Table 3.
Locations of 5′ and 3′ ends of AngHV1 RNAs identified by RACE
| End, method, and expta | ORF | Locationb | Frequencyc | Splicingd |
|---|---|---|---|---|
| 5′ ends, SMARTer RACE | ||||
| 01 | ORF18 | 26335-6 (−) | 4/6 (1) | None |
| 02 | ORF19 | 26232 (+) | 4/6 (2) | D+26343∧A+27106e |
| 03 | ORF19 | 26232 (+) | 8/18 (3) | None |
| 26442 (+) | 3/18 (1) | None | ||
| 04 | ORF25 | 37952 (+)l | 1/18 (1) | None |
| 37967 (+) | 1/18 | None | ||
| 37976 (+)f,m | 5/18 (1) | None | ||
| 37995 (+)f | 1/18 | None | ||
| 38012-3 (+)f,m | 2/18 (1) | None | ||
| 38032-3 (+)f,m | 1/18 | None | ||
| 38052 (+)f | 1/18 | None | ||
| 38099-100 (+)f | 2/18 | None | ||
| 05 | ORF29 | 46424-5 (−)m | 6/18 (4) | D−46317∧A−43244 |
| 46408 (−)l | 2/18 | D−46317∧A−43244 | ||
| 45738 (−) | 1/18 | D−45592∧A−43244g | ||
| 45183 (−) | 1/18 | D−45017∧A−43244h | ||
| 43304-6 (−)m | 2/18 (1) | None | ||
| 06 | ORF43 | 69124 (−)l | 4/6 (2) | None |
| 07 | ORF51 | 82859-60 (−)l | 10/12 (2) | None |
| 08 | ORF51 | 82859-60 (−)l | 5/18 (1) | None |
| 83153-4 (−)l | 4/18 (1) | D−83104∧A−82797 | ||
| 83153-4 (−)l | 4/18 (1) | D−83109∧A−82797 | ||
| 09 | ORF52 | 80341 (+)m | 1/18 | D+80715∧A+82795 |
| 81791-2 (+)l | 6/18 (3) | D+81947∧A+82795h | ||
| 81791-2 (+)l | 3/18 (1) | D+81958∧A+82795 | ||
| 82673-4 (+)m | 1/18 (1) | None | ||
| 10 | ORF59 | 93506-8 (+)m | 3/6 (2) | D+93589∧A+94994 |
| 11 | ORF89asi | 147018-9 (+) | 5/6 (1) | None |
| 12 | ORF97 | 162266-7 (−)m | 2/12 | None |
| 162221-3 (−)m | 3/12 | None | ||
| 162216 (−)l | 1/12 (1) | None | ||
| 162160-1 (−)f,m | 2/12 | None | ||
| 162143 (−)f,m | 2/12 | None | ||
| 13 | ORF100 | 178287 (−) | 1/18 | D−178008∧A−173267g |
| 173550-1 (−)m | 3/18 | None | ||
| 173550-1 (−)m | 3/18 | D−173459∧A−173267 | ||
| 173265 (−) | 3/18 | None | ||
| 14 | ORF105 | 177530 (+)l | 3/6 (2) | None |
| 15 | ORF106 | 186134 (−) | 2/12 (2) | D−185616∧A−182769 |
| 182814 (−) | 6/12 | None | ||
| 16 | ORF115 | 202995 (+)l | 4/6 (2) | None |
| 17 | ORF126 | 220185 (+)l | 5/6 | None |
| 3′ ends, SMARTer RACE | ||||
| 18 | ORF25j | |||
| 19 | ORF42 | 68468 (+)n | 3/6 (2) | None |
| 20 | ORF43 | 68472 (−)n | 3/6 (3) | None |
| 21 | ORF59 | 95631 (+)n | 6/6 | None |
| 22 | ORF126 | 221069 (+)n | 5/6 (1) | None |
| 23 | ORF131 | 227069 (−) | 2/6 (4) | None |
| 5′ ends, ExactSTART | ||||
| 24 | ORF25 | 37952 (+)l | 1/1 | None |
| 25 | ORF43 | 68966 (−)f,k,m | 1/1 | None |
| 26 | ORF100 | 173549 (−)m | 1/1 | D−173459∧A−173267 |
| 27 | ORF126 | 220189 (+)l | 1/1 | None |
| 3′ ends, ExactSTART | ||||
| 28 | ORF25 | 38517 (+)n | 1/1 | None |
| 29 | ORF42 | 68468 (+)n | 1/1 | None |
| 30 | ORF43 | 68471 (−)n | 1/1 | None |
| 31 | ORF59 | 95631 (+)n | 1/1 | None |
| 32 | ORF126 | 221069 (+)n | 1/1 | None |
These numbers correspond to the lane numbers in Fig. 3 and the experiment numbers in Table S2 in the supplemental material.
The most frequently detected genome coordinate is shown; (+), rightward transcription; (−), leftward transcription. Ambiguity is due to the SMARTer RACE method.
Number of plasmids that supported the location/total number sequenced. Parenthetical numbers are the number of additional plasmids from which ends were mapped within a few nucleotides.
D, donor site; A, acceptor site; +, rightward transcription; −, leftward transcription; ∧, splice junction.
Predicted to replace the N-terminal portion of the full-length protein.
Downstream from the first ATG codon. For ORF25, truncated proteins would lack a signal peptide.
Donor site not detected by deep sequencing.
Predicted to extend the N-terminal portion of the annotated protein.
Antisense to ORF89 and ORF90.
No viable bacterial clones were obtained.
A probable artifactual product was analyzed.
Candidate 5′ end also identified from deep sequencing at or within a few nucleotides, supported by >10 reads in library I and included in Table 2.
Candidate 5′ end also identified from deep sequencing at or within a few nucleotides, supported by ≤10 reads in library I and excluded from Table 2.
Candidate 3′ end also identified from deep sequencing at or within a few nucleotides, and included in Table 2.