Sequence
atgc intronic sequence ATGC exonic sequencegtaggttgatatttaattgatacatctattttttacattaatttcagtcttttcattgttatattcaaaatgttgttgcagGGCCTATGGAAGTGGAAAGGAAGATAGTCCACTCTGTGATGTGCCTGGTTTTGAAAACTGCAGGATGAAGTTGCTGCGACATGTATCTTTTGTAGATTGC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv13s0074g00310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os12g41400.1 (Oryza sativa), 3'ss of exon 4
------------------------------gtaggttgatatttaattgatacatctattttttacattaatttcagtcttttcattgttatattcaaaatgttgttgcagGGCCTATGGAAGTGGAAAGGAAGATAGTCCACTCTGTGATGTGCCTGGTTTTGAAAACTGCAGGATGAAGTTGCTGCGACATGTATCTTTTGTAGATTGC
| ||||| | | | || ||| | | | || || | | ||||| | | ||| ||| |||| |||||||||||||| |||||||| || | ||||||||||||||| ||||||||| ||||||||| | ||| ||||||| |||||||| |||||
aattatctgccattcacctacttaggactgctgctttgatgtcaagctaatgcatgtgagctctgcactatatgttgactttttttcctgttatataaa-----------gGGCTTATGGAAGTGGAAAAGAAGATAGCCCTCACTGTGATGTGCCTGGGTTTGAAAACACTAGGATGAAGCTACTGAGACATGTTTCTTTTGTTGATTGT
upper sequence: Vv13s0074g00310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os12g07740.1 (Oryza sativa), 3'ss of exon 4
------------gtaggttgata--tttaat-tgatacatctattttttacattaatttcagtcttttcattgttatattcaaaatgttgttgca----gGGCCTATGGAAGTGGAAAGGAAGATAGTCCACTCTGTGATGTGCCTGGTTTTGAAAACTGCAGGATGAAGTTGCTGCGACATGTATCTTTTGTAGATTGC
|||| | || ||| | ||| | ||| || | | || || ||||| || | | | || || |||| |||||||| ||||| |||||||| || | ||||||||||||||| ||||||||| ||||||||| | ||| ||||||| |||||||| |||||
gccattcacctcttaggattattgctttggtgtgaagctcttatacaatatgtgtgctcttgttcactctttgttgactttagtttcctattacataaagGGCTTATGGAAGCGGAAAAGAAGATAGCCCTCACTGTGATGTGCCTGGGTTTGAAAACACTAGGATGAAGCTACTGAGACATGTTTCTTTTGTTGATTGT
upper sequence: Vv13s0074g00310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G117900_T02 (Zea mays), 3'ss of exon 4
-------------------gtaggttgatatttaattgatacatct--attttttacattaatttcagtcttttcattgttatattcaaaatgttgttgcagGGCCTATGGAAGTGGAAAGGAAGATAGTCCACTCTGTGATGTGCCTGGTTTTGAAAACTGCAGGATGAAGTTGCTGCGACATGTATCTTTTGTAGATTGC
| || | | ||| || | || | | | || | | | | | | |||| || | | || | |||||||||||||| ||||| |||||||| || || |||||||||||||| ||||||||| || |||||| | ||| ||||||| |||||||| ||||||
tatttagcatttgatgatcaaatgtgaagaattatatgctgtgtcatgactcatgacgcccttgttcaccatctgttgattatgtttca--ttttaattaagGGCCTATGGAAGCGGAAAAGAAGATAGCCCTCTATGTGATGTGCCTGGATTTGAAAACACTAGAATGAAGCTCCTGAGACATGTTTCTTTTGTTGATTGC
upper sequence: Vv13s0074g00310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G107654_T01 (Zea mays), 3'ss of exon 4
--------------------------gtaggttgatatttaattgatacatctattttttacattaatttca-gtcttttcattgttatattcaaaatgttgttgcagGGCCTATGGAAGTGGAAAGGAAGATAGTCCACTCTGTGATGTGCCTGGTTTTGAAAACTGCAGGATGAAGTTGCTGCGACATGTATCTTTTGTAGATTGC
||| | ||| || | || || | | | || || || | ||||| ||||||| | |||||||||||||| ||||| |||||||| || || |||||||||||||| ||||||||| || ||||| | ||| ||||||| |||||||| ||||||
tatatattatttagcatttgctgatcaaaggcgaggaattatatgttgtgtc-atgtaacccttgtgcaccatgtgttgactttgtttcattcaaatta-------agGGCCTATGGAAGCGGAAAAGAAGATAGCCCTCTATGTGATGTGCCTGGATTTGAAAACACTAGAATGAAACTCCTGAGACATGTTTCTTTTGTTGATTGC
upper sequence: Vv13s0074g00310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G40750.1 (Glycine max), 3'ss of exon 4
gtaggttgatatttaattgatacatctattttttacattaatttcagtc--ttttcattgttatattcaaaatgttgttgcagGGCCTATGGAAGTGGAAAGGAAGATAGTCCACTCTGTGATGTGCCTGGTTTTGAAAACTGCAGGATGAAGTTGCTGCGACATGTATCTTTTGTAGATTGC
|| | |||||| || | | | || | | || | || | ||| || | |||| | || | |||||| |||||||||||||||||||||||||| | ||||||||||| || ||||||||| ||| |||||| |||||| ||||||| || ||||| |||||
----gtgggtatttattttacatttgccattatgatatcagattatcttaacttttggtgaggtgatcaatttttttctacagGGCTTATGGAAGTGGAAAGGAAGATAGTCCTATGTGTGATGTGCCAGGATTTGAAAACAGCAAGATGAAATTGCTGAGACATGTTTCATTTGTGGATTGT
upper sequence: Vv13s0074g00310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G18240.2 (Glycine max), 3'ss of exon 4
gtaggttgatatttaattg-atacatctat-tttttacattaatttcagtcttttcattgttatattcaaaatgttgttgcagGGCCTATGGAAGTGGAAAGGAAGATAGTCCACTCTGTGATGTGCCTGGTTTTGAAAACTGCAGGATGAAGTTGCTGCGACATGTATCTTTTGTAGATTGC
|| | |||||| ||| | | ||| || | | ||| ||| | ||| || | |||| | || | |||||| |||||||||||||||||||||||||| | ||||| ||||| || ||||||||| ||| |||||| ||||| | ||||| || ||||| |||||
----gtgggtatttatttgtgtgccattatgttatcaagttagtttaa---cttttggtgagctgatcaatttttttctacagGGCTTATGGAAGTGGAAAGGAAGATAGTCCTATGTGTGACGTGCCAGGGTTTGAAAACAGCAAGATGAAATTGCTAAGGCATGTTTCATTTGTGGATTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattttttacattaatttcagtcttttcattgttatattcaaaatgttgttgcagGGCCTATGGAAGTGGAAAGGAAGATAGTCCACTCTGTGATGTGCCTGGTTTTGAAAACTGCAGGATGAAGTTGCTGCGACATGTATCTTTTGTAGATTGC
cattaat putative branch site (score: 3)
ttttcattgttatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggttgatatttaattgatacatctattttttacattaatttcagtcttttcattgttatattcaaaatgttgttgcagGGCCTATGGAAGTGGAAAGGAAGATAGTCCACTCTGTGATGTGCCTGGTTTTGAAAACTGCAGGATGAAGTTGCTGCGACATGTATCTTTTGTAGATTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC