Sequence
atgc intronic sequence ATGC exonic sequencegtaatagtttcgattgtttttctttttggcccacatcccatgtttcagcatcttatgttaatgaaatcatattccctgcagttatttttcttacccattatgattgtttcattgccttgtatagCTGCTTTGAAGCATCCTAGGACTCCTCCAACTAACCCTTCTGTGGACTACCCATCAGGGGATTCTGAGCATGTTGCCAAAAGAGGAAGACCTATGGGAAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0002g08370.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G22910.1 (Glycine max), 3'ss of exon 6
gtaatagtttcgattgtttttctttttggcccacatcccatgtttcagcatcttatgttaatgaaatcatattcc--ctgcagttatttttcttacccattatgattgtttcattgccttgtatagCTGCTTTGAAGCATCCTAGGACTCCTCCAACTAACCCTTCTGTGGACTACCCATCAGGGGATTCTGAGCATGTTGCCAAAAGAGGAAGACCTATGGGAAT
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-------------------------------------gtattgttcactgactctt-taggtgtagtcataatgcgatcatcaaaatttaactttgacttttaacatgtttcattgccttgttaagCTGCTTTGAAGCATCCTAGGACCCCCCCAACTAATCCTTCTGTTGACTATCCATCTGGAGACTCAGATCATGTTGCTAAGAGAACAAGGCCAATGGGAAT
upper sequence: Vv09s0002g08370.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA07G03180.1 (Glycine max), 3'ss of exon 7
gtaatagtttcgattgtttttctttttggcccacatcccatgtttcagca--tcttatgttaatgaaatcatattccctgcagttatttttcttacccattatgattgtttcattgccttgtatagCTGCTTTGAAGCATCCTAGGACTCCTCCAACTAACCCTTCTGTGGACTACCCATCAGGGGATTCTGAGCATGTTGCCAAAAGAGGAAGACCTATGGGAAT
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-------------------------------------gtataattcaccaattctttaggtgcagtcataatgtgatcatcaaaatttatctttgacttttaacat-gtttcattgccttgttaagCTGCTTTGAAGCATCCTAGGACCCCCCCAACTAATCCTTCTGTTGACTATCCATCTGGAGACTCAGATCATGTTGCTAAGAGAACAAGGCCAATGGGAAT
upper sequence: Vv09s0002g08370.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA13G44420.1 (Glycine max), 3'ss of exon 7
gtaatagtttcgattgtttttctttttggcccacatcccatgtttcagcatcttatgttaatgaaatcatattccctgcagttatttttcttacccattatgattgtttcattgccttgtatagCTGCTTTGAAGCATCCTAGGACTCCTCCAACTAACCCTTCTGTGGACTACCCATCAGGGGATTCTGAGCATGTTGCCAAAAGAGGAAGACCTATGGGAAT
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---------------------gtactacattcattttctttctatcattctccaactcttcatgagctatgtttggtttgtataatctt-tgatctctgatg-----ctccttgtctttttaagCTGCTTTGAAGCACCCTAGGACCCCTCCAACTAATCCTTCTGTTGACTATCCATCTGGTGATTCAGATCATGTTTCTAAGAGAACAAGACCAATTGGAAT
upper sequence: Vv09s0002g08370.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA15G00880.1 (Glycine max), 3'ss of exon 6
gtaatagtttcgattgtttt-tctttttggcccacatcccatgtttcagcat-cttatgttaatgaaatcatattccctgcagttatttttcttacccattatgattgtttcattgccttgtatagCTGCTTTGAAGCATCCTAGGACTCCTCCAACTAACCCTTCTGTGGACTACCCATCAGGGGATTCTGAGCATGTTGCCAAAAGAGGAAGACCTATGGGAAT
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gtactacattcatttgctttctatcattctccaattcttcatgactagtagtacttaggtttcatatgctatgtttggtttgtataatctt-tgacctctgatg-----ctccttgcctttttaagCTGCTTTGAAGCACCCTAGGACCCCTCCAACTTATCCTTCTGTTGACTATCCATCTGGTGATTCAGATCATGTTTCTAAGAGAACAAGACCAATGGGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattccctgcagttatttttcttacccattatgattgtttcattgccttgtatagCTGCTTTGAAGCATCCTAGGACTCCTCCAACTAACCCTTCTGTGGACTACCCATCAGGGGATTCTGAGCATGTTGCCAAAAGAGGAAGACCTATGGGAAT
ttcttac putative branch site (score: 2)
ttgcctt putative PPT
agttatttttctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatagtttcgattgtttttctttttggcccacatcccatgtttcagcatcttatgttaatgaaatcatattccctgcagttatttttcttacccattatgattgtttcattgccttgtatagCTGCTTTGAAGCATCCTAGGACTCCTCCAACTAACCCTTCTGTGGACTACCCATCAGGGGATTCTGAGCATGTTGCCAAAAGAGGAAGACCTATGGGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA