Sequence
atgc intronic sequence ATGC exonic sequencegtgagttgatcctttctattttttatctttatttttatttactgcatctttagtgcattgcctgttacacatgcatgatatctatccagctaagttggtgtttctaattctgttttgcaatccaattatagaagcttgaagatttgtttgatctgctattgctttatttatttattttttattacagGACAAGACTATTGCCTATTGGAGGAAATTTGTGGCAGAGTATTATTCACCCCGTGCAAAGAAAAGATGGTGCTTGTCCTTATATGACAATGTTGGAAATC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv16s0100g00500.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA16G32260.1 (Glycine max), 3'ss of exon 3
gtgagttgatcctttctattttttatctttatttttatttactgcatctttagtgcattgcctgttacacatgcatgatatctatccagctaagttggtgtttctaattctgttttgcaatccaattatagaagcttgaagatttgtttgatctgctattgctttatttatttattttttattacagGACAAGACTATTGCCTATTGGAGGAAATTTGTGGCAGAGTATTATTCACCCCGTGCAAAGAAAAGATGGTGCTTGTCCTTATATGACAATGTTGGAAATC
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-------------------------------------------------------------------------------gtttattatgttatatctgaac----acacttgttttatattttggctact----tttgaagttcttgattagttacaactattattcaatttttctttttgcttcagGATAATAGTATTGCCTATTGGAGAAAATTTGTGGCTGAATATTACTCTCCTCGTGCAAAGAAACGGTGGTGCTTGTCATTATATAGTAATGTTGGGCATC
upper sequence: Vv16s0100g00500.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G26970.1 (Glycine max), 3'ss of exon 1
gtgagttgatcctttctattttttatctttatttttatttactgcatctttagtgcattgcctgttacacatgcatgatatctatccagctaagttggtgtttctaattctgttttgcaatccaattatagaagcttgaagatttgtttgatctgctattgctttatttatttattttttattacagGACAAGACTATTGCCTATTGGAGGAAATTTGTGGCAGAGTATTATTCACCCCGTGCAAAGAAAAGATGGTGCTTGTCCTTATATGACAATGTTGGAAATC
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-------------------------------------------------------------------------------gtttattatgttatatctgaac----acacttgttttatgttttggctatt----tttgaagttctcgattagttatgccagttattcaaattttctgtttgcttcagGATAATAGTATTGCCTATTGGAGAAAATTTGTGGCTGAATATTACTCTCTTCGTGCAAAGAAACGATGGTGCTTGTCATTATATAGTAATGTTGGGCATC
upper sequence: Vv16s0100g00500.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G26960.1 (Glycine max), 3'ss of exon 3
gtgagttgatcctttctattttttatctttatttttatttactgcatctttagtgcattgcctgttacacatgcatgatatctatccagctaagttggtgtttctaattctgttttgcaatccaattatagaagcttgaagatttgtttgatctgctattgctttatttatt-tattttttattacagGACAAGACTATTGCCTATTGGAGGAAATTTGTGGCAGAGTATTATTCACCCCGTGCAAAGAAAAGATGGTGCTTGTCCTTATATGACAATGTTGGAAATC
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---------------------------------------------------------------------------------------aggaacttagttatatctgaacacatttgtttatgtg-ttgggtatttctgaagttctagattagttacaactctgttgttgaatgttttgtttgcctcagGATAATAGTATTGCCTATTGGATAAAATTTGTGGCTGAATATTACTCTCCTCGTGCAAAGAAACGGTGGTGCTTGTCATTATATAGCAATGTTGGGCATC
upper sequence: Vv16s0100g00500.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA16G32250.1 (Glycine max), 3'ss of exon 1
gtgagttgatcctttctattttttatctttatttttatttactgcatctttagtgcattgcctgttacacatgcatgatatctatccagctaagttggtgtttctaattctgttttgcaatccaattatagaagcttgaagatttgtttgatctgctattgctttattta-tttattttttattacagGACAAGACTATTGCCTATTGGAGGAAATTTGTGGCAGAGTATTATTCACCCCGTGCAAAGAAAAGATGGTGCTTGTCCTTATATGACAATGTTGGAAATC
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------------------------------------------------------------------------------------ttcagg-aacatggtatatctgaacacatttgtatgt---gttgagtatttttgaagttctagattagttacaactctgctgttgaattttttgtttgcttcagGATAATAGTATTGCCTATTGGAGAAAATTTGTTGCTGAATATTACTCTCCTCGTGCAAAGAAACGGTGGTGCTTGTCATTATATAGCAATGTTGGGCATC
upper sequence: Vv16s0100g00500.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G25520.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgagttgatcctttctattttttatctttatttttatttactgcatctttagtgcattgcctgttacacatgcatgatatctatccagctaagttggtgtttctaattctgttttgcaatccaattatagaagcttgaagatttgtttgatc-tgctattgctttatttatttat-tttttattacagGACAAGACTATTGCCTATTGGAGGAAATTTGTGGCAGAGTATTATTCACCCCGTGCAAAGAAAAGATGGTGCTTGTCCTTATATGACAATGTTGGAAATC
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---------------------------------------------------------------------------------------------------------------gtaagctaatcctaacctatggacttccag--ttatttcatcacatctatgcacccatcgctgatacctcttttctagGAAAATTGCATTACCTATTGGAGGAAATTTGTGGCAGAATACTTTTCACCTCGTGCAAAGCAGAGATTGTGCTTGTCACAGTACGAAAGTGCTGGGCACC
upper sequence: Vv16s0100g00500.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G62090.2 (Arabidopsis thaliana), 3'ss of exon 2
gtgagttgatcctttctattttttatctttatttttatttactgcatctttagtgcattgcctgttacacatgcatgatatctatccagctaagttggtgtttctaattctgttttgcaatccaattatagaagcttgaagatttgtttgatctgctattgctttatttatttattttttattacagGACAAGACTATTGCCTATTGGAGGAAATTTGTGGCAGAGTATTATTCACCCCGTGCAAAGAAAAGATGGTGCTTGTCCTTATATGACAATGTTGGAAATC
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-----------------------------------------------------------------------------gtgagtgtgcatgta-gtcg-----tcaaattttttgttttatgtgtattctagaaa----aaagctcttgacagataccagtcgtgtcattgctgattttgta-----gGAGAGCAGTATTGTTTACTGGAGGAAATTTGTGACGGAGTATTTTTCTCCCCGGGCAAAGAAAAGATGGTGTCTTTCTCATTATGATAATGTGGGGCATA
upper sequence: Vv16s0100g00500.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G25515.1 (Arabidopsis thaliana), 3'ss of exon 1
gtgagttgatcctttctattttttatctttatttttatttactgcatctttagtgcattgcctgttacacatgcatgatatctatccagctaagttggtgtttctaattctgttttgcaatccaattatagaagcttgaagatttgtttgatctgctattgctttatttatttattttttattacagGACAAGACTATTGCCTATTGGAGGAAATTTGTGGCAGAGTATTATTCACCCCGTGCAAAGAAAAGATGGTGCTTGTCCTTATATGACAATGTTGGAAATC
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-----------------------------------------------------------------------------------------gtaagctaata---ctaacc---tatggacttctagttattttatc----acatctattcaa---gttctcccatcactgataccttttctgt---agGAAAATTGCATTACTTATTGGAGGAAATTTGTGGCAGAATACTTCTCACCTCGTGCAAAGCAGAGGTTGTGCTTGTCACAGTACGAAAGTGTTGGGCACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agcttgaagatttgtttgatctgctattgctttatttatttattttttattacagGACAAGACTATTGCCTATTGGAGGAAATTTGTGGCAGAGTATTATTCACCCCGTGCAAAGAAAAGATGGTGCTTGTCCTTATATGACAATGTTGGAAATC
gtttgat putative branch site (score: 5)
tttatttatttttt putative PPT
atctgctattgcttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttgatcctttctattttttatctttatttttatttactgcatctttagtgcattgcctgttacacatgcatgatatctatccagctaagttggtgtttctaattctgttttgcaatccaattatagaagcttgaagatttgtttgatctgctattgctttatttatttattttttattacagGACAAGACTATTGCCTATTGGAGGAAATTTGTGGCAGAGTATTATTCACCCCGTGCAAAGAAAAGATGGTGCTTGTCCTTATATGACAATGTTGGAAATC
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