Sequence
atgc intronic sequence ATGC exonic sequencegtaaagtaggaatgaaatagaagttgctggatcatttattcaacatgtaccctttaatatagaataatgaatattgcaccttgtggtggttctcctctgttactactccttcatgttctgatcattgtattctaatttatttggtattggtggtttgcagCTTACCTTTGTGTTTCTTGTACTGCCTTGCCTTCTGTTGGGCTACCTTGGTCAAGCTGCATACCTTATGGAAAACCATGATCAATATGGTCAACTCTTCT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv12s0142g00170.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G24530.1 (Glycine max), 3'ss of exon 6
gtaaagtaggaatgaaatagaagttgctggatcatttattcaacatgtaccctttaatatagaataatgaatattgcaccttgtggtggttct-cctctgttactactccttcatgttctgatcattgtattctaatttatttggtattggtg-gtttgcagCTTACCTTTGTGTTTCTTGTACTGCCTTGCCTTCTGTTGGGCTACCTTGGTCAAGCTGCATACCTTATGGAAAACCATGATCAATATGGTCAACTCTTCT
|| |||| ||| ||| | | |||| || ||| | || ||||| | | | | |||| | || | || | |||| ||||| ||||||| ||||| |||||||| | || ||||| |||||||| || | ||||||||||||||||||||||||||||||| | | |||| | ||| |
--------------------------------------------------------gtaatgaatgatgtctatgttataattgacaacttctgtttccgttttactttctgtatgttatcaac-taatattttgatgaaactgatggtggtttgtttgtagCTTACATTTGTATTTCTTGTTTTACCATGCCTACTGTTGGGTTATTTGGGTCAAGCTGCATACCTTATGGAAAACCATGCTGATGCTGGTAATGCCTTTT
upper sequence: Vv12s0142g00170.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G07720.1 (Glycine max), 3'ss of exon 4
gtaaagtaggaatgaaatagaagttgctggatcatttattcaacatgtaccctttaatatagaataatgaatattg--caccttgtggtggttctcctctgttactactc--cttcatgt-tctgatca--ttgtattctaatttatttggtattggtg-gtttgcagCTTACCTTTGTGTTTCTTGTACTGCCTTGCCTTCTGTTGGGCTACCTTGGTCAAGCTGCATACCTTATGGAAAACCATGATCAATATGGTCAACTCTTCT
|||||||| || | || | | | | |||||| | | ||| ||| ||| |||| | |||| | || || || | |||| ||||| ||||||| ||||| |||||||| | || ||||| |||||||| || | ||||||||||||||||||||||||||||||| | | |||| | ||| |
---------------------------------------------------------------gtaatgaatgatgtctatgttataattgacaacttctgtttccgttttactttctgtatcttatcaactaatattttgatgtaactgatggtggtttgtttgtagCTTACATTTGTATTTCTTGTTTTACCGTGCCTACTGTTGGGTTATTTGGGTCAAGCTGCATACCTTATGGAAAACCATGCTGATGCTGGTAATGCCTTTT
upper sequence: Vv12s0142g00170.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA15G05880.1 (Glycine max), 3'ss of exon 6
gtaaagtaggaatgaaatagaagttgctggatcatttattcaacatgtaccctttaatatagaataatgaatattgcaccttgtggtggttctcctctgttactactccttcatgttctgatcattgtattctaatttatttggtattggtggtttgcagCTTACCTTTGTGTTTCTTGTACTGCCTTGCCTTCTGTTGGGCTACCTTGGTCAAGCTGCATACCTTATGGAAAACCATGATCAATATGGTCAACTCTTCT
|| | | | || | | |||| | | ||| | | | || || ||| ||| | |||| || || | | ||| || | | || | | | |||||||||| | ||||| |||||||| |||| ||||| || ||||| || | ||||||||||||||||||||||||||||||| | | ||||||| ||| |
-----------------------------------gtagtggattttgtccttgtcatatttatt--tgactgtcatgcttt---------cttatcttttatt--tcctgtgtgatcgcaaactgatatgctggtgaaactgatggggctaatttgcagCTTTCATTTGTCTTTCTTGTTTTGCCGTGCCTACTATTGGGTTATTTGGGTCAAGCTGCATACCTTATGGAAAACCATGCTGATGCTGGTCAAGCCTTTT
upper sequence: Vv12s0142g00170.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G19120.1 (Glycine max), 3'ss of exon 7
gtaaagtaggaatgaaatagaagttgctggatcatttattcaacatgtaccctttaatatagaataatgaatattgcaccttgtggtggttctcctctgttactactccttcatgttc-tgatcattgtattctaatttatttggtattggtggtttgcagCTTACCTTTGTGTTTCTTGTACTGCCTTGCCTTCTGTTGGGCTACCTTGGTCAAGCTGCATACCTTATGGAAAACCATGATCAATATGGTCAACTCTTCT
| ||| ||| | | | || |||| || ||| || || || | | || |||| || || ||| || ||| || | | || | || | |||||||||| | ||||| |||||||| |||| ||||| || ||||| || | ||||||||||||||||||||||||||||||| | | ||||||| ||| |
------------------------------------------gta-gtagattttgtgtttg--tcatatttatttgac--tgtcatgctt-tcatttcttttatttcctgtgtgctcgtgaacaa-atatgctggtgaaactgatgatgctaatttgcagCTTTCATTTGTCTTTCTTGTTTTGCCGTGCCTACTATTGGGTTATTTGGGTCAAGCTGCATACCTTATGGAAAACCATGCTGATGCTGGTCAAGCCTTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctccttcatgttctgatcattgtattctaatttatttggtattggtggtttgcagCTTACCTTTGTGTTTCTTGTACTGCCTTGCCTTCTGTTGGGCTACCTTGGTCAAGCTGCATACCTTATGGAAAACCATGATCAATATGGTCAACTCTTCT
ttctaat putative branch site (score: 2)
atcattgtattctaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagtaggaatgaaatagaagttgctggatcatttattcaacatgtaccctttaatatagaataatgaatattgcaccttgtggtggttctcctctgttactactccttcatgttctgatcattgtattctaatttatttggtattggtggtttgcagCTTACCTTTGTGTTTCTTGTACTGCCTTGCCTTCTGTTGGGCTACCTTGGTCAAGCTGCATACCTTATGGAAAACCATGATCAATATGGTCAACTCTTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC