| No | Gene | Len. | Blast qCov/tCov | Domain qCov/tCov | EST all/spliced | Clean m full/part | Clean r full/part | Clean d full/part | Synteny m/r/d | Dupl. | Incompl. | CpG | OR | lr prob. | Ensemble/nscan/sgp/ eXoniphy/transmap | PET/SAGE/CAGE | id |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | chr1:+225720K | 657 | -/- | -/- | 0.0/0.0 | noaln/noaln | noaln/noaln | noaln/noaln | 0.0/0.0/0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.00 | 0.0/0.0/0.0 | orfchr1.660536 | |
| 2 | chr11:+113999K | 738 | -/- | -/- | 0.0/0.0 | noaln/noaln | noaln/noaln | noaln/noaln | 0.0/0.0/0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.01 | 0.0/0.0/1.0 | orfchr11.136474 | |
| 3 | chr15:-22880K | 642 | -/- | -/- | 0.0/0.0 | noaln/noaln | noaln/noaln | noaln/noaln | 0.0/0.0/0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.01 | 0.0/0.0/0.0 | orfchr15.297152 | |
| 4 | chr16:+34666K | 504 | -/- | -/- | 0.0/0.0 | noaln/noaln | noaln/noaln | noaln/noaln | 0.0/0.0/0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.00 | 0.0/0.0/0.0 | orfchr16.370008 | |
| 5 | chr17:-76494K | 636 | -/- | -/- | 0.0/0.0 | noaln/noaln | noaln/noaln | noaln/noaln | 0.0/0.0/0.0 | 0.0 | 0.0 | 0.4 | 0.0 | 0.01 | 0.0/0.0/1.0 | orfchr17.457935 | |
| 6 | chr2:+235425K | 504 | -/- | -/- | 0.0/0.0 | noaln/noaln | noaln/noaln | noaln/noaln | 0.0/0.0/0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.00 | 0.0/0.0/0.0 | orfchr2.878114 | |
| 7 | chr20:-60465K | 573 | -/- | -/- | 0.0/0.0 | noaln/noaln | noaln/noaln | noaln/noaln | 0.0/0.0/0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.01 | 0.0/0.0/0.0 | orfchr20.708604 | |
| 8 | chr3:+130248K | 765 | 0.1/0.1 | -/- | 0.0/0.0 | noaln/noaln | noaln/noaln | noaln/noaln | 0.0/0.0/0.0 | 0.0 | 639.0 | 0.6 | 0.0 | 0.00 | 0.0/0.0/0.0 | orfchr3.943214 | |
| 9 | chr6:+170311K | 525 | 0.4/0.2 | -/- | 0.0/0.0 | noaln/noaln | noaln/noaln | noaln/noaln | 0.0/0.0/0.0 | 0.0 | 1041.0 | 0.0 | 0.0 | 0.00 | 0.0/0.0/0.0 | orfchr6.1182980 | |
| 10 | chr7:-62210K | 591 | -/- | -/- | 0.0/0.0 | noaln/noaln | noaln/noaln | noaln/noaln | 0.0/0.0/0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.00 | 0.0/0.0/0.0 | orfchr7.1220553 | |
| 11 | chr8:-691K | 606 | 0.8/0.2 | -/- | 0.0/0.0 | noaln/noaln | noaln/noaln | noaln/noaln | 0.0/0.0/0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.00 | 0.0/0.0/0.0 | orfchr8.1267540 | |
| 12 | chrX:+37286K | 771 | -/- | -/- | 0.0/0.0 | noaln/noaln | noaln/noaln | noaln/noaln | 0.0/0.0/0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.01 | 0.0/0.0/0.0 | orfchrX.1411579 |
Blastx run on NCBI website against nr and swissprot database (with e-value threshold 0.01). For each database I list frames that occur among significant matches.
Sequences can be found in the fasta file of all negatives.
ID swissprot nr orfchr1.660536 1 (predicted XP proteins, only first 130a.a. of 450 a.a. target) orfchr11.136474 -1 1,-1,-2,-3 (matches mostly on neg. strand and to predicted proteins) orfchr15.297152 orfchr16.370008 1,3,-2 (mostly XP hypothetical proteins, one NP_ prot on rev. strand) orfchr17.457935 orfchr2.878114 orfchr20.708604 1,2 (short match to XP protein) orfchr3.943214 1,-2 1 (longer match on reverse strand, short match on forward with the same prot.) orfchr6.1182980 1,2,3 1,2 (matches proline-rich proteins in frame 2, fewer matches in frame 1 and 3) orfchr7.1220553 2 1,2 (frame 2, in-frame stop codon, covers a small portion of target) orfchr8.1267540 1,-3 (tandem repeat of HFIVSPYNKFI*) orfchrX.1411579 -1,-2,-3 -1,-2
Also, some of the more questionable RT PCR matches can be found here: orfchr20.708604, orfchr6.1182980, orfchrX.1411579.
Each file contains the original ORF (names starting with orfchr) and two RT PCR matches (names starting with numbers). It is quite confortable to submit the whole file to blat at UCSC server (assembly hg18 from March 2007) and see where the strongest matches occur.