Sequence
atgc intronic sequence ATGC exonic sequence...tatactttaagtcgctgttttggcggctttttcaatacagtttttctcctttacttataaaaaaaaaaagtcctaatgttgatctggcgtcctgttccagATTTGGAATCTCGGCTCCCCTGACCCAAATTTTACTTTGGATGACCACATGAAAGGGGTAAACTGTGTTGATTACTTCACTGGTGGTGACAAGCCATACT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 6
-tatacttta-agtcgctgttttggcggctttttcaatacagtttttctcctttacttataaaa-aaaaaaagtcctaatgttgatctggcgtcctgttccagATTTGGAATCTCGGCTCCCCTGACCCAAATTTTACTTTGGATGACCACATGAAAGGGGTAAACTGTGTTGATTACTTCACTGGTGGTGACAAGCCATACT
| | || | | || || | | || | || ||| | | | | ||| ||| | | | |||||| | | | | ||||| |||| | | || || || || |||||||| || | |||| || || || || ||||||||||| ||||||||||||||||||| ||| || |
gtctgtttcacaatctcttatgcagtggatgttatt-cacaatatatggctttt---tatgaggtgatttgtgcactaatggttctaaaac-tgaaacaacagATATGGAGTTTGGGTTCTCCGGATCCAAATTTCACACTCGATGGACATCAAAAGGGTGTGAACTGTGTTGACTACTTCACTGGTGGTGACAGGCCCTATT
upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G141587_T01 (Zea mays), 3'ss of exon 6
tatactttaagtcgctgttttggcggcttt--ttcaatacagtttttctcctttacttataaaaaa-------aaaaagtcctaatgttgatctggcgtcc-tgttccagATTTGGAATCTCGGCTCCCCTGACCCAAATTTTACTTTGGATGACCACATGAAAGGGGTAAACTGTGTTGATTACTTCACTGGTGGTGACAAGCCATACT
| | | || ||| ||| | | | || ||| | || || | | | | | | | | || | || || | | ||||| |||| ||| || |||||||| |||||||| || | |||| ||| |||||| || |||||||||||||||||||||||||||||| |||||||
-gtttgtgtaatctctgctttaaaagttctggttggtcacaatgttgtattatttgtcgtcattagctttttcatagtttgatggtgatatcctaatttctgtctatcagATATGGAGTCTTGGTTCCCCTGATCCAAATTTCACACTAGATGGCCATTCGAAAGGTGTGAACTGTGTTGATTACTTCACTGGTGGTGACCGACCATACT
upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 6
-tatactttaagtcgctgttttggcggcttt--ttcaatacagtttttc-tcctttacttataaaaaaaaaaag--tcctaatg--ttgatc-tggcgtcctgttc-----------cagATTTGGAATCTCGGCTCCCCTGACCCAAATTTTACTTTGGATGACCACATGAAAGGGGTAAACTGTGTTGATTACTTCACTGGTGGTGACAAGCCATACT
| | ||| || | | ||| | | || ||| | || | | ||| | | | | || | | || ||||| || |||| || ||||| |||| ||| || || |||||||||||||| || | |||| ||| ||||| || ||||||||||||||||||||||||||||| ||||||
gtttgtgtta--tctccgctttaaaaattctggttggccacaatgttgcattatttggtaccgacaggcgacagctttttcatagcttgatggtgatatcctattttttgtcaatatcagATATGGAGTCTTGGTTCTCCTGACCCAAATTTCACACTAGATGGCCATTCCAAAGGTGTGAACTGTGTTGATTACTTCACTGGTGGTGATCGACCATACC
upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G443953_T01 (Zea mays), 3'ss of exon 7
---------tatactttaagtcgctgttttggcggctttttcaatacagtttttctcctttacttataaaaaaaaaaagtcctaatgttgatctggcgtcctgttccagATTTGGAATCTCGGCTCCCCTGACCCAAATTTTACTTTGGATGACCACATGAAAGGGGTAAACTGTGTTGATTACTTCACTGGTGGTGACAAGCCATACT
||| |||| | | | | || | || | | | ||||| |||| || || | | | | || | || | ||| ||||||||| ||| || |||||||| || ||||| || ||||||| || ||||| || || ||||||||||||||||||||||||||| ||||||
gtatacccatatgttttattttgttttaatgataatgtattaatttctcgttttcctctttgctagccttaacgagcaattttc---tttacttgaaat----ttctagATTTGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTGGATGGTCATTCAAAAGGTGTCAATTGTGTTGATTACTTCACTGGTGGTGACCGGCCATATC
upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G419984_T01 (Zea mays), 3'ss of exon 5
tatactttaagtcgctgttttggcggctttttcaatacagtttttctcctttacttataaaaaaaaaaagtcctaatgttgatctggcgtcctgttccagATTTGGAATCTCGGCTCCCCTGACCCAAATTTTACTTTGGATGACCACATGAAAGGGGTAAACTGTGTTGATTACTTCACTGGTGGTGACAAGCCATACT
|| |||| || || | | || | || | ||| || | | || | | | ||| | | | ||||| |||| | | || || || || ||||| || || | |||| || || || || ||||||||||| ||||||||||||||||||| || || |
----------gtatgcctttttgcaatattatgcagcgagatgttaactgcgactcatgatgtgatcttgttcatttatacttcttactttgaactgcagATATGGAGTTTGGGTTCTCCAGATCCAAACTTCACACTTGATGGGCATCAAAAGGGTGTCAACTGTGTTGACTACTTCACTGGTGGTGACAGACCCTATT
upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G000645_T03 (Zea mays), 3'ss of exon 6
tatactttaagtcgctgttttggcggctttttcaatacagtttttctcctttacttataaaaaaaaaaagtcctaatgttgatctggcgtcctgttccagATTTGGAATCTCGGCTCCCCTGACCCAAATTTTACTTTGGATGACCACATGAAAGGGGTAAACTGTGTTGATTACTTCACTGGTGGTGACAAGCCATACT
|| |||| || || | | || | || | ||| || | | || | | | ||| | | | ||||| |||| | | || || || || ||||| || || | |||| || || || || ||||||||||| ||||||||||||||||||| ||| || |
----------gtatgcctttttgcaatattatgcagcgagatgttaactgcgactcatgatgtgatcttgttcatttatacttcttactttgaactgcagATATGGAGTTTGGGTTCTCCAGATCCAAACTTCACACTTGATGGGCATCAAAAGGGTGTCAACTGTGTTGACTACTTCACTGGTGGTGACAGGCCCTATT
upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 6
-tatactttaagtcgctgttttggcggctttttcaatacagtttttctcctttacttataaaaaaaaaaagtcc------taatg--ttgat-------ctggcgtcctgttccagATTTGGAATCTCGGCTCCCCTGACCCAAATTTTACTTTGGATGACCACATGAAAGGGGTAAACTGTGTTGATTACTTCACTGGTGGTGACAAGCCATACT
| || || || | ||| | || || || | || | ||||| | | | ||||| ||||| | | || || |||||||||||||| ||||| |||||||| |||||||||||||||| || |||||| || || ||||||||||| || || ||||||||||| |||||
gtgtaattatgttcttgttcctggatgtttcttttttaaaaaaaaaaaaaagtaaaaagaaaaactatgatcctatgatataatgcattgatgcaactgttatcatctcttttcagATTTGGAATCTTGGCTCTCCTGACCCTAATTTTACTTTGGATGCTCATCAGAAAGGAGTGAATTGTGTTGATTATTTTACAGGTGGTGACAAACCATATC
upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 6
-----------tatactt-taagtcgctgttttggcggctttttcaatacagtttttctcctttacttataaaaaaaaaaagtcctaatgttgatctggcgtcctgttccagATTTGGAATCTCGGCTCCCCTGACCCAAATTTTACTTTGGATGACCACATGAAAGGGGTAAACTGTGTTGATTACTTCACTGGTGGTGACAAGCCATACT
| | ||| | | | ||| | ||| | | | || | | || | ||||||| ||| | || || | | | || |||||||||||||| ||||| |||||||| |||||||| ||||||| ||| ||||| || || |||||||||||||| || ||||||||||| || |||
gtatatacatgtgttcttctcgctagttgtgtcctgaattttctttgtttatttccatacatcta-tgataaaaatttaaaagtaatgtattaatgttatcttcaattgcagATTTGGAATCTTGGCTCTCCTGACCCCAATTTTACGTTGGATGCCCATCAAAAAGGAGTGAATTGTGTTGATTACTTTACAGGTGGTGACAAACCTTACC
upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 6
-tatactttaagtcgctgttttggcggctttttcaatacagtttttctccttt-----acttataaaaaaa---aaaagtcctaatgttgatctggcgtcctgttccagATTTGGAATCTCGGCTCCCCTGACCCAAATTTTACTTTGGATGACCACATGAAAGGGGTAAACTGTGTTGATTACTTCACTGGTGGTGACAAGCCATACT
||||| | || | | | | | | || ||| | | || || ||| | |||| |||| | || || | | | || |||||||||||||| ||||| |||||||| |||||||| ||||||| || ||||| || || |||||||||||||| || |||||||||||||| ||
gtatacatgtgttcttcttgctagttgtgtcctgcattttctttgtttatttccaaacacctatgataaaaattaaaaagtaatgtattaatgttatcttttcttgcagATTTGGAATCTTGGCTCTCCTGACCCCAATTTTACATTGGATGCGCATCAAAAAGGAGTGAATTGTGTTGATTACTTTACAGGTGGTGACAAGCCTTATC
upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 6
tatactttaagtcgctgttttggcggctttttcaatacagtttttctcctttacttataaaaaaaaaaagtcctaatgttgat-ctggcgtcctgttccagATTTGGAATCTCGGCTCCCCTGACCCAAATTTTACTTTGGATGACCACATGAAAGGGGTAAACTGTGTTGATTACTTCACTGGTGGTGACAAGCCATACT
| | || || || ||| || || | | | || | ||||| | || | || || |||||||||||||| ||||| ||||| || |||||||||||||||| || |||||| || || ||||||||||| || || ||||||||||| |||||
----------------------gtagaatt----atgttcttgttcctggttgtttcctatgatataatgcattaatgcacctgttgtcttctcttttcagATTTGGAATCTTGGCTCTCCTGATCCTAATTTTACTTTGGATGCTCATCAGAAAGGAGTGAATTGTGTTGATTATTTTACAGGTGGTGACAAACCATATC
upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 6
tatactttaagtcgctgttttggcggctttttcaatacagtttttctcctttacttataaaaaaaaaaagtcctaatgttgatctg-gcgtcctgttccagATTTGGAATCTCGGCTCCCCTGACCCAAATTTTACTTTGGATGACCACATGAAAGGGGTAAACTGTGTTGATTACTTCACTGGTGGTGACAAGCCATACT
|||| ||| || || ||| || || | | ||| ||| | || || | | |||||||||||||| || ||||| |||||||||||||| ||||||| ||| |||||| ||||| ||||| ||||| ||||| |||||||| ||||| || |
-----------gtgctgaaatggtctaacattgaa-acatcattatggtttagtccgcttagtccgctcattcta-cgtttacatgcatgttcatcttcagATTTGGAATCTTGGTTCCCCAGACCCAAATTTTACATTGGATGCCCATCAGAAAGGAGTAAATTGTGTAGATTATTTCACCGGTGGTGATAAGCCCTATT
upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 10
-------tatactttaagtcgct-gttttggcggctttttcaatacagtttttctcctttacttataaaaaaaaaaagtcctaatgttgatctggcgtc-ctgttccagATTTGGAATCTCGGCTCCCCTGACCCAAATTTTACTTTGGATGACCACATGAAAGGGGTAAACTGTGTTGATTACTTCACTGGTGGTGACAAGCCATACT
|| ||| || | ||| | ||| || || | |||| | || | || | || | ||| | | | || | |||| |||||||| ||||| || || ||||||||||||||||||| || | ||||||||||||||||| || ||||| |||||||| || || ||||||
gtaagattagtcttcaacttttaagttacaccttcttctttcattcccaatttcccattatgagaagcttaacatttgttttcctgtatctacatcttttcttacctagATATGGAATCTTGGCTCTCCGGATCCAAATTTTACTTTGGATGCACATCTCAAAGGGGTAAACTGTGTAGACTACTTTACTGGTGGGGATAAACCATACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcctttacttataaaaaaaaaaagtcctaatgttgatctggcgtcctgttccagATTTGGAATCTCGGCTCCCCTGACCCAAATTTTACTTTGGATGACCACATGAAAGGGGTAAACTGTGTTGATTACTTCACTGGTGGTGACAAGCCATACT
tcctgttcc CT-rich tract
ttacttataaaaaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatactttaagtcgctgttttggcggctttttcaatacagtttttctcctttacttataaaaaaaaaaagtcctaatgttgatctggcgtcctgttccagATTTGGAATCTCGGCTCCCCTGACCCAAATTTTACTTTGGATGACCACATGAAAGGGGTAAACTGTGTTGATTACTTCACTGGTGGTGACAAGCCATACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - caataca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctaatg