Sequence
atgc intronic sequence ATGC exonic sequence...ttctatgattatgcagttctttagttgtgatattgttgatgcaataatccatcataaatgataggaaagataaataaccatttttaatttgtgggggcagTTTATCATACACTGAAGGGAATTATCAAGGCAAAATATGGACAAGATGCATGCAATGTTGGGGATGAGGGGGGATTTGCTCCCAATGTTCAGGATAATAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os09g20820.1 (Oryza sativa), 3'ss of exon 2
--ttctatgattat-gcagttctttagttgtgatattgttgatgcaataatccatcataaatgataggaaagataaataaccatttttaatttgtgggggcagTTTATCATACACTGAAGGGAATTATCAAGGCAAAATATGGACAAGATGCATGCAATGTTGGGGATGAGGGGGGATTTGCTCCCAATGTTCAGGATAATAG
| | | || | | ||| | | ||| ||| | || | | | | | | | | | || | || ||||||| ||| | || ||||| || || ||||| |||||||| |||||||||||||||||||| ||||| || || |||||||| |||||||| || || ||
acattggcaacagttacatctgcgcatttgacttgtagtt--tgctctcgtcttttaattctcaaatgtttgtcttctgagatttacctgtccatgtta-cagTTTACCATGCCCTAAAGGGCATCATTAAGGCGAAATATGGTCAAGATGCATGCAATGTTGGAGATGAAGGTGGCTTTGCTCCTAATGTTCAAGACAACAG
upper sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G034848_T01 (Zea mays), 3'ss of exon 2
--ttctatgattatgcagttctttagttgtgatattg--ttgatgcaataatccatcataaatgataggaaagataaataaccatttttaatttgtgggggcagTTTATCATACACTGAAGGGAATTATCAAGGCAAAATATGGACAAGATGCATGCAATGTTGGGGATGAGGGGGGATTTGCTCCCAATGTTCAGGATAATAG
| ||| | | | ||| || ||| ||| || || | | || | | || | | || || || ||| ||||||| ||| |||||||| || || |||||||||||||| ||||||||||||||||| || ||||| || || |||||||| |||||||| || || ||
tttgttataaaagtaaacatctatatttgggatttttgcttcttctagctggtcacttcatcttctatcctcacttggaa--tatccttg--ttatggtaacagTTTACCATGTCCTGAAGGGCATCATTAAGGCAAAATATGGTCAAGATGCATGCAATGTCGGAGATGAAGGAGGTTTTGCTCCTAATGTTCAAGACAACAG
upper sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G009030_T01 (Zea mays), 3'ss of exon 2
----ttctatgattatgcagttctttagttgtgatattgttgatgcaataatccatcataaatgataggaaagataaataaccatttttaatttgtgggggcagTTTATCATACACTGAAGGGAATTATCAAGGCAAAATATGGACAAGATGCATGCAATGTTGGGGATGAGGGGGGATTTGCTCCCAATGTTCAGGATAATAG
|| ||| | | || | | | | || ||| | ||| || ||| || | | | || | || ||| ||||||| ||| |||||| | || || ||| |||||||||| ||||||||||||||||| || ||||| || || |||||||| |||||||| || || ||
tatgttgtatcagtgaatagctatattgggactat-ttgcttctgc--tagctggtcactt-catcttctaacctcacttggaatatccttgttctggtaacagTTTACCATGTCCTGAAGAGCATCATTAAGTCAAAATATGGTCAAGATGCATGCAATGTCGGAGATGAAGGAGGTTTTGCTCCTAATGTTCAAGACAACAG
upper sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA18G22780.1 (Glycine max), 3'ss of exon 3
ttctatgattatgcagttctttagtt--gtgatattgttgatgcaataatccatcataaatgataggaaagataaataaccatttttaatttgtgggggcagTTTATCATACACTGAAGGGAATTATCAAGGCAAAATATGGACAAGATGCATGCAATGTTGGGGATGAGGGGGGATTTGCTCCCAATGTTCAGGATAATAG
| || ||||| | | | | || |||| || | || | | | ||| || || || | | |||| || | || | ||||||||||| | | |||||||| ||||||||||||||||||||||||||||| |||||||| ||||| || |||||||||||||||||||| ||||| ||
ctgcat-attatctatagcataaattccatgattttttcaatctcaccagcgatc-tacatatggtgacaatcagttaacttggttatttctggtagaacagTTTATCATGTATTAAAGGGAATAATCAAGGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGAAGGAGGATTTGCTCCCAATGTTCAAGATAACAG
upper sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G23080.1 (Glycine max), 3'ss of exon 2
ttctatgattatgcagttctttagtt--gtgatattgttgatgcaataatccatcataaatg-ataggaaagataaataaccatttttaatt-tgtgggggcagTTTATCATACACTGAAGGGAATTATCAAGGCAAAATATGGACAAGATGCATGCAATGTTGGGGATGAGGGGGGATTTGCTCCCAATGTTCAGGATAATAG
| |||||| | | | || | || || | || || | | | || || || | | || | | | | | ||| || || || ||||||||||| | | |||||||| ||||||||||||||||||||||||||||| |||||||| ||||| || |||||||||||||||||||| ||||| ||
--gcac-attatgtatagcacaaattccataattttttcaatctaaca-ccagtgatctatatatggtgacaatcagttaacttggttatttctggtggaacagTTTATCATGTATTAAAGGGAATAATCAAGGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGAAGGAGGATTTGCTCCCAATGTTCAAGATAACAG
upper sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G25390.1 (Glycine max), 3'ss of exon 3
--------------------------------------ttctatgattatgcagt-tctttagt--------tgtgatattgttgatgcaataatccatc-ataaatgataggaaagataaataaccatttttaatttgtgggggcagTTTATCATACACTGAAGGGAATTATCAAGGCAAAATATGGACAAGATGCATGCAATGTTGGGGATGAGGGGGGATTTGCTCCCAATGTTCAGGATAATAG----
|| ||| | | | ||| ||| |||| || | || | | | ||| ||| ||| | || | | |||| || | || | ||||||||||| | | | ||| | ||||||||||||||||||||||||||| |||||||| ||||| || |||||||||||||||||||| ||||| ||
gtattacatatgatttgatagctaatcttaattccatttttcctgactgcatattatctatagcataaattccatgattttttcaatctcaccagcgatctatatatggt--gacaatcagttaacttggttatttctggtagaacagTTTATCATGTATTAAGGGGTA----CAAGGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGACGGAGGATTTGCTCCCAATGTTCAAGATAACAGGAGG
upper sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G24920.1 (Glycine max), 3'ss of exon 1
-----------ttctatgattatgcagttctttagttgtgatattgttgatgcaataatccatcataaatgataggaaagataaataaccatttttaatttgtgggggcagTTTATCATACACTGAAGGGAATTATCAAGGCAAAATATGGACAAGATGCATGCAATGTTGGGGATGAGGGGGGATTTGCTCCCAATGTTCAGGATAATAG-----------------------------
||| | | ||||| || | || ||| | | | | |||| ||||||| || | | |||| ||||| || | | ||| ||||||||||||||||||||||||||||| |||||||| ||||| || ||||||||||||| |||||| ||||| ||
gtagcagagaaaaatattagagtttccttcttctctttctttcttcttgggagggtcctagacctcgaatgctaggaaacattga--gctgatttt------------cagttcataaca----------aataatcaagGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGAAGGAGGATTTGCTCCCAGTGTTCAAGATAACAGGGAGGGGTTTGTTTTACTCGTGGATGCCA
upper sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G74030.1 (Arabidopsis thaliana), 3'ss of exon 2
ttctatgattatgcagttctttagttgtgatattgttgatgcaataatccatcataaatgataggaaagataaataaccatttttaatttgtgggggcagTTTATCATACACTGAAGGGAATTATCAAGGCAAAATATGGACAAGATGCATGCAATGTTGGGGATGAGGGGGGATTTGCTCCCAATGTTCAGGATAATAG
| | | |||| |||| | |||| || || | | || | | || || | | | | | || || |||||||||||||| ||||||| || ||||| | || ||||| |||||||| || ||||| || ||||| || || ||||| || |||||||| ||||| ||
catatttctcttttggttccaaagttcttctattctttggattatcacaaagaattgtttttctgatagtaatgcatttaatgtactttgttgattacagTTTATCATACATTGAAGGGGATAATCAAAACTAAGTATGGTCAAGATGCTTGTAATGTCGGAGATGAAGGAGGGTTTGCGCCGAATGTTCAAGATAACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatccatcataaatgataggaaagataaataaccatttttaatttgtgggggcagTTTATCATACACTGAAGGGAATTATCAAGGCAAAATATGGACAAGATGCATGCAATGTTGGGGATGAGGGGGGATTTGCTCCCAATGTTCAGGATAATAG
aaagataaataaccat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttctatgattatgcagttctttagttgtgatattgttgatgcaataatccatcataaatgataggaaagataaataaccatttttaatttgtgggggcagTTTATCATACACTGAAGGGAATTATCAAGGCAAAATATGGACAAGATGCATGCAATGTTGGGGATGAGGGGGGATTTGCTCCCAATGTTCAGGATAATAG
- - - - -tatgcag
- - - - - - - - - - - - - - - - - - -gatgcaa
- - - - - - - - - - - - - - - - - - - - - - - atccatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taaataa