Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgtttcttttctgcattttcccaatttattggcttttattgtactttttctttttaacaatttccatgaaggtgatgcttgcatatactcaatttattattatacaagatttctcttctttttccctttattttgtgggatatgaatctgtagGCACGACCACTTTTCAAGGACCGTAGGAAGTTCCCTAAGATGGCTGATCCACTACTGCAAGGCCGTTATCCAATGCGAGGACTTTACCAAGCTCTAGCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g71000.1 (Oryza sativa), 3'ss of exon 4
gtaagtgtttcttttctgcattttcccaatttattggcttttattgtactttttctttttaacaatttcc--atgaaggtgatgcttg-catatactcaatttattattatacaagatttctcttctttttccctttattttgtgggat--atgaatctgtagGCACGACCACTTTTCAAGGACCGTAGGAAGTTCCCTAAGATGGCTGATCCACTACTGCAAGGCCGTTATCCAATGCGAGGACTTTACCAAGCTCTAGCAG
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---------------------------------------------------------------aatttgtaaatgaaaccagtttctaatgcaatcttaattgaaaaaaaaacttcgtggacatttttattttggataatcaatacatttcatctgtttgcagGCTCGTCCACTATTCAAGGACCGCAGGAAGTTCCCTAAAATGGCTGATCCAATGCTCCAAGGTCGCTTCCCTATGAGGGGTCTGTATCAGGCTTTAGCTG
upper sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G037585_T02 (Zea mays), 3'ss of exon 3
gtaagtgtttcttttctgcattttcccaatttattggcttttattgtactttttctttttaaca-atttccatgaaggtgatgcttgcatatactcaatttattattatacaagatttctcttctttttccctttattttgtgggatatgaatctgtagGCACGACCACTTTTCAAGGACCGTAGGAAGTTCCCTAAGATGGCTGATCCACTACTGCAAGGCCGTTATCCAATGCGAGGACTTTACCAAGCTCTAGCAG
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----------------------------------------------------tgctgtctgatagactgatactgcagcagcctttaaaacagcaacatctgttggtagacag------tttcatctgtagaactaatacggttcatct-aatctgcagGCTCGTCCACTGTTCAAGGACCGCAGGAAATTCCCTAAAATGGCTGATCCAATGCTTCAGGGCCGCTTCCCTATGAGGGGTCTATATCAGGCCTTAGCTG
upper sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G145709_T01 (Zea mays), 3'ss of exon 4
gtaagtgtttcttttctgcattttcccaatttattggcttttattgtactttttctttttaacaatttccatgaaggtgatgcttgcatatactcaatttattattatacaagatttctcttctttttccctttattttgtgggatatgaatctgtagGCACGACCACTTTTCAAGGACCGTAGGAAGTTCCCTAAGATGGCTGATCCACTACTGCAAGGCCGTTATCCAATGCGAGGACTTTACCAAGCTCTAGCAG
| | | ||| | || || | || | | ||| || | | || ||| ||| || | | | || || || || |||||| |||| || ||||| ||||||||||| ||||| |||||||| |||||||||||| | || || ||||| | || ||| | || || ||||| || |||| |
--------------------------------------atctgataaactgatactgcccc-cagccttcaaaacagaaatgtctgtttgcagacagttt--tatc-tagagaactaatccagttcatc----------------tactaatctgcagGCTCGTCCACTGTTCAAGGACCGAAGGAAATTCCCTAAAATGGCTGATCCAATGCTTCAGGGCCGCTTCCCTATGAGGGGTCTATACCAGGCCTTAGCCG
upper sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G28730.1 (Glycine max), 3'ss of exon 4
gtaagtgtttcttttctgcattttcccaatttattggcttttattgtactttttctttttaacaatttccatgaaggtgatgcttgcatatactcaatttattattata-caagatttctcttctttttccctttattttgtgggatatgaa--tctgtagGCACGACCACTTTTCAAGGACCGTAGGAAGTTCCCTAAGATGGCTGATCCACTACTGCAAGGCCGTTATCCAATGCGAGGACTTTACCAAGCTCTAGCAG
|||| || | || | || || | |||| | | ||| || | | ||| || |||| | ||||| ||| | | |||||||||| || |||||||| ||||||||||||||||| || |||||||| || ||||| ||||||||||| || ||||||||||| |||||||| || ||||
------------------------------------------------------------gtgaattggtttgtatgttaatattttgatcaccttctaaattaacacaacaaatttacaactatttgtcttcatattct-tgggacatggaactttgtagGCACGGCCGCTTTTCAAAGACCGTAGGAAGTTCCCCAAAATGGCTGACCCTCTACTTCAAGGCCGTTACCCGATGCGAGGACTGTACCAAGCACTTGCAG
upper sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G10360.1 (Glycine max), 3'ss of exon 4
gtaagtgtttcttttctgcattttcccaatttattggcttttattgtactttttctttttaacaatttccatgaaggtgatgcttgcatatactcaatttattattatacaagatttctcttctttttccctttattttgtgggatatgaa--tctgtagGCACGACCACTTTTCAAGGACCGTAGGAAGTTCCCTAAGATGGCTGATCCACTACTGCAAGGCCGTTATCCAATGCGAGGACTTTACCAAGCTCTAGCAG
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--------------------------------------------------------tataaatcatgtgaattg-gttggtatgttaatatttctaaattaacacaacatat--ttacaattatttgtcttcatattct-tgggacatggaactttgtagGCACGGCCGCTTTTCAAAGACCGTAGGAAGTTCCCCAAAATGGCTGACCCTCTACTTCAAGGCCGTTACCCGATGCGAGGACTATACCAAGCACTTGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attatacaagatttctcttctttttccctttattttgtgggatatgaatctgtagGCACGACCACTTTTCAAGGACCGTAGGAAGTTCCCTAAGATGGCTGATCCACTACTGCAAGGCCGTTATCCAATGCGAGGACTTTACCAAGCTCTAGCAG
tttattttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgtttcttttctgcattttcccaatttattggcttttattgtactttttctttttaacaatttccatgaaggtgatgcttgcatatactcaatttattattatacaagatttctcttctttttccctttattttgtgggatatgaatctgtagGCACGACCACTTTTCAAGGACCGTAGGAAGTTCCCTAAGATGGCTGATCCACTACTGCAAGGCCGTTATCCAATGCGAGGACTTTACCAAGCTCTAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT