Table 2. Interspecies comparative analyses of pncr genes.
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Dp
|
Dv
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene name | BDGP cDNA ID | cDNA length, bp | Spliced | Dm ORF len. | Dp Ka/Ks* | Dv Ka/Ks† | Dp QRNA‡ | Dm embryo in situ | BLASTN score (%)§ | Northern¶ | Embryo in situ¶ | BLASTN expect (%)§ | Northern |
| pncr001:3R | LD11162 | 1,549 | - | 49 | 0.1156 | 0.1393 | O1040 | Zyg | 5.0e-39 (98)∥ | Pos. | Zyg** | 8.0e-38 (92) | Pos. |
| pncr002:3R | LP03188 | 553 | + | 59 | No TB | No TB | O475 | ND | 7.4e-40 (90)∥†† | Pos. | Zyg | 1.1e-08 (76) | Pos. |
| pncr003:2L | RE28911 | 1,005 | + | 44 | No TB | No TB | O856 | Zyg | 7.3e-67 (100) | Pos. | Zyg** | 18.3e-12 (74) | Pos. |
| pncr004:X | RE54004 | 562 | + | 26 | No TB | No TB | O406 | ND | 1.2e-12 (94) | Pos. | ND | No Dm ortho‡‡ | Pos. |
| pncr005:2R | RE63504 | 331 | + | 38 | No TB | No TB | O96 | ND | 2.4e-18 (56)†† | Pos. | Mat/Zyg | 2.0e-15 (47) | Pos. |
| pncr006:X | RH45340 | 407 | + | 48 | 0.0488 | No TB | P16O129 | Mat/Zyg | 1.9e-15 (31) | Pos. | Mat/Zyg** | 6.1e-08 (64) | Pos. |
| pncr007:3R | RH63361 | 424 | - | 62 | Fχ2 | Fχ2 | Q72 | ND | 4.6e-19 (84) | Pos. | Mat | 1.0e-10 (99) | Pos. |
| pncr008:3L | RH62830 | 326 | + | 40 | 0.1831 | 0.0527 | O259 | ND | 1.3e-11 (79) | Pos. | ND | 1.2e-08 (64) | Neg. |
| pncr009:3L | RH57193 | 981 | + | 33 | 0.2853 | No TB | O684 | Mat/Zyg | 2.5e-08 (39) | Neg. RT-PCR | Neg. RT-PCR | 2.9e-10 (73) | Pos. |
| pncr010:3L | AT24650 | 578 | + | 77 | No TB | No TB | No NT A | ND | No ortho. | — | — | No ortho | — |
| pncr011:3L | GH03576 | 931 | + | 38 | No TB | No TB | O326 | ND | 2.6e-09 (76)∥†† | Neg. RT-PCR | Neg. RT-PCR | No ortho | — |
| pncr012:2L | GH14469 | 695§§ | + | 40 | No TB | No TB | O518 | ND | 1.5e-06 (90)∥ | Neg. RT-PCR | Neg. RT-PCR | No ortho | — |
| pncr013:4 | GM01028 | 1,157§§ | + | 70 | 0.1056 | No TB | No NT A | Mat | No ortho∥ | — | — | No ortho | — |
| pncr014:3L | LD13184 | 2,222 | - | 88 | No TB | No TB | O992 | ND | 3.8e-10 (36) | Neg. RT-PCR | Neg. RT-PCR | No ortho | — |
| pncr015:3L | LP12023 | 313 | - | 59 | No TB | No TB | No NT A | ND | No ortho. | — | — | No ortho | — |
| pncr016:2R | RH09485 | 518 | + | 40 | No TB | No TB | No NT A | ND | No ortho. | — | — | No ortho | — |
| pncr017:3R | SD10988 | 1,415 | + | 80 | No TB | No TB | O1182 | ND | 1.4e-29 (91) | —¶¶ | —¶¶ | No ortho | — |
Analyses of the 17 putative noncoding RNA (pncr) transcripts that appeared on a Northern blot as discrete species, matching the lengths of the corresponding sequenced cDNAs. D. melanogaster (Dm) transcript length, splicing (confirmed by RT-PCR), longest Met-initiated ORF, Ka/Ks, and QRNA result, and embryo in situ hybridization results are shown, as well as sequence similarity of D. melanogaster transcripts to the genomes of D. pseudoobscura (Dp) and D. virilis (Dv) and experimental results in these two species. BDGP, Berkeley Drosophila Genome Project; Zyg, zygotic; Pos., positive; Neg., negative; No TB, no TBLASTN; ND, not detected; Mat, maternal; F χ2, failed χ2 test; No NT A, no NT ALIGN; —, not tested.
Values <0.5 (italics) signify conservation of condon structure; sequences that fail χ2 data fitness test or fail to produce a protein alignment are noted.
As in *, with D. virilis used as the comparative genome.
P, protein coding (italics); Q, RNA secondary structure; O, other. The number after the letter indicates the number of nucleotides assigned by QRNA to this category; sequences that fail to produce a nucleotide alignment are noted (no NT ALIGN).
The fraction of the D. melanogaster sequence (with a BLASTN expectation < 1e-05) aligned as a percentage of transcript length is given in parentheses; transcripts lacking nonrepetitive homology above this cutoff are labeled “no ortholog” (No ortho).
RT-dependent RT-PCR products were used as probes for Northern and in situ analyses. Cases where an orthologous transcript was not detected by RT-PCR are designated “negative RT-PCR” (Neg.), and Northern and in situ experiments were not performed. In cases where no putative ortholog was observed by sequence analysis or where homology was to repetitive regions, RT-PCR was not attempted.
D. melanogaster transcript sequence conserved in A. mellifera.
Patterns of expression for D. pseudoobscura transcripts are similar to those observed in D. melanogaster.
D. melanogaster transcript sequence conserved in A. gambiae.
This D. virilis ortholog could not be identified by homology to the D. melanogaster cDNA; instead, the D. pseudoobscura orthologous sequence was used for this purpose.
Additional longer RNA species are detected by Northern analysis.
D. melanogaster SD10988, pncr017:3R was only detected in Schneider S2 cells; no RT-PCR experiment was performed for this putative D. pseudoobscura ortholog.