Sequence
atgc intronic sequence ATGC exonic sequence...tttttctgagttctatttcttttcaaaaataaaataaaagaaaaaaggaactgaaattaaaatgaaactaaaatgaagctgaagattttgtcctcaacagGTTCCCGGTTGACAAACTTTGTGGGTATACTTAGTCAAGGACTGAGAATAGCTCCTCCTGAAGCTCCAGCAACTGGCTATATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv07s0005g03040.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: LOC_Os07g23110.1 (Oryza sativa), 3'ss of exon 16
tttttctgagttctatttcttttcaaaaataaaataaaagaaaaaaggaactgaaattaaaatgaaactaaaatgaagctgaagattttgtcctca----acagGTTCCCGGTTGACAAACTTTGTGGGTATACTTAGTCAAGGACTGAGAATAGCTCCTCCTGAAGCTCCAGCAACTGGCTATATG
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-cttttt---ttgtaattgtactggagatctacttaacgtccctaagtaactctttccttcctaccatttgaatgattccatgattgcaaaacttaatttatagGTTCAAGGTTGACCAATTATGTTGGAATACTTAGTCAAGGACTAAGAATAGCACCTCCTGAGGCTCCCGTGACAGGCTATATG
upper sequence: Vv07s0005g03040.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GRMZM5G831712_T02 (Zea mays), 3'ss of exon 16
----tttttctgagttctatttcttttcaaaaataaaataaaagaaaaaaggaactgaaattaaaatgaaactaaaatgaagctgaagattttgtcctcaacagGTTCCCGGTTGACAAACTTTGTGGGTATACTTAGTCAAGGACTGAGAATAGCTCCTCCTGAAGCTCCAGCAACTGGCTATATG
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aaaatatagtttgcatgtgtatagttcatttggtagcatttaaggtcttgaacatttcttcataagttattcccttctcacggtaaa-actcgattt---gtagGTTCAAGGTTGACGAATTTTGTGGGAATTCTTAGTCAAGGGCTAAGAATTGCACCTCCTGAGGCACCTGTTACTGGCTATATG
upper sequence: Vv07s0005g03040.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA19G34580.1 (Glycine max), 3'ss of exon 16
tttttctgagttctatttcttttcaaaaataaaataaaag--aaaaaaggaactgaaattaaaatgaaactaaaa--tgaagctgaagattttgtcctcaacagGTTCCCGGTTGACAAACTTTGTGGGTATACTTAGTCAAGGACTGAGAATAGCTCCTCCTGAAGCTCCAGCAACTGGCTATATG
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----atggatggctattttgtattaatgtgcaaactgcagccgtagatgcaaatatgtacaaaattgaattagacacctatgacaaaaatgttctctattttagGTTCTAGGTTGACAAACTTTGTGGGCATTCTTAGCCAAGGACTCAGAATTGCACCTCCTGAAGCCCCCGCGACTGGCTATATG
upper sequence: Vv07s0005g03040.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA03G31820.1 (Glycine max), 3'ss of exon 17
--------tttttctgagttctatttcttttcaaaaataaaataaaagaaaaaaggaactgaaattaaaatgaaactaaaatgaagctgaagattttgtcctcaacagGTTCCCGGTTGACAAACTTTGTGGGTATACTTAGTCAAGGACTGAGAATAGCTCCTCCTGAAGCTCCAGCAACTGGCTATATG
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atggatggctattttgttttcatgtgctatccgcagctg---tagatgaaaatatgtac--aaatttgagttagacacctatga---caaaaatgctctctattatagGTTCTAGGTTGACAAACTTTGTGGGCATTCTTAACCAAGGACTCAGAATTGCACCTCCTGAAGCCCCGGCTACTGGCTATATG
upper sequence: Vv07s0005g03040.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: PP1S114_181V6.1 (Physcomitrella patens), 3'ss of exon 18
tttttctgagtt-ctatttcttttcaaaaataaaataaaagaaaaaaggaactgaaattaaaatgaaactaaaatgaagctgaagattttgtcctcaa--------cagGTTCCCGGTTGACAAACTTTGTGGGTATACTTAGTCAAGGACTGAGAATAGCTCCTCCTGAAGCTCCAGCAACTGGCTATATG
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----tctagtttactcttttaggtagagaacaaaggtattcaattcaagtact----ttcgaaccatgc-aaggtgagcttgaattgtttgttgttgagggatttgcagGTTCTCGAACAACAAATTATGTTGGTATTCTGAGCCAAGGTCTGAGAATTGCTCCTCCTGAAGCTCCAGTAACAGGTTACATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aggaactgaaattaaaatgaaactaaaatgaagctgaagattttgtcctcaacagGTTCCCGGTTGACAAACTTTGTGGGTATACTTAGTCAAGGACTGAGAATAGCTCCTCCTGAAGCTCCAGCAACTGGCTATATG
aactaaa putative branch site (score: 2)
ttttgtcctc putative PPT
aaattaaaatgaaact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttttctgagttctatttcttttcaaaaataaaataaaagaaaaaaggaactgaaattaaaatgaaactaaaatgaagctgaagattttgtcctcaacagGTTCCCGGTTGACAAACTTTGTGGGTATACTTAGTCAAGGACTGAGAATAGCTCCTCCTGAAGCTCCAGCAACTGGCTATATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - -caaaaat
- - - - - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -aaattaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaagct