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author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
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date | Tue, 11 Mar 2014 12:19:13 -0700 |
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# Splice sites and intron regions information for GeneWise-21 # Wed Jan 1 13:42:23 IST 1997 # Created by Mor Amitai (mor@compugen.co.il) # dataset : hum1 and hum2 from embl48 # Consensi are read from top down. The value, for a sequence, # is the number in the line of the first consensus that # matches the sequence. # Note: the set of sequences that are represented by a consensus # are all the sequences that match this consensus and none of the # previous consensi # # the numbers in types 5SS, 3SS, CDS, and the emissions are the number of # occurrences of each sequence in the database. # In case of a consensus this is the number of occurrences of sequences # that are represented by the consensus in the database divided by the # number of sequences that are represented by the consensus. # *stay_prob is the probability of the transition from the state to itself. # No_Spacer_Prob is the probability of transition from Pyrimidine directly # to 3SS (no spacer). type 5SS center 3 phase all begin consensus C-GGTGAGTG 15.75 --GGTGAGTG 8.83333 CAGGTGAG-- 7.6 AAGGTGAG-- 6.86667 CAGGTAAG-- 4.3125 GAGGTGAG-- 4.26667 AAGGTAAG-- 4.1875 --GGTGAGT- 1.71795 ---GTGAGTG 1.66667 --GGTGAG-C 1.51282 -A-GTAAGT- 1.41071 -AGGTG-GT- 1.39583 -TGGTAAG-- 1.39062 CAGGTA-G-- 1.35417 AAGGTA-G-- 1.04167 -GGGTAAG-- 1 --GGTGAG-- 0.91453 -C-GTAAGT- 0.828125 ---GTGAGT- 0.729167 -AGGTAA--- 0.578704 -AGGTG-G-- 0.506944 CAGGTA---- 0.381944 --GGTA-GT- 0.339286 -AGGTGA--- 0.265625 --GGTCAG-- 0.207031 ---GTAAG-- 0.155556 -AGGTA---- 0.134921 -AGGT--G-- 0.111607 --GGT--G-- 0.0369898 -AGGT----- 0.0250947 --GGTA---- 0.0234375 --AGT--G-- 0.0132415 ---GT----- 0.00148067 end consensus type 5SS center 3 phase 0 begin consensus A-GGTGAGTG 8.25 C-GGTGAGTG 7.75 AAGGTGAG-- 3.86667 CAGGTGAG-- 3.46667 AAGGTAAG-- 2.5 GAGGTGAG-- 2.4375 --GGTGAGT- 1.19565 -AGGTAAG-- 1.02083 -A-GTGAGT- 0.916667 -AGGT--GTG 0.785714 AAGGT-GG-- 0.716667 -C-GTGAGT- 0.666667 ---GTAAGTG 0.566667 --GGTGAG-- 0.423077 --GGTAAG-- 0.355556 CAGGT--G-- 0.3 ---GTAAGT- 0.284722 -AGGTAA--- 0.265625 --GGTA-GT- 0.196429 -AGGTAC--- 0.157895 AAGGTG---- 0.13964 -AGGTG---- 0.048048 -AGGT----- 0.0181818 --GGT--G-- 0.0129717 ---GTA---- 0.00291667 ---GT----- 0.000915751 end consensus type 5SS center 3 phase 1 begin consensus --GGTGAGTG 4.375 CAGGTGAG-- 2.8 AAGGTGAG-- 2.26667 -AGGTAAG-- 1.01562 -TGGTAAG-- 0.8125 -TGGTGAG-- 0.7 G-GGTGAG-- 0.755556 CAGGT-GG-- 0.546875 --GGTGAG-- 0.428571 ---GTGAGTG 0.625 ---GTAAGT- 0.223214 AAGGT--G-- 0.200893 -AGGTAA--- 0.1875 --GGTA-G-G 0.175 CAGGT----- 0.0733945 ---GTGAG-- 0.0527778 --GGT--GT- 0.0512129 A-GGTA---- 0.046398 -AGGT----- 0.0137104 ---G-AAG-- 0.00972447 ---GT----- 0.00111909 end consensus type 5SS center 3 phase 2 begin consensus -AGGTGAG-- 0.703125 C--GTGAGT- 0.516667 -AGGTAAG-- 0.5 ---GTAAGT- 0.241667 --GGTGAG-- 0.227778 CAGGTA---- 0.133333 ---GTGAG-- 0.0569444 -AGGT--G-- 0.0483491 ---GTAAG-- 0.0444444 --GGTA---- 0.00896991 ---GT----- 0.000797367 end consensus type 3SS center 3 phase all begin consensus CAGGTG 143 CAGGGT 120 CAGGGC 88 CAGGGA 82 CAGGCT 77 CAGGAG 73 CAGGGG 66 CAGGTA 60 CAGGCC 58 CAGGAA 54 CAGATC 50 CAGCTG 50 CAGG-C 43.5 CAGG-T 38.5 CAGA-C 35.6667 CAGAT- 29.3333 CAGA-A 27.3333 CAG-TC 25.5 TAGG-G 21.75 CAG-CA 21.6667 TAGGA- 21.3333 TAGGG- 20.6667 CAGA-G 19.3333 CAGTG- 18.75 CAGA-- 18 TAGG-- 13.8333 CAG-C- 11.8571 CAG-T- 10.4 CAG-A- 7.375 TAGA-- 6.0625 TAGC-- 3.3125 AAGG-- 3.125 -AGT-- 1.08333 -AG--- 0.714286 end consensus type 3SS center 3 phase 0 begin consensus CAGGGT 88 CAGGTG 64 CAGGAG 43 CAGGG- 40.3333 CAGATC 32 CAGG-C 25 CAGG-A 19 CAGG-T 17.3333 CAGA-C 14.6667 CAG-TG 13 CAGAA- 13 CAGA-T 11.3333 CAGC-C 10.25 TAGG-- 9.8125 CAG--A 4.09091 CAGT-- 4.45455 TAG-T- 3.33333 TAG--- 1.36111 -AGG-- 1.06061 -AG--- 0.342857 end consensus type 3SS center 3 phase 1 begin consensus CAGGTG 71 CAGGCT 36 CAGGG- 24.75 CAG-CC 17.5 CAG-TG 16.6667 CAGAG- 15.75 CAGG-- 14.5556 CAGA-A 13.3333 CAGTG- 10.75 CAG-TC 10.3333 TAGG-G 9.5 CAGA-- 6.16667 TAGG-- 5 CAGC-- 3.69231 TAG--- 1.66667 -AG--- 0.328467 end consensus type 3SS center 3 phase 2 begin consensus CAGG-A 19.25 CAGG-T 14.75 CAG-G- 4.57143 CAG--T 4.66667 TAGG-- 3 CAG--- 2.87879 TAG--- 0.645833 AAG--- 0.25 end consensus type CDS phase all begin consensus AAA 5290.000000 AAC 4795.000000 AAG 8178.000000 AAT 3305.000000 ACA 6240.000000 ACC 7728.000000 ACG 3347.000000 ACT 4930.000000 AGA 8491.000000 AGC 8639.000000 AGG 8997.000000 AGT 4417.000000 ATA 1975.000000 ATC 4973.000000 ATG 6474.000000 ATT 3083.000000 CAA 7057.000000 CAC 6815.000000 CAG 11041.000000 CAT 5779.000000 CCA 10537.000000 CCC 10307.000000 CCG 5621.000000 CCT 10134.000000 CGA 3377.000000 CGC 5146.000000 CGG 5375.000000 CGT 2765.000000 CTA 3502.000000 CTC 7465.000000 CTG 13780.000000 CTT 5453.000000 GAA 7461.000000 GAC 6937.000000 GAG 9975.000000 GAT 4949.000000 GCA 7747.000000 GCC 10890.000000 GCG 4828.000000 GCT 9371.000000 GGA 10143.000000 GGC 10400.000000 GGG 8869.000000 GGT 5567.000000 GTA 2143.000000 GTC 4593.000000 GTG 8189.000000 GTT 3021.000000 TAA 1775.000000 TAC 3687.000000 TAG 1333.000000 TAT 2477.000000 TCA 6180.000000 TCC 7668.000000 TCG 2875.000000 TCT 5767.000000 TGA 7315.000000 TGC 8625.000000 TGG 11718.000000 TGT 5197.000000 TTA 1664.000000 TTC 5462.000000 TTG 4420.000000 TTT 3453.000000 end consensus type CDS phase 0 begin consensus AAA 2167.000000 AAC 2839.000000 AAG 4830.000000 AAT 1616.000000 ACA 1543.000000 ACC 3187.000000 ACG 983.000000 ACT 1484.000000 AGA 995.000000 AGC 2722.000000 AGG 1326.000000 AGT 1093.000000 ATA 585.000000 ATC 3281.000000 ATG 2538.000000 ATT 1584.000000 CAA 1141.000000 CAC 1981.000000 CAG 4796.000000 CAT 1016.000000 CCA 2021.000000 CCC 3183.000000 CCG 1104.000000 CCT 2289.000000 CGA 770.000000 CGC 2011.000000 CGG 1762.000000 CGT 687.000000 CTA 745.000000 CTC 2964.000000 CTG 6980.000000 CTT 1200.000000 GAA 2729.000000 GAC 3946.000000 GAG 6121.000000 GAT 2318.000000 GCA 1767.000000 GCC 4902.000000 GCG 1288.000000 GCT 2556.000000 GGA 2322.000000 GGC 4338.000000 GGG 2688.000000 GGT 1903.000000 GTA 690.000000 GTC 2172.000000 GTG 4546.000000 GTT 1020.000000 TAA 0.000000 TAC 2405.000000 TAG 0.000000 TAT 1323.000000 TCA 990.000000 TCC 2579.000000 TCG 684.000000 TCT 1522.000000 TGA 0.000000 TGC 1747.000000 TGG 1766.000000 TGT 931.000000 TTA 397.000000 TTC 3156.000000 TTG 1313.000000 TTT 1697.000000 end consensus type CDS phase 1 begin consensus AAA 1534.000000 AAC 1140.000000 AAG 2597.000000 AAT 767.000000 ACA 3632.000000 ACC 3429.000000 ACG 1849.000000 ACT 2262.000000 AGA 4427.000000 AGC 4014.000000 AGG 5377.000000 AGT 1927.000000 ATA 953.000000 ATC 1055.000000 ATG 3488.000000 ATT 777.000000 CAA 998.000000 CAC 1332.000000 CAG 3260.000000 CAT 731.000000 CCA 4701.000000 CCC 3908.000000 CCG 2252.000000 CCT 2992.000000 CGA 471.000000 CGC 1361.000000 CGG 1785.000000 CGT 443.000000 CTA 825.000000 CTC 1766.000000 CTG 4378.000000 CTT 882.000000 GAA 924.000000 GAC 843.000000 GAG 1897.000000 GAT 424.000000 GCA 3140.000000 GCC 3275.000000 GCG 1806.000000 GCT 2595.000000 GGA 1911.000000 GGC 2034.000000 GGG 2835.000000 GGT 762.000000 GTA 577.000000 GTC 968.000000 GTG 2506.000000 GTT 563.000000 TAA 622.000000 TAC 561.000000 TAG 912.000000 TAT 322.000000 TCA 3963.000000 TCC 3535.000000 TCG 1466.000000 TCT 2607.000000 TGA 3311.000000 TGC 4099.000000 TGG 6194.000000 TGT 1772.000000 TTA 773.000000 TTC 1353.000000 TTG 2662.000000 TTT 713.000000 end consensus type CDS phase 2 begin consensus AAA 1589.000000 AAC 816.000000 AAG 751.000000 AAT 922.000000 ACA 1065.000000 ACC 1112.000000 ACG 515.000000 ACT 1184.000000 AGA 3069.000000 AGC 1903.000000 AGG 2294.000000 AGT 1397.000000 ATA 437.000000 ATC 637.000000 ATG 448.000000 ATT 722.000000 CAA 4918.000000 CAC 3502.000000 CAG 2985.000000 CAT 4032.000000 CCA 3815.000000 CCC 3216.000000 CCG 2265.000000 CCT 4853.000000 CGA 2136.000000 CGC 1774.000000 CGG 1828.000000 CGT 1635.000000 CTA 1932.000000 CTC 2735.000000 CTG 2422.000000 CTT 3371.000000 GAA 3808.000000 GAC 2148.000000 GAG 1957.000000 GAT 2207.000000 GCA 2840.000000 GCC 2713.000000 GCG 1734.000000 GCT 4220.000000 GGA 5910.000000 GGC 4028.000000 GGG 3346.000000 GGT 2902.000000 GTA 876.000000 GTC 1453.000000 GTG 1137.000000 GTT 1438.000000 TAA 1153.000000 TAC 721.000000 TAG 421.000000 TAT 832.000000 TCA 1227.000000 TCC 1554.000000 TCG 725.000000 TCT 1638.000000 TGA 4004.000000 TGC 2779.000000 TGG 3758.000000 TGT 2494.000000 TTA 494.000000 TTC 953.000000 TTG 445.000000 TTT 1043.000000 end consensus type Intron_Corr_Term phase all 65.6094 type Intron_Corr_Term phase 0 141.429 type Intron_Corr_Term phase 1 172.738 type Intron_Corr_Term phase 2 371.127 type Intron_emission begin consensus A 399845.000000 C 371259.000000 G 393779.000000 T 425926.000000 end consensus type Pyrimidine_emission begin consensus A 2299.000000 C 18610.000000 G 2345.000000 T 17132.000000 end consensus type Spacer_emission begin consensus A 3020.000000 C 3834.000000 G 3644.000000 T 4224.000000 end consensus type Central_Intron_Stay_Prob 0.99853 type Pyrimidine_Stay_Prob 0.944485 type No_Spacer_Prob 0.331508 type Spacer_Stay_Prob 0.902704