SGP2 table

SGP2 predictions for human chr22
Preliminary analysis of the sgp2 predictions along the chromosome 22, not overlapping the 879 genes+pseudogenes annotated in chromosome 22
The annotation taken from http://www.cs.columbia.edu/~vic/sanger2gbd/ (Combined Gene + CDS Set).
There are 115 such sgp2 predictions. We have divided the predictions in: For each gene predicted (the so-called transcript here), we report:
1. chromosome coordinates of the coding exons, and the resulting cDNA and aa sequence
2. length of the transcript
3. number of exons
4. number of exons supported by tblastx hits to mouse trace sequences
5. fraction of the transcript sequence covered by tblastx hits to mouse trace sequences
6. number of exons overlapping genscan predictions
7-10. number of exons overlapping blat, blastz, exonerate (and "mystery") hits.
11-13. number of identical hits (more than 95% identical over at least 100bp) to ensembl cDNAs, human mRNAs and human ests.
14-18. number of similar hits (p<0.1) to mouse ests, rat ests, protein sequences, tetraodon genome sequence, and (not masking) conserved protein domains.


For 11-18 numbers, the blast results are linked (the link maybe not empty even if the reported number is zero).
12-18 numbers are set to zero for predictions identical to ensembl cDNAs, even though the link may not be empty).

SGP predictions identical to ensembl cDNA (95% identity over 100bp)

Gene Length Exons tblastx
exons 		tblastx
coverage 		Genscan Exonerate Blastz Blat "Mystery" Ensembl
cDNA 		GenBank
mRNA 		ESTHum ESTMouse ESTRat PROTNR Genome
Tetraodon 		CDD
chr22_31 249 2 1 95 0 1 1 1 1 2 0 0 0 0 0 0 0
chr22_34 627 4 4 93 4 3 4 4 0 2 0 0 0 0 0 0 0
chr22_48 1095 4 4 99 3 3 4 4 0 3 0 0 0 0 0 0 0
chr22_51 141 2 1 76 0 1 1 1 0 1 0 0 0 0 0 0 0
chr22_74 2373 10 9 79 8 7 9 9 0 4 0 0 0 0 0 0 0
chr22_75 432 3 2 96 2 2 3 2 1 1 0 0 0 0 0 0 0
chr22_76 2973 20 19 92 19 12 17 16 0 3 0 0 0 0 0 0 0
chr22_79 294 2 2 87 1 2 2 2 1 1 0 0 0 0 0 0 0
chr22_80 1287 5 3 91 3 3 2 3 1 2 0 0 0 0 0 0 0
chr22_133 564 2 2 99 2 1 2 2 0 1 0 0 0 0 0 0 0
chr22_135 1005 4 2 95 3 2 3 2 0 1 0 0 0 0 0 0 0
chr22_136 192 1 1 98 1 1 1 1 0 1 0 0 0 0 0 0 0
chr22_137 906 5 5 99 5 5 4 5 0 2 0 0 0 0 0 0 0
chr22_138 1182 11 9 82 10 8 10 10 0 4 0 0 0 0 0 0 0
chr22_147 3543 33 31 94 32 21 30 30 0 7 0 0 0 0 0 0 0
chr22_148 1500 4 4 99 4 4 4 4 0 1 0 0 0 0 0 0 0
chr22_149 1878 16 14 85 11 14 15 15 0 3 0 0 0 0 0 0 0
chr22_152 1674 17 16 96 17 11 16 16 0 3 0 0 0 0 0 0 0
chr22_153 795 8 8 98 8 8 8 8 0 2 0 0 0 0 0 0 0
chr22_159 924 9 7 95 7 3 7 7 0 1 0 0 0 0 0 0 0
chr22_169 1083 8 6 67 6 2 7 6 0 5 0 0 0 0 0 0 0
chr22_170 369 2 2 99 1 1 2 2 0 2 0 0 0 0 0 0 0
chr22_176 1521 10 9 89 8 7 9 8 0 3 0 0 0 0 0 0 0
chr22_178 510 3 3 99 3 0 3 3 0 3 0 0 0 0 0 0 0
chr22_347 270 4 2 91 2 0 2 2 0 1 0 0 0 0 0 0 0
chr22_358 147 1 1 95 1 1 1 1 0 5 0 0 0 0 0 0 0
chr22_374 189 2 1 78 1 1 1 1 0 2 0 0 0 0 0 0 0
chr22_384 195 1 1 81 1 0 1 1 0 3 0 0 0 0 0 0 0
chr22_386 156 2 1 69 1 0 2 0 0 2 0 0 0 0 0 0 0
chr22_685 456 1 1 92 1 1 1 1 0 3 0 0 0 0 0 0 0
chr22_698 288 2 2 100 1 2 1 2 0 1 0 0 0 0 0 0 0
chr22_813 282 2 1 70 2 1 2 1 1 1 0 0 0 0 0 0 0
chr22_830 192 3 1 33 2 1 2 2 0 1 0 0 0 0 0 0 0
chr22_834 1623 14 12 98 12 7 14 12 3 4 0 0 0 0 0 0 0
chr22_835 2460 6 5 91 5 4 5 5 0 3 0 0 0 0 0 0 0

SGP predictions overlapping genscan predictions

Gene Length Exons HSP
support. 		HSP
Cov. % 		Genscan Exonerate Blastz Mus Blat Mus Mystery Ensembl
cDNA 		GenBank
mRNA 		ESTHum ESTMouse ESTRat PROTNR Genome
Tetra 		CDDNCBI
chr22_47 327 2 2 99 2 1 2 1 1 0 0 0 0 0 0 8 0
chr22_49 873 2 2 98 1 1 2 1 0 0 0 1 2 3 10 0 1
chr22_94 1020 2 1 52 1 0 1 0 0 0 0 8 0 0 0 0 167
chr22_98 111 2 1 77 1 0 1 1 0 0 0 0 0 0 0 0 1
chr22_119 87 2 1 86 1 1 1 1 0 0 0 0 0 0 0 0 0
chr22_141 204 2 2 89 1 0 2 2 2 0 0 0 0 0 6 2 0
chr22_165 1296 2 2 42 1 0 2 1 0 0 0 10 0 0 0 0 220
chr22_188 1260 3 2 79 3 1 3 3 1 0 0 2 4 0 8 0 0
chr22_350 393 4 3 64 4 2 3 2 0 0 0 0 0 0 0 3 1
chr22_394 150 2 1 86 1 0 1 1 0 0 0 0 0 0 0 0 0
chr22_404 177 1 1 90 1 1 1 1 0 0 0 0 5 3 6 0 0
chr22_411 1599 3 2 92 2 0 2 2 0 0 0 0 0 0 0 0 1
chr22_453 309 3 2 93 1 2 3 3 0 0 0 5 0 0 0 0 0
chr22_484 1026 3 3 95 3 3 3 3 0 0 3 1 0 0 0 0 51
chr22_532 171 1 1 98 1 1 1 1 0 0 0 1 0 0 0 0 1
chr22_630 234 3 2 93 1 1 2 3 0 0 0 2 0 0 2 0 0
chr22_665 1038 3 2 64 2 1 2 1 1 0 0 0 0 0 0 0 1
chr22_700 294 3 2 88 3 2 3 3 0 0 0 0 0 0 0 0 0
chr22_702 411 5 4 89 3 1 3 2 0 0 0 0 1 0 0 0 0
chr22_706 102 1 1 97 1 0 1 0 0 0 0 2 0 0 0 0 0
chr22_721 333 3 2 91 1 2 3 2 0 0 0 2 0 0 0 0 0
chr22_756 657 1 1 95 1 1 1 1 0 0 0 2 7 2 9 0 0
chr22_764 741 3 2 95 2 0 0 0 0 0 0 0 0 0 0 0 1
chr22_802 69 1 1 95 1 0 1 1 0 0 0 0 0 0 0 0 0
chr22_810 1542 10 8 92 9 5 9 8 0 0 0 2 13 2 81 4 0

SGP predictions NOT overlapping genscan predictions

Gene Length Exons HSP
support. 		HSP
Cov. % 		Genscan Exonerate Blastz Mus Blat Mus Mystery Ensembl
cDNA 		GenBank
mRNA 		ESTHum ESTMouse ESTRat PROTNR Genome
Tetra 		CDDNCBI
chr22_1 54 1 1 100 0 0 1 0 0 0 0 0 0 0 0 0 0
chr22_46 147 1 1 100 0 1 1 1 0 0 0 0 1 4 12 0 1
chr22_69 114 1 1 100 0 1 1 1 0 0 0 0 0 0 0 0 0
chr22_111 381 2 2 85 0 1 2 2 0 0 0 0 12 8 3 0 0
chr22_113 60 1 1 100 0 0 1 1 0 0 0 0 0 0 0 0 0
chr22_125 258 2 1 81 0 0 1 1 0 0 0 2 0 0 0 0 1
chr22_128 6420 3 2 34 0 0 3 0 0 0 0 7 0 0 504 0 493
chr22_161 153 1 1 71 0 0 1 1 0 0 0 0 1 5 0 0 0
chr22_174 894 4 3 68 0 0 2 0 0 0 0 7 0 0 0 0 139
chr22_179 354 2 1 93 0 1 1 1 0 0 1 0 0 0 0 0 12
chr22_185 336 2 1 98 0 1 1 1 0 0 1 0 0 0 0 0 10
chr22_427 144 1 1 97 0 1 1 1 0 0 0 0 0 0 0 0 0
chr22_438 300 2 1 81 0 1 1 1 0 0 0 1 0 0 0 0 0
chr22_439 171 1 1 84 0 1 1 1 1 0 0 0 0 0 0 0 0
chr22_441 396 3 2 86 0 1 2 2 0 0 0 0 0 0 0 0 0
chr22_442 480 3 2 93 0 2 2 2 0 0 0 0 0 0 0 0 0
chr22_443 297 1 1 77 0 1 1 1 1 0 0 0 0 0 0 0 0
chr22_445 177 2 1 93 0 1 1 1 0 0 0 0 0 0 0 0 0
chr22_447 60 1 1 100 0 1 1 1 0 0 0 0 0 0 0 0 0
chr22_451 540 2 2 99 0 1 2 2 0 0 0 0 0 0 0 0 0
chr22_464 489 3 2 91 0 1 3 2 1 0 0 0 15 0 70 0 2
chr22_475 273 5 3 86 0 3 4 4 0 0 0 3 4 0 8 4 1
chr22_534 594 5 5 97 0 3 5 4 1 0 0 1 2 0 25 0 2
chr22_539 126 1 1 100 0 1 1 1 0 0 0 0 0 0 0 0 0
chr22_540 339 2 1 73 0 1 2 1 0 0 0 0 0 0 0 0 0
chr22_541 195 4 1 57 0 0 2 1 0 0 0 0 0 0 1 0 0
chr22_543 174 1 1 93 0 0 0 0 0 0 0 0 0 0 0 0 0
chr22_551 99 1 1 96 0 1 1 1 0 0 0 0 0 0 0 0 0
chr22_557 174 3 2 93 0 0 0 0 0 0 0 0 0 0 0 0 3
chr22_567 168 2 1 85 0 1 1 1 0 0 0 0 0 0 0 0 0
chr22_568 114 1 1 100 0 1 1 1 0 0 0 0 0 0 0 0 0
chr22_571 144 1 1 87 0 1 0 1 0 0 0 0 0 0 0 0 1
chr22_666 276 3 1 78 0 1 1 1 1 0 0 6 0 0 0 0 0
chr22_691 90 2 1 82 0 1 1 1 1 0 0 0 0 0 0 0 0
chr22_722 69 1 1 100 0 0 1 1 0 0 0 0 0 0 0 0 0
chr22_773 264 2 1 67 0 1 1 1 0 0 0 0 0 0 0 0 0
chr22_787 87 1 1 96 0 1 1 1 0 0 0 0 0 0 0 0 0
chr22_788 159 1 1 100 0 1 1 1 0 0 0 0 0 0 0 0 0
chr22_791 135 1 1 97 0 1 1 1 0 0 0 0 0 0 0 0 0
chr22_794 210 1 1 100 0 1 1 1 0 0 0 0 0 0 0 0 0
chr22_796 249 2 1 86 0 1 1 1 0 0 0 0 0 0 0 0 0
chr22_798 69 2 1 84 0 0 2 1 1 0 0 0 0 0 0 0 0
chr22_801 189 1 1 87 0 1 1 1 0 0 0 0 0 0 0 0 0
chr22_803 255 2 1 83 0 1 1 1 1 0 0 0 0 0 0 0 0
chr22_806 258 2 2 88 0 2 2 2 0 0 0 0 0 0 0 0 0
chr22_815 768 3 1 80 0 0 1 0 0 0 0 0 0 0 0 0 10

SGP predictions WITHOUT support from mouse sequence traces

Gene Length Exons HSP
support. 		HSP
Cov. % 		Genscan Exonerate Blastz Mus Blat Mus Mystery Ensembl
cDNA 		GenBank
mRNA 		ESTHum ESTMouse ESTRat PROTNR Genome
Tetra 		CDDNCBI
chr22_82 459 2 0 0 1 0 2 0 0 0 0 1 0 0 13 0 1
chr22_83 807 2 0 0 1 1 1 0 0 0 0 4 0 0 13 0 53
chr22_86 1014 2 0 0 1 0 1 0 0 0 0 4 0 0 7 0 35
chr22_87 426 2 0 0 1 0 1 0 0 0 0 1 0 0 16 0 1
chr22_93 459 2 0 0 1 0 2 0 1 0 0 1 0 0 14 1 0
chr22_123 372 2 0 0 2 0 0 0 0 0 0 0 0 0 0 0 249
chr22_129 345 2 0 0 2 0 2 0 0 0 0 3 0 0 38 0 2
chr22_166 459 2 0 0 1 0 2 0 0 0 0 1 0 0 14 1 0
chr22_805 333 3 0 0 1 0 0 0 0 0 0 0 0 0 0 0 25