Sequence
atgc intronic sequence ATGC exonic sequencegtgagttgttgtttcttttaattttgactttctttgttgaaattgtggttacaattatttacctttcttttattcattgatagttggttttttcataatgcagGTGTCTATGAATCCTTTGACACCATATGCATATACCTCGAGAGTGATCAATCAGTTGGGAGTGATCCTGATAAAAATTTTTGGGTCAGATACAGGATGGC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0008g05690.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G004908_T01 (Zea mays), 3'ss of exon 2
gtgagttgttgtttcttttaattttgactttctttgttgaaattgtggttacaattatttacctttcttttattcattgatagttggttttttcataatgcagGTGTCTATGAATCCTTTGACACCATATGCATATACCTCGAGAGTGATCAATCAGTTGGGAGTGATCCTGATAAAAATTTTTGGGTCAGATACAGGATGGC
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------------gtgaagtaaattt-attcacttgtcttatacagctgcaccaaagctttactttgtgtttacctcatcgtaact-------------tgcagGTGTATATGAGTCGTTTGATACGATCTGCATATACTTGGAGAGTGATCAGTCATCTGGGTATGATCCTGATAAGAACTTTTGGGTGCACTATAAAATGGC
upper sequence: Vv04s0008g05690.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G06960.1 (Glycine max), 3'ss of exon 2
gtgagttgttgtttcttttaattttgactttct-----ttgttga-----aattgtggttacaattatttacctttcttttattc--attgatagttggttttttcataatgcagGTGTCTATGAATCCTTTGACACCATATGCATATACCTCGAGAGTGATCAATCAGTTGGGAGTGATCCTGATAAAAATTTTTGGGTCAGATACAGGATGGC
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gtaggt-gttctatcacacaaattttatctcctgcattttattcactaccagttgtagttgtgaacttttactttttttattctctgattgaaaggttatgtttccatgacccagGTGTATATGAGTCGTTTGACACCATATGTATTTATTTAGAGAGTGACCAGGCTGTTGGTAGTGACCCGGATAAAAATTTCTGGGTCAGATACAGGATGGC
upper sequence: Vv04s0008g05690.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G07050.1 (Glycine max), 3'ss of exon 2
gtgagttgttgtttcttttaattttgactttctttgtt------------gaaattgtggttacaattatttacctttct--tttattcattgatagttggttttttcataatgcagGTGTCTATGAATCCTTTGACACCATATGCATATACCTCGAGAGTGATCAATCAGTTGGGAGTGATCCTGATAAAAATTTTTGGGTCAGATACAGGATGGC
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gtaggt-gttctatcacacaaatttgatctcctgtattttttattcacaggcagtagtagttgtgaacatttactttttttattctttgattgaaagcttatgttcccatgacccagGTGTATACGAGTCGTTTGACACCATATGTATTTATTTAGAGAGTGACCAGGCTGTTGGTAGTGACCCGGATAAAAATTTCTGGGTCAGATACAGAATGGC
upper sequence: Vv04s0008g05690.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT2G25320.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgagttgttgtttcttttaattttgactttctttgttgaaattgtggttacaattatttacctttcttttattcattgatagttggttttttcataatgcagGTGTCTATGAATCCTTTGACACCATATGCATATACCTCGAGAGTGATCAATCAGTTGGGAGTGATCCTGATAAAAATTTTTGGGTCAGATACAGGATGGC
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gtgagtggttagattttttccatatctctaatcctg----------gattattaatgtttatgat-ctccaattgcttaatgtgtgcctcgt--ataatgcagGTGTATATGAGTCCTTTGACACCATATGCATATATTTAGAGAGTGATCAATCTGCGGGTACAGATGTGGACAATAATTTCTGGGTTAAGTACAAGATGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttacaattatttacctttcttttattcattgatagttggttttttcataatgcagGTGTCTATGAATCCTTTGACACCATATGCATATACCTCGAGAGTGATCAATCAGTTGGGAGTGATCCTGATAAAAATTTTTGGGTCAGATACAGGATGGC
cattgat putative branch site (score: 4)
ttttttcat putative PPT
attatttacctttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttgttgtttcttttaattttgactttctttgttgaaattgtggttacaattatttacctttcttttattcattgatagttggttttttcataatgcagGTGTCTATGAATCCTTTGACACCATATGCATATACCTCGAGAGTGATCAATCAGTTGGGAGTGATCCTGATAAAAATTTTTGGGTCAGATACAGGATGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG