Sequence
atgc intronic sequence ATGC exonic sequence...tttactagaactgaagtttatctaatttttatttccttcttttcctttttttgggttaaaagattgaagttctctagtcatcgaagttgtgtttttatagGTTCTTTTGCGAATGCTTCCAAACTATCATCATCATGTGCGGTCCCATGAGAACACACTCATAACAAAATTTTTTGGTCTTCACAGGATCAAACCTTCAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os02g57660.2 (Oryza sativa), 3'ss of exon 5
--------------------------------------------------tttactagaactgaagtttatc-taatttttatttccttcttttc----ctttttttgggttaaaagattgaagttctctagtcatcgaagttgtgtttttatagGTTCTTTTGCGAATGCTTCCAAACTATCATCATCATGTGCGGTCCCATGAGAACACACTCATAACAAAATTTTTTGGTCTTCACAGGATCAAACCTTCAA
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gttctgttttatgcttaaattttcagagatcatataagcgtgctagaaaattctttaatggtagattcttcgataaattatacattataagtaacaccacctacttagcaagcggaagttaaaaacatttcatgactctatatg-atccttgcagGTTCTTTTACGAATGCTTCCAAAATATTACCATCATGTCCGTACTTATGAGAACACCCTCATAACTAAGTTTTTTGGCCTCCACAGGGTGAAGCCTTCTA
upper sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G050309_T01 (Zea mays), 3'ss of exon 4
--------------------------------tttactagaactgaagtttatctaattt-ttatttccttcttttcctttttttgggttaaaagattgaagttctctagtcatcgaagttgtgtttttatagGTTCTTTTGCGAATGCTTCCAAACTATCATCATCATGTGCGGTCCCATGAGAACACACTCATAACAAAATTTTTTGGTCTTCACAGGATCAAACCTTCAA
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gtccattttctatatggattacagagattgtatttcttagctttcatgattgttggatagattgtgcatgtatagtacggccatttgcctaggaagcgaaattgaacttttcat-gactctactaccctgtagGTTCTTTTACGAATGCTTCCAAACTATTATGATCATGTCCGTACCTATGAGAACACCCTCATAACTAAGTTTTTTGGCCTCCACAGGGTGAAACCTTCTA
upper sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G374973_T01 (Zea mays), 3'ss of exon 4
--------------------------------tttactagaactgaagtttatc---taatttttatttccttctt---ttcctttttttgggttaaaagattgaagttctctagtcatcgaagttgtgtttttatagGTTCTTTTGCGAATGCTTCCAAACTATCATCATCATGTGCGGTCCCATGAGAACACACTCATAACAAAATTTTTTGGTCTTCACAGGATCAAACCTTCAA
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gtccattttctgtttacactacagggattgtatttcttagctgtcacgattgttggatagtttgtgcatgtatagtgcggccatttgccttggaagcaaaattgaacttttcatgac-tctatactat---cctgtagGTTCTTTTACGAATGCTTCCAAAGTATTATGATCATGTCCGTACCTATGAGAACACCCTCATAACCAAGTTTTTTGGCCTCCACAGGGTGAAACCTTCTA
upper sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G076392_T02 (Zea mays), 3'ss of exon 3
tttactagaactgaagtttatctaatttttatttccttcttttcctttttttgggttaaaagattga-agttctctagtcatcgaagttgt------gtttttatagGTTCTTTTGCGAATGCTTCCAAACTATCATCATCATGTGCGGTCCCATGAGAACACACTCATAACAAAATTTTTTGGTCTTCACAGGATCAAACCTTCAA
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-------ttactcagcttgttgtcatgggtaatatttttcgatcttttttatggttaaattgtttgacagttcataccagttctaaactgtcaaaaaattcttgcagGTTCTTCTACGAATGCTTCCAGAGTATTATCACCATGTCCGTACCTATGAGAACACACTCATAACTAAGTTTTTTGGCCTCCACAGGGTTAAACCGTCCA
upper sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA03G34340.1 (Glycine max), 3'ss of exon 3
-tttactaga--actgaagtttatctaatttttatttcct-tcttttcctttttttgggttaaaagattgaagttctctagtcatcgaagttgtgtttttatagGTTCTTTTGCGAATGCTTCCAAACTATCATCATCATGTGCGGTCCCATGAGAACACACTCATAACAAAATTTTTTGGTCTTCACAGGATCAAACCTTCAA
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ttttaaatgtttagtaatgatatcttagtatttacctgctattttctacttgcttttcagtataaaatactaattcccttgtc--caaaatttgacat--gcagGTCCTTCTAAGAATGCTTCCAGACTATCATCATCATGTGAAGTCATATGAAAATACACTTATCACAAAATTTTTTGGTCTGCACAGGATTAAACCTTCAA
upper sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G06800.1 (Glycine max), 3'ss of exon 4
-------tttactagaactgaagtttatctaatttttattt--ccttcttttcctttttttgggttaaaagattgaagttctctagtcatcgaagttgtgtttttatagGTTCTTTTGCGAATGCTTCCAAACTATCATCATCATGTGCGGTCCCATGAGAACACACTCATAACAAAATTTTTTGGTCTTCACAGGATCAAACCTTCAA
|| | | | | | | || | || | || ||||| | | | ||||| | |||| | | | | | | | ||| | ||||||||| | ||||||||||| |||||||||| |||||| | | |||| || ||||| || ||||||||||||||||| |||||||| | |||||| |
attggagcatatgcttagtaatgatattttagtattcacttgctcttctctacttctttttcactaaaaaaaattgtgataaccaaattttgaaat---------gtagGTTCTTCTAAGAATGCTTCCAGACTATCATCACCATGTGAAGACATATGATAATACACTTATCACAAAATTTTTTGGTCTGCACAGGATTATACCTTCGA
upper sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G20980.1 (Glycine max), 3'ss of exon 4
----tttactagaactgaagtttatctaatttttatttccttcttttcctttt-tttgggttaaaagattgaagttctctagtcatcgaagttgtgtttttatagGTTCTTTTGCGAATGCTTCCAAACTATCATCATCATGTGCGGTCCCATGAGAACACACTCATAACAAAATTTTTTGGTCTTCACAGGATCAAACCTTCAA
| | || | | ||| | || || ||||| | | ||| ||| || || || || || | | | | | || || | ||||||||| | ||||||||||| |||||||||| |||||| | | |||| || ||||| || ||||||||||||||||| |||||||| | |||||||
tcaagtctttggagcatatattttagtg-ttcacatgctcttctgtacttttcgttttcactataaaatacaaattgt--aatgaccaaattttgaaat--gtagGTTCTTCTAAGAATGCTTCCAGACTATCATCACCATGTGAAGACATATGATAATACACTTATCACAAAATTTTTTGGTCTGCACAGGATTATTCCTTCAA
upper sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT3G09920.1 (Arabidopsis thaliana), 3'ss of exon 3
----------------tttactagaactgaagtttatctaatttttatttccttcttttcctttttttgggttaaaagattgaagttctctagtcatcgaagttgtgttttta-----tagGTTCTTTTGCGAATGCTTCCAAACTATCATCATCATGTGCGGTCCCATGAGAACACACTCATAACAAAATTTTTTGGTCTTCACAGGATCAAACCTTCAA
| | | | |||| | | | | || || | | | | | |||| || | ||| ||| ||| || || |||| ||||||||| || | ||||||||| | || |||||||||||| | | |||||||||| ||||| || ||||| ||||| |||||||| |||||||| ||||
gtttgtgactacttacatatccaccatctctgttttcacattatcttcttagttttctccatgtctttgcgtagactctttgt--ccgtctgcccattgagcttccagatttactgtgtagGTTCTTCTGAGGATGCTTCCAGATTACCATCATCATGTGAAGACATATGAGAACACCCTCATTACTAAATTCTTTGGCCTTCACAGAATCAAACCATCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttttgggttaaaagattgaagttctctagtcatcgaagttgtgtttttatagGTTCTTTTGCGAATGCTTCCAAACTATCATCATCATGTGCGGTCCCATGAGAACACACTCATAACAAAATTTTTTGGTCTTCACAGGATCAAACCTTCAA
tgttttt CT-rich tract
ttaaaagatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttactagaactgaagtttatctaatttttatttccttcttttcctttttttgggttaaaagattgaagttctctagtcatcgaagttgtgtttttatagGTTCTTTTGCGAATGCTTCCAAACTATCATCATCATGTGCGGTCCCATGAGAACACACTCATAACAAAATTTTTTGGTCTTCACAGGATCAAACCTTCAA
- - - - - - - - - - - - - - - - -tccttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaagat