Conservation of the Exon-Intron Structure of Long Intergenic Non-Coding RNA Genes in Eutherian Mammals
Abstract
:1. Introduction
2. Materials and Methods
3. Results
3.1. Datasets
3.2. Evolutionary Conservation of Splicing Signals
3.3. Evolutionary Conservation of the Exon-Intron Structure
4. Discussion
5. Conclusions
Acknowledgments
Author Contributions
Conflicts of Interest
Abbreviations
lncRNA | long non-coding RNA |
lincRNA | long intergenic non-coding RNA |
nt | nucleotide |
References
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Features of lincRNA Genes | Mouse | Human |
---|---|---|
Number of all lincRNAs | 2,390 | 589 |
Number of intron-containing lincRNAs | 979 | 245 |
Number of exons | 3,439 | 1,194 |
Number of introns | 2,462 | 949 |
Number of exons shorter than 15 nt | 41 | 7 |
Number of introns per lincRNA | 2.52 | 3.86 |
Average gene length, nt (standard error) | 11,775 (712) | 17,192 (1,921) |
Median gene length, nt | 2,535 | 2,626 |
Average exon length, nt (standard error) | 524 (21) | 409 (48) |
Median exon length, nt | 464 | 356 |
Average intron length, nt (standard error) | 9,621 (1,631) | 10,562 (4,539) |
Median intron length, nt | 2,615 | 2,116 |
Species | Common Name (Number of Orthologs) | Splice Site Pairwise Comparison with Mouse or Human as a Reference | |||||
---|---|---|---|---|---|---|---|
Donor Splicing Site (GT or GC dinucleotide) | Acceptor Splicing Site (AG dinucleotide) | ||||||
Number of Matches | Number of Mismatches | Percent Matches | Number of Matches | Number of Mismatches | Percent Matches | ||
Mouse as a reference | |||||||
Rattus norvegicus | Rat (2285) | 1555 | 569 | 73% | 1448 | 669 | 68% |
Oryctolagus cuniculus | Rabbit (1522) | 518 | 258 | 67% | 419 | 306 | 58% |
Homo sapiens | Human (2091) | 902 | 619 | 59% | 746 | 715 | 51% |
Pan troglodytes | Chimp (2068) | 826 | 606 | 58% | 703 | 692 | 50% |
Macaca mulatta | Macaque (1971) | 807 | 543 | 60% | 682 | 647 | 51% |
Bos taurus | Cow (1815) | 694 | 402 | 63% | 560 | 498 | 53% |
Canis lupus familiaris | Dog (1897) | 714 | 512 | 58% | 627 | 581 | 52% |
Loxodonta africana | Elephant (1485) | 499 | 247 | 67% | 428 | 312 | 58% |
Echinops telfairi | Tenrec (1256) | 368 | 179 | 67% | 283 | 193 | 59% |
Takifugu Rubripes | Fugu (203) | 36 | 28 | 56% | 24 | 28 | 46% |
Monodelphis domestica | Opossum (1068) | 249 | 169 | 60% | 162 | 150 | 52% |
Dasypus novemcinctus | Armadillo (1426) | 469 | 260 | 64% | 382 | 322 | 54% |
Gallus gallus | Chicken (472) | 113 | 36 | 76% | 75 | 43 | 64% |
Danio rerio | Zebrafish (207) | 44 | 27 | 62% | 26 | 32 | 45% |
Tetraodon nigroviridis | Tetraodon (226) | 46 | 24 | 66% | 29 | 28 | 51% |
Xenopus tropicalis | Frog (312) | 74 | 37 | 67% | 51 | 40 | 56% |
Human as a reference | |||||||
Pan troglodytes | Chimp (575) | 870 | 19 | 98% | 867 | 15 | 98% |
Macaca mulatta | Macaque (564) | 800 | 53 | 94% | 828 | 42 | 95% |
Mus musculus | Mouse (488) | 368 | 120 | 75% | 364 | 105 | 78% |
Rattus norvegicus | Rat (476) | 369 | 112 | 77% | 342 | 102 | 77% |
Oryctolagus cuniculus | Rabbit (463) | 445 | 86 | 84% | 415 | 114 | 78% |
Bos taurus | Cow (527) | 531 | 122 | 81% | 484 | 144 | 77% |
Canis lupus familiaris | Dog (476) | 546 | 121 | 82% | 543 | 118 | 82% |
Loxodonta africana | Elephant (458) | 364 | 82 | 82% | 341 | 83 | 80% |
Echinops telfairi | Tenrec (419) | 196 | 59 | 77% | 175 | 68 | 72% |
Dasypus novemcinctus | Armadillo (468) | 362 | 95 | 79% | 320 | 122 | 72% |
Monodelphis domestica | Opossum (287) | 213 | 35 | 86% | 189 | 62 | 75% |
Gallus gallus | Chicken (131) | 33 | 10 | 77% | 23 | 18 | 56% |
Takifugu Rubripes | Fugu (80) | 48 | 7 | 87% | 51 | 11 | 82% |
Danio rerio | Zebrafish (79) | 43 | 7 | 86% | 44 | 9 | 83% |
Tetraodon nigroviridis | Tetraodon (87) | 49 | 16 | 75% | 52 | 18 | 74% |
Xenopus tropicalis | Frog (89) | 29 | 4 | 88% | 29 | 10 | 74% |
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Chernikova, D.; Managadze, D.; Glazko, G.V.; Makalowski, W.; Rogozin, I.B. Conservation of the Exon-Intron Structure of Long Intergenic Non-Coding RNA Genes in Eutherian Mammals. Life 2016, 6, 27. https://doi.org/10.3390/life6030027
Chernikova D, Managadze D, Glazko GV, Makalowski W, Rogozin IB. Conservation of the Exon-Intron Structure of Long Intergenic Non-Coding RNA Genes in Eutherian Mammals. Life. 2016; 6(3):27. https://doi.org/10.3390/life6030027
Chicago/Turabian StyleChernikova, Diana, David Managadze, Galina V. Glazko, Wojciech Makalowski, and Igor B. Rogozin. 2016. "Conservation of the Exon-Intron Structure of Long Intergenic Non-Coding RNA Genes in Eutherian Mammals" Life 6, no. 3: 27. https://doi.org/10.3390/life6030027
APA StyleChernikova, D., Managadze, D., Glazko, G. V., Makalowski, W., & Rogozin, I. B. (2016). Conservation of the Exon-Intron Structure of Long Intergenic Non-Coding RNA Genes in Eutherian Mammals. Life, 6(3), 27. https://doi.org/10.3390/life6030027