Sequence
atgc intronic sequence ATGC exonic sequence...tttttaaagatcctaacttttgtcataattcattagccctttagtacgtggcataatcacatgtaactaaaattttctatgttgtgttgctattgtgcagAGCAACAATGAAAAGCTGTTAGAGAATCCATACCTTCAGATGCGTGGCATAATTCAGCTGTCAAATGATCTTGGGACTGGGTTATAATCTGATGTTTTTT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv13s0019g00680.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: LOC_Os01g74310.5 (Oryza sativa), 3'ss of exon 6
------------------------------------------------------------------------------tttttaaa---gatcctaacttt-tgtcataattcattagccctttagtacgtggcataatcacatgtaactaaaatttt--ctatgttg---------tgttgct---attgtg--cagAGCAACAATGAAAAGCTGTTAGAGAATCCATACCTTCAGATGCGTGGCATAATTCAGCTGTCAAATGATCTTGGGACTGGGTTATAA-TCTGATGTTTTTT
| | || | | | || || | || || ||| | || ||| ||| || || | || | ||||| | |||| | ||||| ||| | ||||||||||| ||| | ||||| ||||||||||| |||||||| ||| | ||| ||||||| ||||| || | | || | || |||| |
gtggagcctcttttttcctatctcattatgggggtgaaatttgaagtattacatgaatgccatccatatgcatcggtttatctagattagtttctggtttcacgccaggtgcttcaagtgtcgtaggaggtttcatt-tcatgcatatctgatatctcaattatgtcggtactgacatgttatttacattgttgccagTGTAACAATGAAAAACTGCTGGAGAACCCATACCTTCAAATGCGTGGGATACTGCAGTTGTCAAACGATCTAGGAGTTCAATAATCACTCGAATGTGCTA-
upper sequence: Vv13s0019g00680.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA10G43560.2 (Glycine max), 3'ss of exon 16
-tttttaaagatcctaacttttgtcataattcattagccctttagtacgtggcataatcacatgtaa---ctaaaattttctatgttgtgttgctattgtgcagAGCAACAATGAAAAGCTGTTAGAGAATCCATACCTTCAGATGCGTGGCATAATTCAGCTGTCAAATGATCTTGGGACTGGGTTATAATCTGATGTTTTTT
| ||| || | || ||||| | || ||| |||||| | || | | ||| | | ||| | || | ||| | || |||| |||||||||||| |||||||||||||| |||||||| ||| |||||||| |||| || ||||||||||||| || || | || | | | ||
ttattttaaatttct---ctttgtt-tgtttgcttaataatttagtgttcttggtgattaattataaatgtttcatgtttgtgctttttattggcactgcacagACCAACAATGAAAAACTGTTAGAGAATCCTTACCTTCAAATGTGTGGCATACTTCAATTGGCAAATGATCTTGGATTTGACTTGTGATGTTAAACTCTTG
upper sequence: Vv13s0019g00680.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA20G23240.1 (Glycine max), 3'ss of exon 19
----tttttaaagatcctaactt-ttgtcataattcattagccctttagtacgtggcataatcacatgtaactaaaattttctatgttgtgttgctattgtgcagAGCAACAATGAAAAGCTGTTAGAGAATCCATACCTTCAGATGCGTGGCATAATTCAGCTGTCAAATGATCTTGGGACTGGGTTATAATCTGATGTTTTTT
||||||| || | || || | |||| |||| ||| | ||| |||| | | | || | ||| | |||| || | || ||||||||||||||||| |||||||||||||| |||||||| ||| |||||||| |||| || |||||||||||| || || | |
ccttattttaaatttctttgtttgtttgcttaataatttagtatttttg---gtgat-taattataaatg-ttacatgtttgtgctttgtatttgcactgcacagAGCAACAATGAAAAACTGTTAGAGAATCCTTACCTTCAAATGTGTGGCATACTTCAATTGGAAAATGATCTTGGATTTGACTTGTGA-------------
upper sequence: Vv13s0019g00680.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA02G10370.1 (Glycine max), 3'ss of exon 16
tttttaaagatcctaacttttgtcataattcattagccctttagtacgtggcataatcacatgtaactaaaattttctatgttgtgttgctattgtgcagAGCAACAATGAAAAGCTGTTAGAGAATCCATACCTTCAGATGCGTGGCATAATTCAGCTGTCAAATGATCTTGGGACTGGGTTATAATCT----GATGTTTTTT------------------
|| | ||||| | || | | | || | | | | || ||| | || ||| || | || |||| ||||||||||| |||||||||||||| || ||||| ||| |||||||| |||| ||| |||||||||| |||| || ||| |||| | || ||
------------------ttcttaataatatagtatttttggccaatttaatatttactattatgattatgattatgcat--tgtatt--tgcaatgtagagtaacaatgaaaaactgttagAGAATCCGTATCTTCAAATGTGTGGCATACTTCAACTGGCAAATGATCTGGGGATTGACCTATGATCTTCAAGGCGTGACTTTCTGGGAGATTGTTATAC
upper sequence: Vv13s0019g00680.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA18G52540.1 (Glycine max), 3'ss of exon 15
----tttttaaagatcctaacttttgtcataattcattagccctttagtacgtggcataatcacatgtaactaaaattttctatgttgtgttgctattgtgcagAGCAACAATGAAAAGCTGTTAGAGAATCCATACCTTCAGATGCGTGGCATAATTCAGCTGTCAAATGATCTTGGGACTGGGTTATAATCTGATGTTTTTT
||||| | | ||| | ||| | | || ||| || | ||| | || || || | || | |||| || | || |||| ||||||||||| ||||||||||| || || ||||| ||| |||||||| |||| ||| |||||||||| |||| || | | |
gtttttttttttttttgcagttttcttaatagtgtacta--tttttggtgaatttaatatttactattacttatatgattatgcattgtatt--tgccatgtagAGTAACAATGAAAAACTGTTAGAGAACCCGTATCTTCAAATGTGTGGCATACTTCAACTGGCAAATGATCTGGGGATTGACCTGTGA-------------
upper sequence: Vv13s0019g00680.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: AT3G12590.1 (Arabidopsis thaliana), 3'ss of exon 16
---------------------------------------tttttaaagatcctaacttttgtcataattcattagcc--ctttagtacgtggcataatcacatgtaactaaaattttctatgttgtgttgctattgtgcagAGCAACAATGAAAAGCTGTTAGAGAATCCATACCTTCAGATGCGTGGCATAATTCAGCTGTCAAATGATCTTGGGACTGGGTTATAATCTGATGTTTTTT-
||| ||| | ||| ||| | ||| |||| | || ||| | | | | ||| | | || | || | ||||||||||||| ||||| || ||| ||||||||||||| || |||||| |||| ||| ||||||| ||||| || || | ||| | || | | |
gtattgctatcgtcataattcagggtgtagatgcgtagaaccggaaatatcaaagagaacctcaaaatcaaagagctttctttgttttgtttcatgtataataatgatccacattgattgtattct--tgtt-ttgtgcagAGCAATAATGAGAAACTGCTAGAGAATCCATATCTGCAGATGTGTGGTATACTTCAGCTATCAAACGAGCTCTGAACTCG-CGGCTCTCATAAGCCTCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acgtggcataatcacatgtaactaaaattttctatgttgtgttgctattgtgcagAGCAACAATGAAAAGCTGTTAGAGAATCCATACCTTCAGATGCGTGGCATAATTCAGCTGTCAAATGATCTTGGGACTGGGTTATAATCTGATGTTTTTT
aactaaa putative branch site (score: 2)
taactaaaattttcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttttaaagatcctaacttttgtcataattcattagccctttagtacgtggcataatcacatgtaactaaaattttctatgttgtgttgctattgtgcagAGCAACAATGAAAAGCTGTTAGAGAATCCATACCTTCAGATGCGTGGCATAATTCAGCTGTCAAATGATCTTGGGACTGGGTTATAATCTGATGTTTTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - tcctaac
- - - - - - - - - - - - - - - - - -gcccttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tcacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aactaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgttgc