Sequence
atgc intronic sequence ATGC exonic sequencegtacgccttctcctcattgtagcatatttagatattgtcctatgtttacttccaaatgttctaaatgaaaaaaacttctcgagacgggtcttagtttttttaatattctttgttgcaaggcttgctgaaatgactgtttctttgttccaagattaagatttcacatgctaatggtttcagGAAGAGAGTTGCGATTGTTGGAAGTGGACCAGCCGGGTTGGCTGCTGCTGATCAGCTAAACAGAATGGGCCATTTTGTGACAGTGTTTGAGCGTGCTGAC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv16s0098g00290.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA14G32500.1 (Glycine max), 3'ss of exon 20
gtacgccttctcctcattgtagcatatt-tagatattgtcctatgtttacttccaaatgttctaaatgaaaaaaacttctcgagacgggtcttagtttttttaatattctttgttgcaaggcttgctgaaatgactgtttctttgttccaagattaagatttcacatgctaatggtttcagGAAGAGAGTTGCGATTGTTGGAAGTGGACCAGCCGGGTTGGCTGCTGCTGATCAGCTAAACAGAATGGGCCATTTTGTGACAGTGTTTGAGCGTGCTGAC
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gtatgctgtttt-tctttttaacatctcatcagtttcattttcgttattctgctgttccttttcagccaaatatgcataaccctccaagttgatgtgccataatttttctatctttaaa---ctgttcaact--ttgttacaataattagcgttatttgactaatatctttaccgatacagGAAAAGAGTAGCCATCGTTGGAAGTGGACCATCTGGCTTGGCAGCTGCTGATCAGCTAAATAAAATGGGTCATACAGTAACCGTGTATGAAAGAGCTGAT
upper sequence: Vv16s0098g00290.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA06G13280.2 (Glycine max), 3'ss of exon 19
----gtacgccttctcctcattgtagcatatttagatattgtcctatgtttacttccaaatgttctaaatgaaaaaaacttctcgagacgggtcttagtttttttaatattctttgttgcaaggctt-gctgaaatgactgtttctttgttccaagattaagatttcacatgctaatggtttcagGAAGAGAGTTGCGATTGTTGGAAGTGGACCAGCCGGGTTGGCTGCTGCTGATCAGCTAAACAGAATGGGCCATTTTGTGACAGTGTTTGAGCGTGCTGAC
| || ||| || | || || | | ||| ||| ||| || || | | |||||| | || | | | || || ||||| |||| | | | ||| ||||| | || | | | | || || | ||| || |||| | || | |||||| ||||| || ||||||||||||||||| |||| |||| ||||||||||| || || | |||||||||| ||| || |||| ||| | |||||
gtatgcactttttcacccctttccgttatttct-gatgttgct-----tttcaatcgaataggtataaatgtacaa---tccacaagttggtgtttagtgattttcagttattaaactgcttggctttgttgtagttattattaaactggctcg---ttag---ttaacatcttcattaatacagGAAAAGAGTGGCCGTTGTTGGAAGTGGACCATCCGGCCTGGCAGCTGCTGATCAACTGAATAAAATGGGCCATACTGTAACTGTGTATGAAAGAGCTGAT
upper sequence: Vv16s0098g00290.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA19G16450.1 (Glycine max), 3'ss of exon 15
gtacgccttctcctcattgtagcat-atttagatattgtcctatgtttacttccaaatgttctaaatgaaaaa--aacttctcgagacgggtcttagtttttttaatattctttgt-tgca-aggcttgctgaaatgactgtttctttgttccaagattaagatttcacatgctaatggtttcagGAAGAGAGTTGCGATTGTTGGAAGTGGACCAGCCGGGTTGGCTGCTGCTGATCAGCTAAACAGAATGGGCCATTTTGTGACAGTGTTTGAGCGTGCTGAC
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gtatgctgtttt-tctttctaatatcacgtcggtttcatttttgttattctgctgttccttttcagccaaacatgtaccctccaagttgatgtgcagtaatttttctgtttttaatctgctcaactttgttacaataattagatttattt-----aactaatatctt---tactgata----cagGAAAAGAGTAGCCATCGTTGGCAGTGGACCATCTGGCTTGGCAGCTGCTGATCAGCTAAATAAAATGGGTCATACAGTAACCGTGTATGAAAGAGCTGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaaatgactgtttctttgttccaagattaagatttcacatgctaatggtttcagGAAGAGAGTTGCGATTGTTGGAAGTGGACCAGCCGGGTTGGCTGCTGCTGATCAGCTAAACAGAATGGGCCATTTTGTGACAGTGTTTGAGCGTGCTGAC
tgctaat putative branch site (score: 2)
attaagattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgccttctcctcattgtagcatatttagatattgtcctatgtttacttccaaatgttctaaatgaaaaaaacttctcgagacgggtcttagtttttttaatattctttgttgcaaggcttgctgaaatgactgtttctttgttccaagattaagatttcacatgctaatggtttcagGAAGAGAGTTGCGATTGTTGGAAGTGGACCAGCCGGGTTGGCTGCTGCTGATCAGCTAAACAGAATGGGCCATTTTGTGACAGTGTTTGAGCGTGCTGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT