Sequence
atgc intronic sequence ATGC exonic sequence...gtggtggaggtgggggtgggaggaaagttgatgttttaacttgtagaagtaaaaacttgaaattggttgggaaatcaaggcactgacattgtcatttcagGTGGTTCATCATCTTTTATCTATAGCTGCAGTGGCATATGCAATGTTGACTGGGGAAGGGCAACTTTACACCTACATGGTTCTTATCTCTGAGACAACAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv12s0028g01000.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G016184_T02 (Zea mays), 3'ss of exon 5
-------------------------------------------------------------------------gtggtggaggtgggggtgggaggaaagttgatgttttaacttgtagaagtaaaaacttgaaat---tggttgg-gaaatcaaggcactg-acattgtcatttcagGTGGTTCATCATCTTTTATCTATAGCTGCAGTGGCATATGCAATGTTGACTGGGGAAGGGCAACTTTACACCTACATGGTTCTTATCTCTGAGACAACAA
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gtaggtgacaacttgagaattaaattatgtgcacaagagccaataatcataagttattctgatttaacatgacattttttcagaataagttcacacgtcaccagtttggcaacacgttagaatgttgacaggtggtccctagctggcgttatcttatggttatgtgttgtcatttcagGTCCTCCACCATACTGTTTCCCTGGTTGCAATAGCTTACACAATGTTGTCTGGGGAAGGGCAGTTTTACACATACATGGTTCTCATTTCAGAGACAACCA
upper sequence: Vv12s0028g01000.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G132084_T04 (Zea mays), 3'ss of exon 6
------------------------------------------------------------------------gtggtggaggtgggggtgggaggaaagttgatgttttaacttgtagaagtaaa---aacttgaaattggttggga--aatcaaggcactgacattgtcatttcagGTGGTTCATCATCTTTTATCTATAGCTGCAGTGGCATATGCAATGTTGACTGGGGAAGGGCAACTTTACACCTACATGGTTCTTATCTCTGAGACAACAA
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gtaggtgccaacttaaactaatttcacaagaaccaataatcataagctagtctgatttaacataacaattttttttttcagaataagttcacatgcca-ccagtttctcaacatgttagaatattctcaggtggtccctagctagtattatcttatggttacgtgttgccatttcagGTCCTCCACCATACTCTTTCTCTGGTTGCAATAGCTTACACAATGTTGTCTGGGGAAGGGCAGTTTTACACATACATGGTTCTCATTTCAGAGACAACCA
upper sequence: Vv12s0028g01000.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G41750.1 (Glycine max), 3'ss of exon 6
---------------------------------------------gtggtggaggtgggggtgggaggaaagtt----gatgttttaacttgtagaagtaaaaacttgaaat-----tggttgggaaatcaaggcactg-acattgtcat---ttcagGTGGTTCATCATCTTTTATCTATAGCTGCAGTGGCATATGCAATGTTGACTGGGGAAGGGCAACTTTACACCTACATGGTTCTTATCTCTGAGACAACAA
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gtaaggataatatttttttaacttacatagtttaagccaacctttcatgtgaagttaaactctcttaatcaattttaagaaatttcacttgataggaacccag-ctggagatgattatggtcgggatttaacctgacttcatattaacattggttcagGTGATTCATCATCTGTTTTCTTTGGTAGCAGTAGCATATGCAATGTTGACTGGGGAAGGACAGCTTTACACATTCATGGTCCTGATCTCTGAGACAACTA
upper sequence: Vv12s0028g01000.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G45240.3 (Glycine max), 3'ss of exon 5
---------------------------------------------------------------------------gtggtggaggtgggggtgggaggaaagttgatgttttaacttgtaga---agtaaaaacttgaaattggttgggaaatcaaggcactgacattgtcatttcagGTGGTTCATCATCTTTTATCTATAGCTGCAGTGGCATATGCAATGTTGACTGGGGAAGGGCAACTTTACACCTACATGGTTCTTATCTCTGAGACAACAA
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gtaaggatcatatcttttgacttgcatagtttaaaccaacctaaccttgttcatctgaactcattcaatttttagatattccacttgattatggcaagagt-ttgatttccttccttgttcactctatttggttgtaaatatggatttaacatgacttca-taataacattgatttagGTGATTCATCATTTGCTTTCTTTAGTAGCAGTATCATTTTCAATGTTGACTGGGGAGGGTCAGCTATACACATACATGGTCCTGATCTCTGAGACAACTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaagtaaaaacttgaaattggttgggaaatcaaggcactgacattgtcatttcagGTGGTTCATCATCTTTTATCTATAGCTGCAGTGGCATATGCAATGTTGACTGGGGAAGGGCAACTTTACACCTACATGGTTCTTATCTCTGAGACAACAA
cactgac putative branch site (score: 2)
tcatttc putative PPT
aaaaacttgaaatt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtggtggaggtgggggtgggaggaaagttgatgttttaacttgtagaagtaaaaacttgaaattggttgggaaatcaaggcactgacattgtcatttcagGTGGTTCATCATCTTTTATCTATAGCTGCAGTGGCATATGCAATGTTGACTGGGGAAGGGCAACTTTACACCTACATGGTTCTTATCTCTGAGACAACAA
gtggtgg
- - - - - - -gggtggg
- - - - - - - - - - aggaaag
- - - - - - - - - - - - - - - - - - - - - - - - gtaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggttggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgacat