3857:
3810:
3761:
3702:
3643:
3594:
3530:
3476:
3458:
3427:
3368:
3317:
3260:
3214:
3147:
3106:
3071:
3022:
2965:
2906:
2880:
2849:
2787:
2736:
2718:
2659:
2491:
2473:
2357:
2301:
2228:
2163:
2114:
2052:
2017:
1998:
1950:
1909:
1844:
1787:
1740:
1607:
1527:
1467:
1375:
1090:
1024:
962:
894:
510:, a protein encoded by an overprinted gene. The protein specifically binds
4116:
4036:"Packaging of the bacteriophage λ chromosome: Effect of chromosome length"
3792:
3299:
2617:
2594:
2531:
2247:
2179:
Evolution of Living
Organisms: Evidence for a New Theory of Transformation
1665:
1565:
1419:
1266:
1199:
1137:
1063:
27:
A gene whose sequence partially overlaps the reading frame of another gene
4752:"Definitive demonstration by synthesis of genome annotation completeness"
4139:
4083:"Effects of genome size on bacteriophage phi X174 DNA packaging in vitro"
4067:
3918:
Jaschke PR, Lieberman EK, Rodriguez J, Sierra A, Endy D (December 2012).
3053:
2823:
2633:
2405:
2145:
1626:"Constrained evolution with respect to gene overlap of hepatitis B virus"
1624:
Mizokami M, Orito E, Ohba Ki, Ikeo K, Lau JY, Gojobori T (January 1997).
735:
675:
573:
333:
82:
4155:
2807:
2455:
1625:
1494:"Properties of overlapping genes are conserved across microbial genomes"
875:
449:. Which member of an overlapping gene pair is younger can be identified
135:
in databases. Overprinted genes are particularly common features of the
3625:
3036:
Rancurel C, Khosravi M, Dunker AK, Romero PR, Karlin D (29 July 2009).
1859:
1649:
1509:
808:
783:
543:
136:
116:
3447:
Philosophical
Transactions of the Royal Society B: Biological Sciences
2554:
1883:
2578:
2515:
2397:
1974:"The origin of a novel gene through overprinting in Escherichia coli"
1411:
742:
623:
555:
within the genome replication gene A of ΦX174 was shown to express a
527:
522:
The existence of overlapping genes was first identified in the virus
375:
90:
58:
50:. Overlapping genes are present in and a fundamental feature of both
3122:"Size Selective Recognition of siRNA by an RNA Silencing Suppressor"
4750:
Jaschke PR, Dotson GA, Hung KS, Liu D, Endy D (12 November 2019).
861:
663:
587:
578:
511:
497:
487:
473:
396:
329:
268:
However, these overlap regions are known to be less important for
237:
204:
190:
176:
172:
151:
66:
55:
2555:"Intragenic regulation of the synthesis of ΦX174 gene A proteins"
1687:
Allison JR, Lechner M, Hoeppner MP, Poole AM (12 February 2016).
534:
in 1977. Previous analysis of ΦX174, a small single-stranded DNA
486:, though with varying frequencies. They are especially common in
425:
proposed that one of the genes in the pair could have originated
2324:"Evolution of Viral Proteins Originated De Novo by Overprinting"
39:
1330:
Pavesi A, Magiorkinis G, Karlin DG, Wilke CO (15 August 2013).
3824:
Wright BW, Ruan J, Molloy MP, Jaschke PR (20 November 2020).
362:
By generation of a novel ORF within an existing one due to a
348:(ORF) downstream into a contiguous gene due to the loss of a
3120:
Vargason JM, Szittya G, Burgyán J, Hall TM (December 2003).
3969:"Redundancy, antiredundancy, and the robustness of genomes"
2616:
Roznowski AP, Doore SM, Kemp SZ, Fane BA (6 January 2020).
1860:"Substitution rate and natural selection in parvovirus B19"
3718:"De Novo Origin of Protein-Coding Genes in Murine Rodents"
3610:"Mammalian Overlapping Genes: The Comparative Perspective"
2922:"Gene overlapping and size constraints in the viral world"
2808:"Properties and abundance of overlapping genes in viruses"
2752:"Gene overlapping and size constraints in the viral world"
983:"Comparative study of overlapping genes in the genomes of
126:
from existing sequences, either older genes or previously
2071:"Evolutionary Dynamics of Overlapped Genes in Salmonella"
2069:
Luo Y, Battistuzzi F, Lin K, Gibas C (29 November 2013).
2869:
Proceedings of the Royal
Society B: Biological Sciences
2707:
Proceedings of the Royal
Society B: Biological Sciences
1215:"Origins of genes: "big bang" or continuous creation?"
1156:"Origins of genes: "big bang" or continuous creation?"
773:
Methods in identifying overlapping genes and ORFs
111:
within an expressible pre-existing gene, which can be
4376:
Pavesi A, Magiorkinis G, Karlin DG (15 August 2013).
3777:"Recent de novo origin of human protein-coding genes"
3716:
Murphy DN, McLysaght A, Carmel L (21 November 2012).
921:"Overlapping genes in natural and engineered genomes"
4034:
Feiss M, Fisher R, Crayton M, Egner C (March 1977).
1754:
Fujii Y, Kiyotani K, Yoshida T, Sakaguchi T (2001).
590:
genomes. Some studies attribute this observation to
586:
virus. Overlapping genes are particularly common in
3282:Fonseca MM, Harris DJ, Posada D (5 November 2013).
919:Wright BW, Molloy MP, Jaschke PR (5 October 2021).
3544:
3542:
3540:
3495:"Overlapping genes in the human and mouse genomes"
3171:"Overlapping genes: a window on gene evolvability"
2490:Barrell BG, Air GM, Hutchison CA (November 1976).
461:. Younger members of the pair tend to have higher
3551:"Birth and death of gene overlaps in vertebrates"
1972:Delaye L, DeLuna A, Lazcano A, Becerra A (2008).
2863:Chirico N, Vianelli A, Belshaw R (7 July 2010).
2701:Chirico N, Vianelli A, Belshaw R (7 July 2010).
4756:Proceedings of the National Academy of Sciences
4140:"Effect of Genome Size on AAV Vector Packaging"
3973:Proceedings of the National Academy of Sciences
1581:
1579:
1577:
1575:
1539:
1537:
1487:
1485:
1483:
1481:
1479:
1477:
1219:Proceedings of the National Academy of Sciences
855:Nelson, Chase W, et al. (1 October 2020).
2430:Ye K, Malinina L, Patel DJ (3 December 2003).
2371:
2369:
2367:
2317:
2315:
2313:
2311:
2261:
2259:
2257:
1925:"Stability and Evolution of Overlapping Genes"
1441:
1439:
1437:
1288:, Cambridge University Press, pp. 76–90,
3488:
3486:
2322:Sabath N, Wagner A, Karlin D (19 July 2012).
1325:
1323:
1321:
1319:
976:
974:
972:
850:
848:
749:by >1% results in almost complete loss of
8:
3775:Knowles DG, McLysaght A (2 September 2009).
3226:
3224:
1149:
1147:
211:Overlapping genes can also be classified by
3967:Krakauer DC, Plotkin JB (29 January 2002).
2064:
2062:
646:distributions and high levels of intrinsic
530:was the first DNA genome ever sequenced by
3549:Makałowska I, Lin CF, Hernandez K (2007).
3441:McLysaght A, Guerzoni D (31 August 2015).
2492:"Overlapping genes in bacteriophage φX174"
2425:
2423:
981:Y. Fukuda, M. Tomita et T. Washio (1999).
822:catalytically dead Cas9 (dCas9) disruption
642:. Overprinted proteins often have unusual
638:to viral proliferation, but contribute to
4793:
4775:
4726:
4708:
4667:
4589:
4543:
4497:
4451:
4419:
4401:
4352:
4334:
4285:
4220:
4171:
4098:
4010:
3992:
3935:
3800:
3751:
3741:
3692:
3682:
3633:
3584:
3574:
3520:
3510:
3466:
3417:
3407:
3358:
3348:
3331:Pallejà A, Harrington ED, Bork P (2008).
3307:
3204:
3186:
3137:
3061:
3012:
2955:
2937:
2896:
2839:
2777:
2767:
2726:
2649:
2463:
2347:
2291:
2237:
2227:
2153:
2104:
2094:
2007:
1997:
1940:
1899:
1826:
1730:
1712:
1517:
1365:
1355:
1282:"In search of the origins of viral genes"
1256:
1238:
1189:
1179:
1080:
1062:
1014:
952:
884:
874:
559:with an identical coding sequence to the
3879:Pradhan P, Li W, Kaur P (January 2009).
683:, permitting the overlapped genes to be
662:and a novel binding mode in recognizing
4138:Wu Z, Yang H, Colosi P (January 2010).
2806:Schlub TE, Holmes EC (1 January 2020).
844:
4616:
4605:
4562:
4551:
4516:
4505:
4470:
4459:
4081:Aoyama A, Hayashi M (September 1985).
340:. They may originate in three ways:
3169:Huvet M, Stumpf MP (1 January 2014).
2801:
2799:
2797:
2485:
2483:
1619:
1617:
1280:Gibbs A, Keese PK (19 October 1995),
1213:Keese PK, Gibbs A (15 October 1992).
1154:Keese PK, Gibbs A (15 October 1992).
7:
3608:Veeramachaneni V (1 February 2004).
3493:C. Sanna, W. Li et L. Zhang (2008).
1809:Guyader S, Ducray DG (1 July 2002).
1040:
1038:
1036:
1034:
914:
912:
910:
908:
906:
904:
576:of viruses. Another example is the
445:, contributing to the prevalence of
378:size and due to the opportunity for
2920:Brandes N, Linial M (21 May 2016).
2750:Brandes N, Linial M (21 May 2016).
2128:Wei X, Zhang J (31 December 2014).
1558:10.1146/annurev.ge.17.120183.002435
1122:10.1146/annurev.ge.17.120183.002435
546:produced during infection required
457:distribution, or by less optimized
4252:Willis S, Masel J (19 July 2018).
2266:Willis S, Masel J (19 July 2018).
1942:10.1111/j.0014-3820.2000.tb00075.x
1286:Molecular Basis of Virus Evolution
175:end of one gene overlaps with the
25:
316:for one frame while mostly being
4580:Bazzini A, Wu Q (6 March 2020).
2553:LINNEY E, HAYASHI M (May 1974).
514:produced as part of the plant's
433:. It was later substantiated by
215:, which describe their relative
4534:Ben-Tal N, ed. (23 June 2017).
4087:Journal of Biological Chemistry
3657:Behura SK, Severson DW (2013).
2673:Dockrill P (11 November 2020).
2328:Molecular Biology and Evolution
722:in a given eukaryotic lineage.
482:Overlapping genes occur in all
3233:Journal of Molecular Evolution
2865:"Why genes overlap in viruses"
2703:"Why genes overlap in viruses"
1630:Journal of Molecular Evolution
1492:Johnson Z, Chisholm S (2004).
374:advantage due to reduction in
103:from another gene at the same
1:
4591:10.3410/f.737484924.793572056
4100:10.1016/s0021-9258(17)39144-5
3139:10.1016/S0092-8674(03)00984-X
1600:10.1016/S0168-9525(02)02649-5
777:Standardized methods such as
674:Estimates of gene overlap in
463:intrinsic structural disorder
4403:10.1371/journal.pcbi.1003162
4336:10.1371/journal.pone.0202513
4052:10.1016/0042-6822(77)90425-1
3885:Journal of Molecular Biology
3743:10.1371/journal.pone.0048650
3288:G3: Genes, Genomes, Genetics
3099:10.1016/j.biochi.2015.08.008
2134:Genome Biology and Evolution
2096:10.1371/journal.pone.0081016
1714:10.1371/journal.pone.0147619
1357:10.1371/journal.pcbi.1003162
1294:10.1017/cbo9780511661686.008
652:RNA silencing suppressor p19
504:RNA silencing suppressor p19
453:either by a more restricted
407:human T-lymphotropic virus 1
344:By extension of an existing
4270:10.1534/genetics.118.301249
4213:10.1016/j.ymthe.2021.03.023
3937:10.1016/j.virol.2012.09.020
2997:10.1016/j.virol.2020.03.007
2284:10.1534/genetics.118.301249
1828:10.1099/0022-1317-83-7-1799
1815:Journal of General Virology
620:single-stranded DNA genomes
538:that infected the bacteria
4841:
4719:10.1038/s41467-020-20841-6
4652:10.1038/s41587-020-00806-2
4382:PLOS Computational Biology
2045:10.1016/j.gene.2016.02.002
1460:10.1016/j.gene.2003.09.021
1336:PLOS Computational Biology
937:10.1038/s41576-021-00417-w
4710:10.1101/2020.03.04.977314
4488:Ahmed N (27 March 2009).
4453:10.7717/peerj.6447/supp-2
3897:10.1016/j.jmb.2008.11.027
3842:10.1021/acssynbio.0c00323
3409:10.1186/s12862-015-0558-z
3253:10.1007/s00239-006-0180-1
2939:10.1186/s13062-016-0128-3
2769:10.1186/s13062-016-0128-3
1923:Krakauer DC (June 2000).
1546:Annual Review of Genetics
1110:Annual Review of Genetics
658:, which has both a novel
279:while the other is under
4499:10.3410/f.1157743.618965
3684:10.1186/1471-2148-13-124
3663:BMC Evolutionary Biology
3555:BMC Evolutionary Biology
3388:BMC Evolutionary Biology
3188:10.1186/1471-2164-15-721
1978:BMC Evolutionary Biology
1045:Pavesi A (26 May 2021).
755:adeno-associated viruses
518:defense against viruses.
508:tomato bushy stunt virus
109:nucleotide substitutions
69:overlap must be between
4777:10.1073/pnas.1905990116
4545:10.7554/elife.27860.082
3576:10.1186/1471-2148-7-193
3512:10.1186/1471-2164-9-169
3350:10.1186/1471-2164-9-335
1772:10.1023/a:1008130318633
1240:10.1073/pnas.89.20.9489
1181:10.1073/pnas.89.20.9489
925:Nature Reviews Genetics
228:alternative start sites
18:Overprinting (genetics)
4615:Cite journal requires
4561:Cite journal requires
4515:Cite journal requires
4469:Cite journal requires
3994:10.1073/pnas.032668599
3459:10.1098/rstb.2014.0332
2979:Pavesi A (July 2020).
2881:10.1098/rspb.2010.1052
2719:10.1098/rspb.2010.1052
2229:10.1073/pnas.81.8.2421
1999:10.1186/1471-2148-8-31
598:, particularly one of
553:alternative start site
519:
479:
470:Taxonomic distribution
418:
157:
124:emergence of new genes
4697:Nature Communications
3830:ACS Synthetic Biology
3793:10.1101/gr.095026.109
3300:10.1534/g3.113.005652
2340:10.1093/molbev/mss179
2202:Ohno S (April 1984).
1064:10.3390/genes12060809
1007:10.1093/nar/27.8.1847
989:Mycoplasma pneumoniae
985:Mycoplasma genitalium
565:polypeptide synthesis
542:, suggested that the
501:
477:
417:through overprinting.
400:
320:for the other frame.
302:potato leafroll virus
234:Out-of-phase overlaps
155:
4640:Nature Biotechnology
3054:10.1128/JVI.00595-09
2634:10.1128/jvi.01593-19
816:techniques, such as
793:bottom-up proteomics
393:Origins of new genes
142:evolutionary history
87:untranslated regions
4768:2019PNAS..11624206J
4762:(48): 24206–24213.
4394:2013PLSCB...9E3162P
4327:2018PLoSO..1302513P
4156:10.1038/mt.2009.255
4093:(20): 11033–11038.
3985:2002PNAS...99.1405K
3734:2012PLoSO...748650M
3675:2013BMCEE..13..124B
3567:2007BMCEE...7..193M
3400:2015BMCEE..15..283F
3245:2007JMolE..64..457C
3048:(20): 10719–10736.
3042:Journal of Virology
2875:(1701): 3809–3817.
2713:(1701): 3809–3817.
2622:Journal of Virology
2571:1974Natur.249..345L
2508:1976Natur.264...34B
2456:10.1038/nature02213
2448:2003Natur.426..874Y
2390:1977Natur.265..687S
2220:1984PNAS...81.2421O
2087:2013PLoSO...881016L
1990:2008BMCEE...8...31D
1876:2016NatSR...635759S
1705:2016PLoSO..1147619A
1642:1997JMolE..44S..83M
1404:1981Natur.290..457A
1348:2013PLSCB...9E3162P
1231:1992PNAS...89.9489K
1172:1992PNAS...89.9489K
1106:"Overlapping Genes"
876:10.7554/eLife.59633
281:purifying selection
246:selection pressures
115:to express a novel
44:nucleotide sequence
3626:10.1101/gr.1590904
3453:(1678): 20140332.
2824:10.1093/ve/veaa009
2181:. Academic Press.
2177:Grassé PP (1977).
2146:10.1093/gbe/evu294
1864:Scientific Reports
1650:10.1007/pl00000061
1588:Trends in Genetics
1510:10.1101/gr.2433104
797:ribosome profiling
607:genes in viruses.
592:selective pressure
520:
480:
423:Pierre-Paul Grassé
419:
346:open reading frame
277:positive selection
158:
89:(UTRs) along with
42:whose expressible
4201:Molecular Therapy
4144:Molecular Therapy
3836:(11): 3079–3090.
3787:(10): 1752–1759.
2565:(5455): 345–348.
2442:(6968): 874–878.
2334:(12): 3767–3780.
2188:978-1-4832-7409-6
1884:10.1038/srep35759
1398:(5806): 457–465.
1303:978-0-521-45533-6
1225:(20): 9489–9493.
995:Nucleic Acids Res
779:genome annotation
685:transcriptionally
618:and viruses with
557:truncated protein
451:bioinformatically
255:hepatitis B virus
230:of the same gene.
16:(Redirected from
4832:
4808:
4807:
4797:
4779:
4747:
4741:
4740:
4730:
4712:
4688:
4682:
4681:
4671:
4631:
4625:
4624:
4618:
4613:
4611:
4603:
4593:
4577:
4571:
4570:
4564:
4559:
4557:
4549:
4547:
4531:
4525:
4524:
4518:
4513:
4511:
4503:
4501:
4485:
4479:
4478:
4472:
4467:
4465:
4457:
4455:
4440:
4434:
4433:
4423:
4405:
4373:
4367:
4366:
4356:
4338:
4321:(10): e0202513.
4306:
4300:
4299:
4289:
4249:
4243:
4242:
4224:
4192:
4186:
4185:
4175:
4135:
4129:
4128:
4102:
4078:
4072:
4071:
4031:
4025:
4024:
4014:
3996:
3979:(3): 1405–1409.
3964:
3958:
3957:
3939:
3915:
3909:
3908:
3876:
3870:
3869:
3821:
3815:
3814:
3804:
3772:
3766:
3765:
3755:
3745:
3713:
3707:
3706:
3696:
3686:
3654:
3648:
3647:
3637:
3605:
3599:
3598:
3588:
3578:
3546:
3535:
3534:
3524:
3514:
3490:
3481:
3480:
3470:
3438:
3432:
3431:
3421:
3411:
3379:
3373:
3372:
3362:
3352:
3328:
3322:
3321:
3311:
3279:
3273:
3272:
3228:
3219:
3218:
3208:
3190:
3166:
3160:
3159:
3141:
3117:
3111:
3110:
3082:
3076:
3075:
3065:
3033:
3027:
3026:
3016:
2976:
2970:
2969:
2959:
2941:
2917:
2911:
2910:
2900:
2860:
2854:
2853:
2843:
2803:
2792:
2791:
2781:
2771:
2747:
2741:
2740:
2730:
2698:
2692:
2691:
2689:
2687:
2670:
2664:
2663:
2653:
2613:
2607:
2606:
2579:10.1038/249345a0
2550:
2544:
2543:
2516:10.1038/264034a0
2487:
2478:
2477:
2467:
2427:
2418:
2417:
2398:10.1038/265687a0
2384:(5596): 687–95.
2373:
2362:
2361:
2351:
2319:
2306:
2305:
2295:
2263:
2252:
2251:
2241:
2231:
2199:
2193:
2192:
2174:
2168:
2167:
2157:
2125:
2119:
2118:
2108:
2098:
2066:
2057:
2056:
2028:
2022:
2021:
2011:
2001:
1969:
1963:
1962:
1944:
1920:
1914:
1913:
1903:
1855:
1849:
1848:
1830:
1821:(7): 1799–1807.
1806:
1800:
1799:
1751:
1745:
1744:
1734:
1716:
1684:
1678:
1677:
1621:
1612:
1611:
1583:
1570:
1569:
1541:
1532:
1531:
1521:
1489:
1472:
1471:
1443:
1432:
1431:
1412:10.1038/290457a0
1386:
1380:
1379:
1369:
1359:
1327:
1314:
1313:
1312:
1310:
1277:
1271:
1270:
1260:
1242:
1210:
1204:
1203:
1193:
1183:
1151:
1142:
1141:
1101:
1095:
1094:
1084:
1066:
1042:
1029:
1028:
1018:
1001:(8): 1847–1853.
978:
967:
966:
956:
916:
899:
898:
888:
878:
852:
814:reverse genetics
706:Escherichia coli
548:coding sequences
540:Escherichia coli
532:Frederick Sanger
443:gene duplication
439:subfunctionalize
357:initiation codon
224:In-phase overlap
71:coding sequences
32:overlapping gene
21:
4840:
4839:
4835:
4834:
4833:
4831:
4830:
4829:
4815:
4814:
4811:
4749:
4748:
4744:
4690:
4689:
4685:
4633:
4632:
4628:
4614:
4604:
4579:
4578:
4574:
4560:
4550:
4533:
4532:
4528:
4514:
4504:
4487:
4486:
4482:
4468:
4458:
4442:
4441:
4437:
4388:(8): e1003162.
4375:
4374:
4370:
4308:
4307:
4303:
4251:
4250:
4246:
4194:
4193:
4189:
4137:
4136:
4132:
4080:
4079:
4075:
4033:
4032:
4028:
3966:
3965:
3961:
3917:
3916:
3912:
3878:
3877:
3873:
3823:
3822:
3818:
3781:Genome Research
3774:
3773:
3769:
3715:
3714:
3710:
3656:
3655:
3651:
3614:Genome Research
3607:
3606:
3602:
3548:
3547:
3538:
3492:
3491:
3484:
3440:
3439:
3435:
3381:
3380:
3376:
3330:
3329:
3325:
3281:
3280:
3276:
3230:
3229:
3222:
3168:
3167:
3163:
3119:
3118:
3114:
3084:
3083:
3079:
3035:
3034:
3030:
2978:
2977:
2973:
2919:
2918:
2914:
2862:
2861:
2857:
2812:Virus Evolution
2805:
2804:
2795:
2749:
2748:
2744:
2700:
2699:
2695:
2685:
2683:
2672:
2671:
2667:
2615:
2614:
2610:
2552:
2551:
2547:
2502:(5581): 34–41.
2489:
2488:
2481:
2429:
2428:
2421:
2375:
2374:
2365:
2321:
2320:
2309:
2265:
2264:
2255:
2201:
2200:
2196:
2189:
2176:
2175:
2171:
2127:
2126:
2122:
2068:
2067:
2060:
2030:
2029:
2025:
1971:
1970:
1966:
1922:
1921:
1917:
1857:
1856:
1852:
1808:
1807:
1803:
1753:
1752:
1748:
1699:(2): e0147619.
1686:
1685:
1681:
1636:(S1): S83–S90.
1623:
1622:
1615:
1585:
1584:
1573:
1543:
1542:
1535:
1504:(11): 2268–72.
1491:
1490:
1475:
1445:
1444:
1435:
1388:
1387:
1383:
1342:(8): e1003162.
1329:
1328:
1317:
1308:
1306:
1304:
1279:
1278:
1274:
1212:
1211:
1207:
1166:(20): 9489–93.
1153:
1152:
1145:
1103:
1102:
1098:
1044:
1043:
1032:
980:
979:
970:
918:
917:
902:
854:
853:
846:
842:
830:
775:
728:
715:
689:translationally
681:gene regulation
672:
496:
484:domains of life
472:
411:deltaretrovirus
395:
380:transcriptional
326:
287:, the proteins
150:
28:
23:
22:
15:
12:
11:
5:
4838:
4836:
4828:
4827:
4817:
4816:
4810:
4809:
4742:
4683:
4646:(6): 697–704.
4626:
4617:|journal=
4572:
4563:|journal=
4526:
4517:|journal=
4480:
4471:|journal=
4435:
4368:
4301:
4264:(1): 303–313.
4244:
4207:(1): 223–237.
4187:
4130:
4073:
4046:(1): 281–293.
4026:
3959:
3930:(2): 278–284.
3910:
3891:(3): 831–842.
3871:
3816:
3767:
3728:(11): e48650.
3708:
3649:
3620:(2): 280–286.
3600:
3536:
3482:
3433:
3374:
3323:
3274:
3239:(4): 457–462.
3220:
3161:
3132:(7): 799–811.
3112:
3077:
3028:
2971:
2926:Biology Direct
2912:
2855:
2818:(1): veaa009.
2793:
2756:Biology Direct
2742:
2693:
2665:
2608:
2545:
2479:
2419:
2363:
2307:
2278:(1): 303–313.
2253:
2194:
2187:
2169:
2140:(1): 381–390.
2120:
2081:(11): e81016.
2058:
2039:(2): 143–147.
2023:
1964:
1935:(3): 731–739.
1915:
1850:
1801:
1746:
1679:
1613:
1594:(5): 228–232.
1571:
1533:
1473:
1433:
1381:
1315:
1302:
1272:
1205:
1143:
1116:(1): 499–525.
1096:
1030:
968:
931:(3): 154–168.
900:
843:
841:
838:
837:
836:
829:
826:
809:RNA sequencing
801:DNA sequencing
774:
771:
727:
724:
714:
711:
702:model organism
671:
668:
628:mutation rates
495:
492:
471:
468:
394:
391:
368:
367:
364:point mutation
360:
353:
325:
322:
314:non-synonymous
306:parvovirus B19
261:domain of the
242:
241:
231:
217:reading frames
209:
208:
194:
180:
165:Unidirectional
149:
148:Classification
146:
26:
24:
14:
13:
10:
9:
6:
4:
3:
2:
4837:
4826:
4823:
4822:
4820:
4813:
4805:
4801:
4796:
4791:
4787:
4783:
4778:
4773:
4769:
4765:
4761:
4757:
4753:
4746:
4743:
4738:
4734:
4729:
4724:
4720:
4716:
4711:
4706:
4702:
4698:
4694:
4687:
4684:
4679:
4675:
4670:
4665:
4661:
4657:
4653:
4649:
4645:
4641:
4637:
4630:
4627:
4622:
4609:
4601:
4597:
4592:
4587:
4583:
4576:
4573:
4568:
4555:
4546:
4541:
4537:
4530:
4527:
4522:
4509:
4500:
4495:
4491:
4484:
4481:
4476:
4463:
4454:
4449:
4445:
4439:
4436:
4431:
4427:
4422:
4417:
4413:
4409:
4404:
4399:
4395:
4391:
4387:
4383:
4379:
4372:
4369:
4364:
4360:
4355:
4350:
4346:
4342:
4337:
4332:
4328:
4324:
4320:
4316:
4312:
4305:
4302:
4297:
4293:
4288:
4283:
4279:
4275:
4271:
4267:
4263:
4259:
4255:
4248:
4245:
4240:
4236:
4232:
4228:
4223:
4218:
4214:
4210:
4206:
4202:
4198:
4191:
4188:
4183:
4179:
4174:
4169:
4165:
4161:
4157:
4153:
4149:
4145:
4141:
4134:
4131:
4126:
4122:
4118:
4114:
4110:
4106:
4101:
4096:
4092:
4088:
4084:
4077:
4074:
4069:
4065:
4061:
4057:
4053:
4049:
4045:
4041:
4037:
4030:
4027:
4022:
4018:
4013:
4008:
4004:
4000:
3995:
3990:
3986:
3982:
3978:
3974:
3970:
3963:
3960:
3955:
3951:
3947:
3943:
3938:
3933:
3929:
3925:
3921:
3914:
3911:
3906:
3902:
3898:
3894:
3890:
3886:
3882:
3875:
3872:
3867:
3863:
3859:
3855:
3851:
3847:
3843:
3839:
3835:
3831:
3827:
3820:
3817:
3812:
3808:
3803:
3798:
3794:
3790:
3786:
3782:
3778:
3771:
3768:
3763:
3759:
3754:
3749:
3744:
3739:
3735:
3731:
3727:
3723:
3719:
3712:
3709:
3704:
3700:
3695:
3690:
3685:
3680:
3676:
3672:
3668:
3664:
3660:
3653:
3650:
3645:
3641:
3636:
3631:
3627:
3623:
3619:
3615:
3611:
3604:
3601:
3596:
3592:
3587:
3582:
3577:
3572:
3568:
3564:
3560:
3556:
3552:
3545:
3543:
3541:
3537:
3532:
3528:
3523:
3518:
3513:
3508:
3504:
3500:
3496:
3489:
3487:
3483:
3478:
3474:
3469:
3464:
3460:
3456:
3452:
3448:
3444:
3437:
3434:
3429:
3425:
3420:
3415:
3410:
3405:
3401:
3397:
3393:
3389:
3385:
3378:
3375:
3370:
3366:
3361:
3356:
3351:
3346:
3342:
3338:
3334:
3327:
3324:
3319:
3315:
3310:
3305:
3301:
3297:
3293:
3289:
3285:
3278:
3275:
3270:
3266:
3262:
3258:
3254:
3250:
3246:
3242:
3238:
3234:
3227:
3225:
3221:
3216:
3212:
3207:
3202:
3198:
3194:
3189:
3184:
3180:
3176:
3172:
3165:
3162:
3157:
3153:
3149:
3145:
3140:
3135:
3131:
3127:
3123:
3116:
3113:
3108:
3104:
3100:
3096:
3092:
3088:
3081:
3078:
3073:
3069:
3064:
3059:
3055:
3051:
3047:
3043:
3039:
3032:
3029:
3024:
3020:
3015:
3010:
3006:
3002:
2998:
2994:
2990:
2986:
2982:
2975:
2972:
2967:
2963:
2958:
2953:
2949:
2945:
2940:
2935:
2931:
2927:
2923:
2916:
2913:
2908:
2904:
2899:
2894:
2890:
2886:
2882:
2878:
2874:
2870:
2866:
2859:
2856:
2851:
2847:
2842:
2837:
2833:
2829:
2825:
2821:
2817:
2813:
2809:
2802:
2800:
2798:
2794:
2789:
2785:
2780:
2775:
2770:
2765:
2761:
2757:
2753:
2746:
2743:
2738:
2734:
2729:
2724:
2720:
2716:
2712:
2708:
2704:
2697:
2694:
2682:
2681:
2676:
2669:
2666:
2661:
2657:
2652:
2647:
2643:
2639:
2635:
2631:
2627:
2623:
2619:
2612:
2609:
2604:
2600:
2596:
2592:
2588:
2584:
2580:
2576:
2572:
2568:
2564:
2560:
2556:
2549:
2546:
2541:
2537:
2533:
2529:
2525:
2521:
2517:
2513:
2509:
2505:
2501:
2497:
2493:
2486:
2484:
2480:
2475:
2471:
2466:
2461:
2457:
2453:
2449:
2445:
2441:
2437:
2433:
2426:
2424:
2420:
2415:
2411:
2407:
2403:
2399:
2395:
2391:
2387:
2383:
2379:
2372:
2370:
2368:
2364:
2359:
2355:
2350:
2345:
2341:
2337:
2333:
2329:
2325:
2318:
2316:
2314:
2312:
2308:
2303:
2299:
2294:
2289:
2285:
2281:
2277:
2273:
2269:
2262:
2260:
2258:
2254:
2249:
2245:
2240:
2235:
2230:
2225:
2221:
2217:
2214:(8): 2421–5.
2213:
2209:
2205:
2198:
2195:
2190:
2184:
2180:
2173:
2170:
2165:
2161:
2156:
2151:
2147:
2143:
2139:
2135:
2131:
2124:
2121:
2116:
2112:
2107:
2102:
2097:
2092:
2088:
2084:
2080:
2076:
2072:
2065:
2063:
2059:
2054:
2050:
2046:
2042:
2038:
2034:
2027:
2024:
2019:
2015:
2010:
2005:
2000:
1995:
1991:
1987:
1983:
1979:
1975:
1968:
1965:
1960:
1956:
1952:
1948:
1943:
1938:
1934:
1930:
1926:
1919:
1916:
1911:
1907:
1902:
1897:
1893:
1889:
1885:
1881:
1877:
1873:
1869:
1865:
1861:
1854:
1851:
1846:
1842:
1838:
1834:
1829:
1824:
1820:
1816:
1812:
1805:
1802:
1797:
1793:
1789:
1785:
1781:
1777:
1773:
1769:
1765:
1761:
1757:
1750:
1747:
1742:
1738:
1733:
1728:
1724:
1720:
1715:
1710:
1706:
1702:
1698:
1694:
1690:
1683:
1680:
1675:
1671:
1667:
1663:
1659:
1655:
1651:
1647:
1643:
1639:
1635:
1631:
1627:
1620:
1618:
1614:
1609:
1605:
1601:
1597:
1593:
1589:
1582:
1580:
1578:
1576:
1572:
1567:
1563:
1559:
1555:
1551:
1547:
1540:
1538:
1534:
1529:
1525:
1520:
1515:
1511:
1507:
1503:
1499:
1495:
1488:
1486:
1484:
1482:
1480:
1478:
1474:
1469:
1465:
1461:
1457:
1453:
1449:
1442:
1440:
1438:
1434:
1429:
1425:
1421:
1417:
1413:
1409:
1405:
1401:
1397:
1393:
1385:
1382:
1377:
1373:
1368:
1363:
1358:
1353:
1349:
1345:
1341:
1337:
1333:
1326:
1324:
1322:
1320:
1316:
1305:
1299:
1295:
1291:
1287:
1283:
1276:
1273:
1268:
1264:
1259:
1254:
1250:
1246:
1241:
1236:
1232:
1228:
1224:
1220:
1216:
1209:
1206:
1201:
1197:
1192:
1187:
1182:
1177:
1173:
1169:
1165:
1161:
1157:
1150:
1148:
1144:
1139:
1135:
1131:
1127:
1123:
1119:
1115:
1111:
1107:
1100:
1097:
1092:
1088:
1083:
1078:
1074:
1070:
1065:
1060:
1056:
1052:
1048:
1041:
1039:
1037:
1035:
1031:
1026:
1022:
1017:
1012:
1008:
1004:
1000:
996:
992:
990:
986:
977:
975:
973:
969:
964:
960:
955:
950:
946:
942:
938:
934:
930:
926:
922:
915:
913:
911:
909:
907:
905:
901:
896:
892:
887:
882:
877:
872:
868:
864:
863:
858:
851:
849:
845:
839:
835:
832:
831:
827:
825:
823:
819:
815:
810:
806:
802:
798:
794:
790:
789:Proteogenomic
785:
784:RAST pipeline
780:
772:
770:
767:
763:
760:
759:gene delivery
756:
752:
748:
744:
739:
737:
734:
733:bacteriophage
725:
723:
721:
712:
710:
708:
707:
703:
699:
698:misannotation
695:
690:
686:
682:
677:
669:
667:
665:
661:
657:
656:Tombusviruses
653:
649:
645:
641:
640:pathogenicity
637:
632:
629:
625:
621:
617:
613:
608:
606:
601:
597:
593:
589:
585:
581:
580:
575:
574:pathogenicity
570:
566:
562:
558:
554:
549:
545:
541:
537:
536:bacteriophage
533:
529:
525:
517:
516:RNA silencing
513:
509:
505:
500:
493:
491:
489:
485:
476:
469:
467:
464:
460:
456:
452:
448:
444:
440:
436:
432:
428:
424:
416:
412:
408:
404:
399:
392:
390:
388:
387:co-regulation
385:
384:translational
381:
377:
373:
365:
361:
358:
354:
351:
347:
343:
342:
341:
339:
335:
331:
323:
321:
319:
315:
311:
307:
303:
299:
294:
290:
286:
285:tombusviruses
282:
278:
273:
271:
267:
264:
260:
256:
251:
247:
239:
235:
232:
229:
225:
222:
221:
220:
218:
214:
206:
203:overlap: the
202:
198:
195:
192:
189:overlap: the
188:
184:
181:
178:
174:
171:overlap: the
170:
166:
163:
162:
161:
154:
147:
145:
143:
138:
134:
129:
125:
123:
118:
114:
110:
106:
102:
101:reading frame
98:
94:
92:
88:
84:
80:
76:
72:
68:
64:
60:
57:
53:
49:
48:gene products
45:
41:
37:
33:
19:
4812:
4759:
4755:
4745:
4700:
4696:
4686:
4643:
4639:
4629:
4608:cite journal
4575:
4554:cite journal
4529:
4508:cite journal
4483:
4462:cite journal
4438:
4385:
4381:
4371:
4318:
4314:
4304:
4261:
4257:
4247:
4204:
4200:
4190:
4150:(1): 80–86.
4147:
4143:
4133:
4090:
4086:
4076:
4043:
4039:
4029:
3976:
3972:
3962:
3927:
3923:
3913:
3888:
3884:
3874:
3833:
3829:
3819:
3784:
3780:
3770:
3725:
3721:
3711:
3666:
3662:
3652:
3617:
3613:
3603:
3558:
3554:
3505:(169): 169.
3502:
3499:BMC Genomics
3498:
3450:
3446:
3436:
3391:
3387:
3377:
3340:
3337:BMC Genomics
3336:
3326:
3294:(1): 19–27.
3291:
3287:
3277:
3236:
3232:
3178:
3175:BMC Genomics
3174:
3164:
3129:
3125:
3115:
3090:
3086:
3080:
3045:
3041:
3031:
2988:
2984:
2974:
2929:
2925:
2915:
2872:
2868:
2858:
2815:
2811:
2759:
2755:
2745:
2710:
2706:
2696:
2684:. Retrieved
2680:ScienceAlert
2678:
2668:
2625:
2621:
2611:
2562:
2558:
2548:
2499:
2495:
2439:
2435:
2381:
2377:
2331:
2327:
2275:
2271:
2211:
2207:
2197:
2178:
2172:
2137:
2133:
2123:
2078:
2074:
2036:
2032:
2026:
1981:
1977:
1967:
1932:
1928:
1918:
1870:(1): 35759.
1867:
1863:
1853:
1818:
1814:
1804:
1766:(1): 47–52.
1763:
1759:
1749:
1696:
1692:
1682:
1633:
1629:
1591:
1587:
1549:
1545:
1501:
1497:
1451:
1447:
1395:
1391:
1384:
1339:
1335:
1307:, retrieved
1285:
1275:
1222:
1218:
1208:
1163:
1159:
1113:
1109:
1099:
1054:
1050:
998:
994:
988:
984:
928:
924:
866:
860:
805:perturbation
776:
740:
729:
719:
716:
704:
673:
660:protein fold
633:
616:retroviridae
609:
604:
596:viral capsid
582:gene in the
577:
521:
481:
455:phylogenetic
447:orphan genes
431:overprinting
430:
426:
420:
414:
372:evolutionary
369:
338:mitochondria
327:
304:, and human
298:Sendai virus
274:
266:
243:
233:
223:
212:
210:
200:
196:
186:
182:
168:
164:
159:
121:
97:Overprinting
96:
95:
35:
31:
29:
3093:: 231–243.
2686:11 November
1760:Virus Genes
1552:: 499–525.
1454:: 181–187.
834:Nested gene
818:CRISPR-Cas9
751:infectivity
670:Prokaryotes
612:RNA viruses
600:icosahedral
459:codon usage
435:Susumu Ohno
409:(HTLV1), a
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