Sequence
atgc intronic sequence ATGC exonic sequence...tgtcacacttcacttctcttgttcctgtagccagcactaaatatttagtatatggcttaggagaaatggcttggaatgactattattgctctccatccagGGTTGTAATCGGCTATGATGAAGGAAGTATTATGGTAAAACTTGGTAGAGAAGTGCCTGTGGCAAGTATGGACAACAGTGGAAAAATAATATGGGCTAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 9
--tgtcacacttcac-----ttctcttgttcctgtagccagcactaaatatttagtatatggcttaggagaaatggcttggaatgactattattgctctccatccagGGTTGTAATCGGCTATGATGAAGGAAGTATTATGGTAAAACTTGGTAGAGAAGTGCCTGTGGCAAGTATGGACAACAGTGGAAAAATAATATGGGCTAAG
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caatttgctcttcacagaaacccttttcttttcat-gttttcattaacttcttccttttcaagttaatttagtgatacgggaaaaaacttgact------tgtgcagGGTTGTGATCGGATATGATGAAGGGACAATAATGATAAAAATTGGCCGTGAAGTTCCTGTTGCTAGCATGGACAGCAGTGGAAAAATCATATGGTCAAAA
upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 9
tgtcacacttcacttctcttgttcctgtagccagcactaaatatttagtatatggctt-----aggagaaat--ggcttggaatgactattattgctctccatccagGGTTGTAATCGGCTATGATGAAGGAAGTATTATGGTAAAACTTGGTAGAGAAGTGCCTGTGGCAAGTATGGACAACAGTGGAAAAATAATATGGGCTAAG
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-------aagaatttctctcattgaaacatgttgtgtgagattttcattgacttgttctttcctgcataagtcaagttaatgatatggaatattttattttgtgtagGGTTGTGATTGGATATGATGAAGGGACAATAATGATAAAAATTGGTCGTGAAGTTCCTGTTGCTAGCATGGATAGCAGTGGAAAAATTATATGGGCAAAG
upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 9
----------------------tgtcacacttcacttctcttgttcctg--tagccagcactaaatatt--------tagtatatggcttaggaga-------------aa----tggcttggaatgactattattgc---tctccatccagGGTTGTAATCGGCTATGATGAAGGAAGTATTATGGTAAAACTTGGTAGAGAAGTGCCTGTGGCAAGTATGGACAACAGTGGAAAAATAATATGGGCTAAG
| | | | | |||| | || || | | | | | | || || ||| || | || | || ||| | ||| | | | || ||||||||| || |||||||||||||||| |||||||| ||||||||| ||||||| |||||||| || |||||||||||||| ||||| || ||| |||||
gtaagttttttctggatagaaattttgtaagtaatttcttaggccgttgaataatctgagtgggaaactgtgtcaaattgtgcctgaattatgaaattttcttatctttaactcttttctcataatcaaaattttcgggtgcattcaaacagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGAAGTACCTGTGGCTAGCATGGACAACAGTGGGAAAATTATTTGGTCTAAG
upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 9
----------------------------------tgtcacacttcacttctcttgttcctgtagccagcactaaat-------------atttagtatatggcttaggagaaatggcttggaatgactattattgctc----------tccatccagGGTTGTAATCGGCTATGATGAAGGAAGTATTATGGTAAAACTTGGTAGAGAAGTGCCTGTGGCAAGTATGGACAACAGTGGAAAAATAATATGGGCTAAG
| || | | | || | | ||| | || || | | | | || || ||| || | | | | ||| || | | | || ||||||||| || |||||||||||||||| |||||||| ||||||||| ||||||| |||||||| || ||||||||||| || ||||| || ||| |||||
gtaagttttttgtggatagaatttttgcaattaatttcttaatataattttttaagccct-tgaatagtgctgagtgggaagctgtgccaaattgtgcctgaattatgaaattttcttatccttaactcttttctcgtatcgggtgcattcaaacagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGAAGTTCCTGTGGCTAGCATGGACAACAGCGGGAAAATTATTTGGTCTAAG
upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 9
tgtcacacttcactt-ctcttgttcctgtagccagcactaaatatttagtatatggcttaggagaaatggcttggaatgactattattgctctccatccagGGTTGTAATCGGCTATGATGAAGGAAGTATTATGGTAAAACTTGGTAGAGAAGTGCCTGTGGCAAGTATGGACAACAGTGGAAAAATAATATGGGCTAAG
|| | | | | || || || | || | | | | | | | | | || || | | ||| || | | || || | ||||||||| || |||||||||||||| | ||||||||| |||||||| |||||| ||||| || || ||||| |||||||| |||||||| |||||||||
tgccgaatattatttactttttcttctcttgagaaatcagtgtctctctcttttccctccttcttcgtgaccta-aattaccaaaacctctttctttgcagGGTTGTGATAGGCTATGATGAAGGTACTATTATGGTCAAACTTGGCCGAGAAGAACCTGTAGCCAGCATGGATAACAGTGGGAAAATAATTTGGGCTAAG
upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 9
--tgtcacacttcacttctcttgttcctgtagccagcactaaatatttagtatatggcttaggagaaatggcttggaatgactattattgctctccatccagGGTTGTAATCGGCTATGATGAAGGAAGTATTATGGTAAAACTTGGTAGAGAAGTGCCTGTGGCAAGTATGGACAACAGTGGAAAAATAATATGGGCTAAG
|| | | | | || || ||| | | | | | | | ||| | | || ||| | | ||| ||| | || | | |||||| || || |||||||||||||| | ||||||||| |||||||| |||||| ||||| || || ||||| |||||||| |||||||| |||||||||
gatgccgaatattatttacttt-ttcttctcttgaaaaatcagtgtttctcttttcactcgttcttcatgaccta-aattactgaaacctctttttttgcagGGTCGTGATAGGCTATGATGAAGGTACTATTATGGTCAAACTTGGCCGAGAAGAACCTGTAGCCAGCATGGATAACAGTGGGAAAATAATTTGGGCTAAG
upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 9
--------tgtcacacttcacttctcttgttcctgtagccagcactaaatatttagtatatggcttaggagaaatggcttggaatgactattattgctctccatccagGGTTGTAATCGGCTATGATGAAGGAAGTATTATGGTAAAACTTGGTAGAGAAGTGCCTGTGGCAAGTATGGACAACAGTGGAAAAATAATATGGGCTAAG
||| | | | | | | || || | | ||| | | | | | | | || ||| || | | | | | || ||||||||| ||||| ||||||||||||| || ||||| |||||||| ||||| | ||||| || || |||||||| | |||||||| ||||||||||||
cttagatttgttagaaatgatattgagaggtc---tacctggttctagtactccattgagttgtcctgcaaaac---cttaccttgtccacattctcatttca--cagGGTTGTGATCGGATATGATGAAGGAACCATCATGGTTAAACTTGGACGAGAAATTCCTGTCGCTAGCATGGACAATACCGGAAAAATCATATGGGCTAAG
upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 9
----tgtcacacttcacttctcttgttcctgtagccagcactaaatatttagtatatggcttaggagaaatggcttggaatgactattattgctctccatccagGGTTGTAATCGGCTATGATGAAGGAAGTATTATGGTAAAACTTGGTAGAGAAGTGCCTGTGGCAAGTATGGACAACAGTGGAAAAATAATATGGGCTAAG
|| | || | || | ||| || ||| || | | | | | | || || | | ||||| | || ||||||| || || ||||||||||||| || ||||| |||||||| ||||| | ||||| || || ||||||| || |||||||| ||||||||||||
agggcgtttagagtggctaggagttttttagggatcagtgttagcaccttattaaactgatcatacgggaccatcaacaacgaatgtgtttgctttaca----gGGTTGTGATTGGATATGATGAAGGAACCATCATGGTTAAACTTGGACGAGAAATTCCTGTCGCTAGCATGGACAGTAGCGGAAAAATCATATGGGCTAAG
upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 13
----------------------tgtca-cacttcacttctcttgttcctgta-gccagcactaaatatttagtatatggcttaggagaa----------atggctt--ggaatgactattattgctctccatccagGGTTGTAATCGGCTATGATGAAGGAAGTATTATGGTAAAACTTGGTAGAGAAGTGCCTGTGGCAAGTATGGACAACAGTGGAAAAATAATATGGGCTAAG
||||| | || || || | || | ||| ||| ||| | | | || | || ||| | ||| | || | ||| |||||||||||||| || ||||| |||||| || ||||| |||||||| | ||| | || ||||| |||||||| ||||| |||||||| || ||||||||
gtaagtttctgatcttttactatgtcaatatttattccctattaaagatatatatcttcacatcataattatttctttgtgtaaatttatgtttccttcataacttacgagatggcaataccttgtctttttccagGGTTGTAATTGGTTATGACGAAGGATCCATAATGGTGAAACTTGGCCGTGAAATACCAGTGGCTAGTATGGATAACAGCGGAAAAATTATTTGGGCTAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagtatatggcttaggagaaatggcttggaatgactattattgctctccatccagGGTTGTAATCGGCTATGATGAAGGAAGTATTATGGTAAAACTTGGTAGAGAAGTGCCTGTGGCAAGTATGGACAACAGTGGAAAAATAATATGGGCTAAG
ctctccatcc CT-rich tract
actattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtcacacttcacttctcttgttcctgtagccagcactaaatatttagtatatggcttaggagaaatggcttggaatgactattattgctctccatccagGGTTGTAATCGGCTATGATGAAGGAAGTATTATGGTAAAACTTGGTAGAGAAGTGCCTGTGGCAAGTATGGACAACAGTGGAAAAATAATATGGGCTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - -cacttca
- - - - - - - - - - -ttcctgt
- - - - - - - - - - - - - - - - -gcactaa
- - - - - - - - - - - - - - - - - - - - - - - - - tatggct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggcttg