Sequence
atgc intronic sequence ATGC exonic sequencegtatattatttcctttaacattggtttttgtggaatttgttctaattttgaaatcatctcagctgaaaacttgttgctgaattaatcgactatgctttcctttagGTTTATGAAATATTGGATAATGCCATTGATGAGGCTCAAGCTGGATTTGCTTCAAAGGTAGACGTTGTTTTACTTGCTGATGATTCTGTAAGCATCACTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv08s0007g05120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g16290.1 (Oryza sativa), 3'ss of exon 3
gtatattatttcctttaacattggtttttgtggaatttgttctaattttgaaatcatctcagctgaaaacttgttgctgaattaatcgactatgctttcctttagGTTTATGAAATATTGGATAATGCCATTGATGAGGCTCAAGCTGGATTTGCTTCAAAGGTAGACGTTGTTTTACTTGCTGATGATTCTGTAAGCATCACTG
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gtatattgaatgc---agattaggctactgtt---ttttttctgtggtacaaagtattccatattgttcttttctgatcattcgtctga--atggtgtatcacagGTTTATGAAATATTGGATAATGCCGTGGATGAAGCTCAAGCAGGCTACGCCACTAAGGTTGATGTTATCCTTCATGGCGACAATTCAGTTAGTGTAACAG
upper sequence: Vv08s0007g05120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA19G31030.1 (Glycine max), 3'ss of exon 3
gtatattatttcctttaacattggtttttgtggaatttgttctaattttgaaatcatctcag-ctgaaaacttgttgctgaattaatcgactatgctttcctttagGTTTATGAAATATTGGATAATGCCATTGATGAGGCTCAAGCTGGATTTGCTTCAAAGGTAGACGTTGTTTTACTTGCTGATGATTCTGTAAGCATCACTG
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--gtattgtcttct--agcttttgtttttttgcagct-gttttgttgatgctttgtttttgttctgaggtttttcttattgaagaagtgtttatgtggtgtcatagGTGTATGAAATTTTGGATAATGCTGTTGATGAAGCTCAAGCTGGGTTTGCTTCCAAGATTGATGTTGTTTTACTTGCGGATGATTCTGTGAGCATCACAG
upper sequence: Vv08s0007g05120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA03G28290.1 (Glycine max), 3'ss of exon 3
gtatattatttcctttaacattggtttttgtggaatttgttctaattttgaaatcatctcag--ctgaaaacttgttgctgaattaatcgactatgctttcctttagGTTTATGAAATATTGGATAATGCCATTGATGAGGCTCAAGCTGGATTTGCTTCAAAGGTAGACGTTGTTTTACTTGCTGATGATTCTGTAAGCATCACTG
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--gtattgtgttct--agcttttgtttttttgcagct-gttttggttgatgttttgttcttgttctgaggtttttctgatcgaagaagagttcatgtggtgtcttagGTGTACGAAATTTTGGATAATTCTGTTGACGAAGCTCAAGCTGGGTTTGCTTCCAAGATTTATGTTGTTTTGCATGCGGATGATTCTGTGAGCATCACAG
upper sequence: Vv08s0007g05120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT3G10270.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatattatttcctttaacattggtttttgtggaatttgttctaattttgaaatcatctcagctgaaaacttgttgctgaattaatcgactatgctttcctttagGTTTATGAAATATTGGATAATGCCATTGATGAGGCTCAAGCTGGATTTGCTTCAAAGGTAGACGTTGTTTTACTTGCTGATGATTCTGTAAGCATCACTG
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-------------gtaaatgcctttttcttttga---cgttcttggtc-gtgactggctc--ctatcaactggttatatccttcccaatacatgttgtttcttagGTTTATGAGATCCTTGACAACGCAATTGACGAGGCCCAAGCTGGTTTTGCTTCAAAGATCGACGTTGTTTTACATTCAGATGATTCAGTCAGCATTTCAG
upper sequence: Vv08s0007g05120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G04130.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatattatttcctttaacattggtttttgtggaatttgttctaattttgaaatcatctcagctgaaaacttgttgctgaattaatcgactatgctttccttt---agGTTTATGAAATATTGGATAATGCCATTGATGAGGCTCAAGCTGGATTTGCTTCAAAGGTAGACGTTGTTTTACTTGCTGATGATTCTGTAAGCATCACTG
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-----------------------gtaaatgctttatccgttgaaacccctcgtttgaactggctcttgacatctttttatgtttttctaatgtaatctcttttcttagGTTTATGAGATACTTGACAACGCAATTGATGAGGCTCAAGCTGGTTATGCCTCAAAGGTTGATGTCGTCCTACATGCAGATGGCTCAGTTAGTGTTGTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatcatctcagctgaaaacttgttgctgaattaatcgactatgctttcctttagGTTTATGAAATATTGGATAATGCCATTGATGAGGCTCAAGCTGGATTTGCTTCAAAGGTAGACGTTGTTTTACTTGCTGATGATTCTGTAAGCATCACTG
aattaat putative branch site (score: 3)
ctatgctttccttt putative PPT
tgaattaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatattatttcctttaacattggtttttgtggaatttgttctaattttgaaatcatctcagctgaaaacttgttgctgaattaatcgactatgctttcctttagGTTTATGAAATATTGGATAATGCCATTGATGAGGCTCAAGCTGGATTTGCTTCAAAGGTAGACGTTGTTTTACTTGCTGATGATTCTGTAAGCATCACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT