Sequence
atgc intronic sequence ATGC exonic sequence...cagaactccttttagactgaaacatgttcatcattgtttacctttttggttaactgccttgctgtgctcatgggacttctcatgtgatgtcaaattgtagAATCGGGCTGGACTACGTCAATTCTTAGACTCATTTGGTGGAACAGAACAGTCTGCGGCAAGTGGTAATTCTATATCTGCTGGTCTTGCTCAGGAGTCAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv12s0055g00490.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA08G07990.1 (Glycine max), 3'ss of exon 12
----------------------------------------------------------------------cagaact-ccttttagactg---aaacatgttcatcattgtttacctttttggttaa--ctgccttgctgtgctcatgggac-ttctcatgtga-tgtcaaatt-gtagAATCGGGCTGGACTACGTCAATTCTTAGACTCATTTGGTGGAACAGAACAGTCTGCGGCAAGTGGTAATTCTATATCTGCTGGTCTTGCTCAG--GAGTCAT
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gtatacttgatttaaggggcatttacagagacatgctccctactttgaattttagctaggcttgtataattatatccaccacttaaactgtaagagcaaatgaataatatattatctgctaagctaagttttcatggctcattttatatttcattctattgtcactgtcaactttgtagAGTCGGGCTGGGTTACGTCAGTTCTTAGATTCATTTGGTGGAACAGAACATTCCAATGCTTGTAATAATCCTACAGCAACTGTTCTATCACAAACAAGTG--
upper sequence: Vv12s0055g00490.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA05G24890.1 (Glycine max), 3'ss of exon 10
-----------------------------------------------------------------------------------------------cagaactccttttagactgaaacatgttcatcattgtttacctttttggttaa--ctgccttgctgtgctcatgggac-ttctcatgtga-tgtcaa-attgtagAATCGGGCTGGACTACGTCAATTCTTAGACTCATTTGGTGGAACAGAACAGTCTGCGGCAAGTGGTAATTCTATATCTGCTGGTCTTGCTCAG--GAGTCAT
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gtattgatttaagggacatttgcagagacatgctttggtatgctgcattttgaaagtatctcgctccctactttgaattttagctaggctcgtatgattatatccaccacttaagagcaaaagagtaatatattatttgctaagctaagttttcatggctcattttatatctcactctagtgtgactgtcaacattgtagAGTCGGGCTGGGTTACGTCTGTTCTTAGATTCTTTTGGTGGAACAGAACATTCCAATGCTTGTAATAATCCTACATCAACTGTTCTATCACAAACAAGTG--
upper sequence: Vv12s0055g00490.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: AT3G19720.2 (Arabidopsis thaliana), 3'ss of exon 14
-------cagaactccttttagactgaaacatgttcatcattgtttacctttttggttaactgccttgctgtgctcatgggacttctcatgtgatgtcaaattgtagAATCGGGCTGGACTACGTCAATTCTTAGACTCATTTGGTGGAACAGAACAGTCTGCGGCAAGTGGTAATTCTATATCTGCTGGTCTTGCTCAGGAGTCAT
| | ||| | ||| || || | | | | || | | | || | | | || || | | ||||||| || ||||| |||||||||||||| |||||||||||||||||||| || | || || |
gtcattgctacagccctatagctctgtttcaatccaattgagttgtgtacataccatcaagtatccgtttctgattg-agtagttttcgtttctcaatgttatgtagAACCGAGCTGGTCTACGTCAATTCTTGGACTCATTTGGTGGAACAGAGCATAATACGACATCAG------------------------------------
upper sequence: Vv12s0055g00490.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: AT3G19720.1 (Arabidopsis thaliana), 3'ss of exon 14
-------cagaactccttttagactgaaacatgttcatcattgtttacctttttggttaactgccttgctgtgctcatgggacttctcatgtgatgtcaaattgtagAATCGGGCTGGACTACGTCAATTCTTAGACTCATTTGGTGGAACAGAACAGTCTGCGGCAAGTGGTAATTCTATATCTGCTGGTCTTGCTCAGGAGTCAT
| | ||| | ||| || || | | | | || | | | || | | | || || | | ||||||| || ||||| |||||||||||||| |||||||||||||||||||| || | || || |||||| | ||| | ||||| | || || |||
gtcattgctacagccctatagctctgtttcaatccaattgagttgtgtacataccatcaagtatccgtttctgattg-agtagttttcgtttctcaatgttatgtagAACCGAGCTGGTCTACGTCAATTCTTGGACTCATTTGGTGGAACAGAGCATAATACGACATCAGGTAATGCCATAGGATTTAGTCTTCCCCAAGATGCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggttaactgccttgctgtgctcatgggacttctcatgtgatgtcaaattgtagAATCGGGCTGGACTACGTCAATTCTTAGACTCATTTGGTGGAACAGAACAGTCTGCGGCAAGTGGTAATTCTATATCTGCTGGTCTTGCTCAGGAGTCAT
ggttaac putative branch site (score: 3)
aaattgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cagaactccttttagactgaaacatgttcatcattgtttacctttttggttaactgccttgctgtgctcatgggacttctcatgtgatgtcaaattgtagAATCGGGCTGGACTACGTCAATTCTTAGACTCATTTGGTGGAACAGAACAGTCTGCGGCAAGTGGTAATTCTATATCTGCTGGTCTTGCTCAGGAGTCAT
- - - - - - - - - - - catgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - actgcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtga