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tRNAscan-SE Analysis of Cryptococcus neoformans var JEC21

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tRNAs Sorted by Genome Locus plain text version Sequence Name tRNA # tRNA Bounds tRNA Isotype Anticodon Upstream Region Downstream Region Intron Bounds Scores First-Pass Scanner Begin End Begin End Total (Cove) HMM 2' Str chr1 1 559251 559336 Thr TGT tcaacaacaa tcattttttt 559288 559300 66.12 43.46 22.66 Both chr1 2 574947 575041 Ser AGA aaaactactc actttttttt 574984 574997 51.80 18.23 33.57 tRNAscan chr1 3 594060 594154 Ser AGA taccgcatat ttttttccct 594097 594110 51.80 18.23 33.57 tRNAscan chr1 4 848246 848341 Ala AGC aaacatcatc aagttctttt 848283 848305 57.37 33.58 23.79 Both chr1 5 853475 853569 Ala AGC gaacactgac ttttttttct 853512 853533 58.51 34.73 23.78 Both chr1 6 855458 855550 Ala AGC cggcagcagc tatttttttc 855495 855514 57.48 33.70 23.78 Both chr1 7 1052585 1052656 Gly TCC attttgactt catttttttt 0 0 63.13 32.64 30.49 Both chr1 8 1208523 1208623 Leu AAG aacatccaat atatttttgt 1208561 1208581 50.60 20.48 30.12 Both chr1 9 1511516 1511605 Ile TAT gtactgttga tttctttttg 1511553 1511569 56.60 24.58 32.02 Both chr1 10 2281275 2281185 Glu CTC ctgtaacacc tatctttttg 2281238 2281220 53.84 25.73 28.11 Both chr1 11 2211873 2211771 Val CAC tcaacgagct tatttttttg 2211835 2211807 73.69 48.82 24.87 Both chr1 12 1955472 1955384 Val AAC ccaacaaaat tctttttcca 1955434 1955420 55.49 30.37 25.12 Eufind chr1 13 1832935 1832844 Ala TGC tcatcagatc aaacaaatct 1832898 1832880 53.81 27.24 26.57 Both chr1 14 1375591 1375521 Gly GCC aagttctcat atttcttttt 0 0 56.25 23.36 32.89 Both chr1 15 1199520 1199420 Leu AAG acattttaat atatttttgt 1199482 1199462 50.60 20.48 30.12 Both chr1 16 1197701 1197601 Leu AAG aatatctgat atattttttg 1197663 1197643 50.74 20.62 30.12 Both chr1 17 870640 870545 Pseudo CGA aattcttgct tttccttttt 870601 870589 39.93 3.95 35.98 tRNAscan chr1 18 605104 605010 Ser AGA aacaccaatt gtttttactt 605067 605054 51.80 18.23 33.57 tRNAscan chr1 19 575303 575209 Ser AGA tctattggtt actttttttt 575266 575253 51.80 18.23 33.57 tRNAscan   chr10 1 116270 116359 Arg TCG atatcgtcaa gactttttga 116306 116323 58.51 40.58 17.93 Eufind chr10 2 119342 119438 Glu CTC tttaccaata ttacttttta 119379 119403 54.87 26.76 28.11 Both chr10 3 639486 639601 Arg ACG aaaggagtaa gtttcttttt 639522 639565 63.92 34.26 29.66 Both chr10 4 909953 910034 His GTG aatatcaaaa tttttttggt 909990 909999 67.21 39.09 28.12 Both chr10 5 938025 937943 Met CAT aacatcacaa tttttttttt 937989 937979 54.40 24.02 30.38 Both chr10 6 745195 745116 Arg CCG gagttgattt ttctttttga 745159 745152 56.40 30.54 25.86 Both chr10 7 499931 499829 Arg ACG aaattaagga ttttacattt 499895 499865 65.40 35.75 29.65 tRNAscan chr10 8 473280 473178 Gly CCC ttaaaatgag tacattttgc 473244 473213 42.37 12.10 30.27 Both chr10 9 120117 120021 Glu CTC tcaacaagtg ttactttttg 120080 120056 56.15 28.04 28.11 Both chr10 10 100305 100211 Glu CTC tctaatagta tttttttttc 100268 100246 54.47 26.36 28.11 Both chr10 11 27134 27045 Arg TCG atattgtcaa gactttttgg 27098 27081 58.51 40.58 17.93 Eufind   chr11 1 573294 573396 Leu AAG tgtatgacac attcttttgc 573332 573354 51.63 23.23 28.40 Both chr11 2 975753 975671 Asp GTC taaaaacaag tttctttttt 975716 975706 46.86 19.15 27.71 Eufind chr11 3 334687 334593 Ala AGC taataacttt tttccttttt 334650 334629 52.85 29.07 23.78 Both chr11 4 226495 226387 Gly CCC aaagttggac gattcctttc 226459 226422 43.41 13.14 30.27 Both chr11 5 206701 206609 Glu TTC tcatcaagca gatctttttt 206664 206644 64.52 39.82 24.70 Both chr11 6 95282 95190 Tyr GTA tttcaacaag tattttttgg 95242 95226 56.83 33.60 23.23 tRNAscan   chr12 1 97210 97297 Phe GAA ttacgtaaat acatttttgt 97247 97261 71.00 54.19 16.81 Both chr12 2 464299 464389 Ile AAT acaaatgatc tttctttttg 464338 464353 57.52 15.65 41.87 Both chr12 3 497760 497849 Val AAC tccataaaat tggctttttt 497798 497813 54.98 29.86 25.12 Eufind chr12 4 511669 511757 Val AAC ttaacaggat tttttttttc 511707 511721 55.85 30.72 25.13 Eufind chr12 5 529453 529543 Val AAC tttggaaaat ttctttttga 529491 529507 55.88 30.75 25.13 Eufind chr12 6 580145 580234 Val AAC accataaaat ttcttttttg 580183 580198 55.48 30.35 25.13 Eufind chr12 7 593521 593603 Trp CCA tttaacaaat ttctttttgc 593557 593567 62.30 40.99 21.31 Both chr12 8 863174 863067 Lys CTT aaatacacag ttctttttga 863137 863103 66.95 51.59 15.36 Both chr12 9 790780 790688 Glu TTC tcacaatgaa gatctttttg 790743 790723 64.66 39.96 24.70 Both chr12 10 512524 512436 Val AAC gttacacaat tttctttttt 512486 512472 55.35 30.22 25.13 Eufind   chr13 1 679249 679341 Tyr GTA ttcatccgaa ttcaaatttg 679289 679305 56.83 33.60 23.23 tRNAscan chr13 2 679351 679469 Lys CTT attcaaattt tttttttaat 679388 679433 68.14 52.78 15.36 Both   chr14 1 198564 198634 Gly GCC attacctgat tttttttttg 0 0 56.25 23.36 32.89 Both chr14 2 408731 408828 Asn GTT gttcaacaat gattcttttt 408769 408792 68.44 48.23 20.21 Both chr14 3 461000 461087 Cys GCA ttgacagttg ttctttttca 461040 461051 66.26 43.66 22.60 tRNAscan chr14 4 461156 461246 Cys GCA caactatgct gtgcttttta 461196 461210 66.29 43.69 22.60 tRNAscan chr14 5 376661 376554 Lys CTT gacaccgaaa tctcttttta 376624 376590 66.95 51.59 15.36 Both chr14 6 96795 96725 Gly GCC tggacacaaa tctttttttg 0 0 56.25 23.36 32.89 Both   chr2 1 1294403 1294502 Ser TGA catctgatga tttaattttt 1294439 1294458 42.93 17.06 25.87 Eufind chr2 2 1500828 1500924 Leu TAA ttttactcgg acagcttttt 1500865 1500878 54.54 26.81 27.73 Both chr2 3 1542184 1542088 Glu CTC caaaatggaa ttactttttg 1542147 1542123 55.01 26.90 28.11 Both chr2 4 1277694 1277608 Thr CGT atttaagaaa gttctttttt 1277657 1277649 54.05 41.19 12.86 Both chr2 5 924355 924246 Pseudo GCT aaacaatcca ttttcttttt 924318 924290 49.95 8.86 41.09 tRNAscan chr2 6 721098 720992 Pro CGG ttaagttgta aaatttaatt 721062 721027 37.30 13.88 23.42 tRNAscan chr2 7 221818 221747 His GTG tccatccaaa tgcctttttg 0 0 73.65 45.52 28.13 Both chr2 8 79263 79172 Cys GCA acaagtgtgc tttttccttg 79223 79208 66.91 44.31 22.60 tRNAscan   chr3 1 272703 272784 Gln TTG aaatacacga tctatttttt 272740 272749 52.32 38.28 14.04 Both chr3 2 296457 296538 Gly GCC tcataggaac tacctttttg 296493 296503 49.80 16.91 32.89 Both chr3 3 1780260 1780174 Leu CAG aacatccaat acagattttt 1780223 1780215 52.61 28.17 24.44 Both chr3 4 436970 436889 Met CAT atttaattaa atttttttgt 436934 436925 56.04 25.66 30.38 Both   chr4 1 82130 82234 Val CAC tgtcacgaac tactttttct 82168 82198 73.79 48.93 24.86 Both chr4 2 168188 168283 Glu CTC gacagaaaac ttatcttttt 168225 168248 53.97 25.86 28.11 Both chr4 3 439469 439576 Lys CTT gcatcaagaa ttcttttttg 439506 439540 66.95 51.59 15.36 Both chr4 4 772440 772532 Tyr GTA acccaataag ttttttttgg 772480 772496 56.83 33.60 23.23 tRNAscan chr4 5 1277557 1277654 Asn GTT tttcaaccat tttctttttg 1277595 1277618 68.42 48.21 20.21 Both chr4 6 1322357 1322449 Glu TTC aatataacca tattttttgc 1322394 1322414 65.16 40.46 24.70 Both chr4 7 1713962 1714044 Trp CCA atataacaat attttttttc 1713998 1714008 63.08 41.77 21.31 Both chr4 8 1477070 1476973 Arg CCT cattatttaa tttttttttt 1477033 1477009 59.67 44.06 15.61 Both chr4 9 1471206 1471109 Arg CCT tatattgaaa tattttttgc 1471169 1471145 57.76 42.15 15.61 Both chr4 10 1115277 1115179 Gly GCC atgaaagtag attttttaat 1115241 1115214 50.33 17.44 32.89 Both chr4 11 1111136 1111046 Asn GTT gttcaattat ggtttttttt 1111098 1111082 67.74 47.53 20.21 Both chr4 12 752920 752829 Tyr GTA acataaatcg tttacttttt 752880 752865 57.34 34.11 23.23 tRNAscan chr4 13 97719 97632 Phe GAA aaaccaagaa cactttttgc 97682 97668 70.06 53.73 16.33 Both chr4 14 75509 75422 Phe GAA ttatatgact atgtttttgt 75472 75458 70.06 53.73 16.33 Both   chr5 1 38007 38114 Lys CTT aacatagcaa tttttacact 38044 38078 67.58 52.22 15.36 Both chr5 2 357639 357721 Ala CGC tgtcatgttc tttttgtgct 357675 357686 47.81 25.25 22.56 Eufind chr5 3 1279571 1279485 Pro TGG caacaagttg caaacaattt 1279535 1279521 53.52 32.81 20.71 Both chr5 4 1048157 1048066 Phe GAA tttcaaggaa attttttctt 1048120 1048102 68.16 51.83 16.33 Both chr5 5 514325 514236 Phe GAA ttttctattc ttatttttag 514288 514272 71.37 55.04 16.33 Both chr5 6 481955 481873 Ala CGC tacacgtgtc ctttttgtac 481919 481908 47.18 29.03 18.15 Eufind chr5 7 330187 330090 Met CAT aactataaaa ttttaaattt 330151 330125 55.40 34.66 20.74 Both chr5 8 293214 293127 Trp CCA aatctcgtct aactttactt 293177 293163 65.57 41.90 23.67 Both   chr6 1 33888 33985 Glu CTC aagttaagtt tactttttac 33925 33950 55.85 28.83 27.02 Both chr6 2 726516 726586 Gly GCC cagttcagta tttcttttta 0 0 56.25 23.36 32.89 Both chr6 3 980363 980460 Met CAT aattcaacaa tttatttttt 980399 980425 58.37 37.62 20.75 Both chr6 4 1126736 1126826 Lys TTT ggacatcaaa aagatacaac 1126774 1126790 70.24 50.75 19.49 Both chr6 5 1237837 1237935 Thr AGT ttgcatggaa ttcaactttt 1237875 1237899 62.75 30.54 32.21 Both chr6 6 1270980 1271069 Arg TCG ctacgatgaa cactttttta 1271016 1271033 58.51 40.58 17.93 Eufind chr6 7 1250086 1249997 Arg TCG gtatcaacct cgttattttt 1250050 1250033 58.51 40.58 17.93 Eufind chr6 8 1170436 1170329 Lys CTT acaactgaaa tccttttttt 1170399 1170365 66.95 51.59 15.36 Both chr6 9 1164559 1164488 Gly TCC actgtacaag cacgattttt 0 0 63.13 32.64 30.49 Both chr6 10 1111357 1111276 Gly GCC tcatggattc attttttact 1111321 1111311 49.66 16.77 32.89 Both chr6 11 1060538 1060457 Gly GCC catcgagtaa ttttttcctc 1060502 1060492 49.51 16.62 32.89 Both chr6 12 1054135 1054043 Ala AGC attcgacaat aagctttttt 1054098 1054079 54.78 31.00 23.78 Both chr6 13 999439 999343 Thr AGT aaacatcaaa tttctttttt 999401 999379 64.83 32.62 32.21 Both chr6 14 991640 991543 Met CAT aacacagcaa tttgaagttt 991604 991578 54.41 33.66 20.75 Both chr6 15 642881 642786 Glu CTC tgtatgatac tttttttata 642844 642821 55.09 28.07 27.02 Both chr6 16 275639 275540 Arg CCT aactgtcgca cttctttttg 275602 275576 55.71 40.10 15.61 Both chr6 17 232120 232020 Leu AAG ataaacaaat attctttttg 232082 232062 50.60 20.48 30.12 Both chr6 18 12772 12677 Glu CTC cttaggcaat accttttttt 12735 12712 53.68 26.66 27.02 Both   Sequence Name tRNA # tRNA Bounds tRNA Isotype Anticodon Upstream Region Downstream Region Intron Bounds Scores First-Pass Scanner Begin End Begin End Total (Cove) HMM 2' Str chr7 1 52439 52529 Arg ACG cattaaacaa tctttttgct 52475 52493 64.39 34.73 29.66 Both chr7 2 54419 54490 Gln CTG ggttattact gacatttttg 0 0 63.50 42.86 20.64 Both chr7 3 64079 64150 Gln CTG agctgaaaac gatatttttg 0 0 63.50 42.86 20.64 Both chr7 4 1124405 1124493 Arg TCT gcagtagtaa tccctttttg 1124442 1124457 64.22 49.03 15.19 Both chr7 5 1243078 1243172 Ser AGA tttatcaatt gttttctttt 1243115 1243128 51.80 18.23 33.57 tRNAscan chr7 6 1284832 1284930 Pro AGG tggcatagcc caatatcttt 1284868 1284894 52.94 32.88 20.06 Both chr7 7 1286695 1286792 Pro AGG tggcatagcc cattatattt 1286731 1286756 53.30 33.25 20.05 Both chr7 8 1287455 1287552 Pro AGG tggcatagcc caatatcttt 1287491 1287516 53.94 33.89 20.05 Both chr7 9 1297850 1297753 Pro AGG tggcatagcc caatatcttt 1297814 1297789 53.94 33.89 20.05 Both chr7 10 1296964 1296867 Pro AGG tggcatagcc caatatcttt 1296928 1296903 53.30 33.25 20.05 Both chr7 11 1104590 1104482 Leu CAA tttggcggaa tttttttgtt 1104553 1104524 56.09 22.78 33.31 Both chr7 12 1059118 1059047 His GTG atatcccaaa tccacaattt 0 0 74.67 47.66 27.01 Both chr7 13 1040734 1040648 His GTG ttttctgtcc taatcttttt 1040695 1040683 45.23 20.01 25.22 tRNAscan chr7 14 661424 661319 Ser GCT cataaccgat atctttttgc 661387 661363 49.41 18.62 30.79 Both chr7 15 519045 518952 Thr AGT actatatcgg tttccctttt 519007 518988 64.37 32.16 32.21 Both   chr8 1 155881 155952 Gln CTG aagtatgcag gatacttttg 0 0 63.50 42.86 20.64 Both chr8 2 995349 995438 Val AAC tttcaacaat tatttttgcc 995387 995402 55.26 30.14 25.12 Eufind chr8 3 1016920 1017028 Leu CAA gtaattcgtt tttatttttt 1016957 1016986 56.09 22.78 33.31 Both chr8 4 1099913 1099819 Ser AGA ttcaaccgtt ttcttttttg 1099876 1099863 51.94 18.38 33.56 tRNAscan chr8 5 93289 93182 Lys CTT aaatataaaa tctttttgct 93252 93218 66.95 51.59 15.36 Both   chr9 1 119969 120057 Ile AAT aaaaatgatc tttttttaat 120008 120021 57.62 15.76 41.86 Both chr9 2 139526 139615 Ile AAT acaaatgatc tttcttttta 139565 139579 57.12 15.25 41.87 Both chr9 3 511851 511947 Thr AGT aatctgtcga ttttttttag 511889 511911 62.14 29.92 32.22 Both chr9 4 666869 666977 Leu CAA agttgtatta tttttttgca 666906 666935 56.73 23.42 33.31 Both chr9 5 912580 912677 Asn GTT tgcaatcaat ttttcttttt 912618 912641 68.30 48.09 20.21 Both chr9 6 946754 946836 Met CAT agaattatga taatcttttt 946790 946800 55.53 25.15 30.38 Both chr9 7 1145686 1145765 Gly TCC ttcactttat cattcttttt 1145723 1145730 56.66 26.17 30.49 Both chr9 8 1071772 1071683 Arg TCG caacgaacaa gtttcttttt 1071736 1071719 58.51 40.58 17.93 Eufind chr9 9 964404 964302 Leu AAG aaacaaggaa gtatttttgt 964366 964344 52.91 23.34 29.57 Both chr9 10 819632 819529 Gln TTG gaatatacag tgactttttg 819595 819564 56.74 38.40 18.34 Both chr9 11 515804 515708 Thr AGT aaacatcgaa atttcttttt 515766 515744 63.91 31.69 32.22 Both chr9 12 183511 183423 Ile AAT acaaatgatc tttctttttg 183472 183459 56.70 14.84 41.86 Both chr9 13 161830 161749 Gly GCC ataactagag tatctttttg 161794 161784 48.74 15.85 32.89 Both chr9 14 127579 127491 Ile AAT acaaatgatc ttatttttat 127540 127527 58.12 16.25 41.87 Both chr9 15 108254 108166 Ile AAT acaaatgatc tttctttttt 108215 108202 56.70 14.84 41.86 Both chr9 16 81257 81166 Ala AGC ttttaatcaa ttactttttg 81220 81202 55.16 31.38 23.78 Both chr9 17 59158 59067 Ala AGC aaacaacaat cagcttttta 59121 59103 55.58 31.80 23.78 Both

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The Genomic tRNA Database is curated by Todd Lowe and Patricia Chan. Please email lowe@soe.ucsc.edu with any questions and comments. To submit corrections, please use our Bug and Request Tracking System.