Sequence
atgc intronic sequence ATGC exonic sequence...tttggcattactaataccacactttttaaatgaattctctatattccatactcttattctgtaccctgacctgatttttttgaatatctattgactatagGCCCGTAGAGGTGGTATTGATGAACCATTTGCATGGGATAGTAGAGAGTATTTGAGGAAACTCTGCATAGGAAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0068g00720.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os02g32350.2 (Oryza sativa), 3'ss of exon 2
tttggcattactaataccacactttttaaatgaattctctatattccatactcttattctgtaccctgacctgatttttt-----tgaatatctat-tgactatagGCCCGTAGAGGTGGTATTGATGAACCATTTGCATGGGATAGTAGAGAGTATTTGAGGAAACTCTGCATAGGAAAG
||| | | || | | | |||| | ||| ||||| ||||| | |||| || | | | || | || | || | | | || |||| || | ||||| | |||||||||||||| ||||| || || |||| | | |||||||||||||||||||||
tttctcgtg--tagttcaaaacttat-gaatttattct---tattctccagtctttccctccctttttgctttatgtattgaaactaaaactttgtgctgctcaagGCTCGCCGTGGTGGAGTGGATGAACCATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAG
upper sequence: Vv14s0068g00720.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G136296_T02 (Zea mays), 3'ss of exon 2
tttggcattactaataccacactttttaaatgaattctctatattccatactcttattctgtaccctgacctgattttt---ttgaatatctattg-actatagGCCCGTAGAGGTGGTATTGATGAACCATTTGCATGGGATAGTAGAGAGTATTTGAGGAAACTCTGCATAGGAAAG
||| | || | | | || | |||| | | | | | |||| | | | | | | |||||| ||| ||| || | |||||||| ||| | ||||| ||||||| || ||||||||||| || ||||||| | ||||||| ||||||||||| |||
--tggaactatttactgagtatcaattg--tagcttcttgacaattgacattcttctcatttctctagttttcatttttcgcttgtttattcatggtgctatagGCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG
upper sequence: Vv14s0068g00720.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA06G17050.4 (Glycine max), 3'ss of exon 2
tttggcattactaataccacactttttaaatgaatt----------ctctatattccatactcttattctg--taccctgacctgatttttttgaatatctattgacta---tagGCCCGTAGAGGTGGTATTGATGAACCATTTGCATGGGATAGTAGAGAGTATTTGAGGAAACTCTGCATAGGAAAG
| | ||| | || || ||||| | || ||| | ||| | | | || | | | | | | ||||||| | | | | | ||||| |||||||||||| | || || || ||||||||||| || ||||||| | ||||||| ||||||||||| |||
-gtagttttagttatttgactttttttcattggattaattaatcaattaaataatttaaagctttgtgttaattgctttagtgttttttttttttttttttgcgaattgtggtagGCGCGTAGAGGTGGTGTGGACGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG
upper sequence: Vv14s0068g00720.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA04G38010.1 (Glycine max), 3'ss of exon 2
-------------tttggcattactaataccacactttttaaatgaattctctatattccatactct-tattctgtaccctgacctgatttttttgaatat--ctattgactatagGCCCGTAGAGGTGGTATTGATGAACCATTTGCATGGGATAGTAGAGAGTATTTGAGGAAACTCTGCATAGGAAAG
|||| | || | | | | |||| | |||| || ||| | |||| | || | | | | ||||||| | | | | | | | ||||| |||||||||||| | || || || ||||||||||| || ||||||| | ||||||| ||||||||||| |||
gtacttttagttatttgacttttttt-cattggattaattaa-tcaattaaata-atttaaggctctgtgttaattgctttagtgttgttttttttttttttgcgaattattgtagGCGCGTAGAGGTGGTGTGGACGAGCCTTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG
upper sequence: Vv14s0068g00720.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA05G33320.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------------------------------------------------tttggcat-tactaataccacactttttaaatgaattctcta-tattccatactcttattctgtaccctgacctgatttttttgaatatctattgactatagGCCCGTAGAGGTGGTATTGATGAACCATTTGCATGGGATAGTAGAGAGTATTTGAGGAAACTCTGCATAGGAAAG
||| | | | ||||| | | || || || || | | || | | | | | ||| | | ||| ||| || | ||| ||| ||| |||||||||||| | ||||| || ||||||||||| |||||||||| | | |||| |||||||| || |||
gtaattttacttgattcatggatattttgttgtaactatgaactgaaattgttttgaaatgcttctgtatcgattttgtgttaataatgttttccgtgttctaatttcgaaattgaaaattgctttttgtgctacttctggggtgtttacattacgttaaagctctttgtttaaaaa---atttgcta--gGCGCGTAGAGGTGGTGTAGATGAGCCGTTTGCATGGGAAAGTAGAGAGTTTCTACGGAAGCTCTGCATTGGGAAG
upper sequence: Vv14s0068g00720.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G00910.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------------------------------------------tttggcattactaataccacactttttaaat---gaattctctatattccatactcttattctgtaccctgacctgatttttttgaatatctattgactatagGCCCGTAGAGGTGGTATTGATGAACCATTTGCATGGGATAGTAGAGAGTATTTGAGGAAACTCTGCATAGGAAAG
| || || || | ||| |||| ||| || | | | | | | | ||| | | | ||| ||| || || | |||||| |||||||||||| | ||||| || ||||| ||||| |||||||||| | | |||| || ||||| || |||
gtaattttacttggttcatggaattgaaattgctgtgactgtgaattgaaattcttttgaaattctgttgtaccgattttgtggtttatgatgttttccgtattctaatttcaaaattgaaaatgctttctgtgctactgctgaggtgtttacattaaagttctttgtttaaaaattt-----tgatagGCGCGTAGAGGTGGTGTAGATGAGCCGTTTGCGTGGGAAAGTAGAGAGTTTCTACGGAAGCTTTGCATTGGGAAG
upper sequence: Vv14s0068g00720.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G07350.2 (Arabidopsis thaliana), 3'ss of exon 2
-------------------------------------------------------------------------------------------tttggcattactaataccacactttttaaatgaattctc------tatattccatactcttattctgtaccctgacctgatttttttgaatatctattgactatagGCCCGTAGAGGTGGTATTGATGAACCATTTGCATGGGATAGTAGAGAGTATTTGAGGAAACTCTGCATAGGAAAG
||| || | | || ||| ||| |||| ||| | ||| || | || | || | | | || || || | | | | | ||||| || ||||| ||||| ||||| || ||||||||||| || | ||| | |||||||||||| ||||||||||||
gtgagttttaatctcaagttttttttaccagatattagtgtttgaaacaaaagcttgtgatcatcacaaccaatcaaaaaatctttttgatattgatttttttcttttcatactgctta--tgaagtcttaaaccgcagattatattattttttgttggaattaaatgtcatgttgtttgttttttcctctttttagGCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAAAGAATTTTTGAGGAAACTTTGCATAGGAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccatactcttattctgtaccctgacctgatttttttgaatatctattgactatagGCCCGTAGAGGTGGTATTGATGAACCATTTGCATGGGATAGTAGAGAGTATTTGAGGAAACTCTGCATAGGAAAG
tattgac putative branch site (score: 2)
tgatttttttgaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttggcattactaataccacactttttaaatgaattctctatattccatactcttattctgtaccctgacctgatttttttgaatatctattgactatagGCCCGTAGAGGTGGTATTGATGAACCATTTGCATGGGATAGTAGAGAGTATTTGAGGAAACTCTGCATAGGAAAG
- -ggcatta
- - - - - - - - ccacact
- - - - - - - - - - - - - -aaatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctgac