Sequence
atgc intronic sequence ATGC exonic sequencegtcagccatggcatttcatttacttcagattatctcacagattttggtctatgaagaaagaaatggtattcaaactaagttcttcagcaaggataattgcttttgaatttttatgtggcaatccaggtatatttcaaggatgtagCTGGCTGGCTGTGATGAGGCAAAGCAAGAAATCATGGAGTTTGTGCACTTCCTCAAGAAGCCAAAGAAATATGAGGAGTTGGGAGCAAAAATTCCAAAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv08s0007g00560.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os05g38400.2 (Oryza sativa), 3'ss of exon 5
----------------------------------------gtcagccatggcattt---------catttact-tcagattat-ctcacagattttggtctatgaagaaagaaatggtattcaaactaagttcttcagcaaggataattgctt--ttgaatttttatgtggcaatccaggtatatttcaaggatgtagCTGGCTGGCTGTGATGAGGCAAAGCAAGAAATCATGGAGTTTGTGCACTTCCTCAAGAAGCCAAAGAAATATGAGGAGTTGGGAGCAAAAATTCCAAAAG
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gttagttcattctcttcttctgttctactttgaaacgactgtcaaatatgaaatatatacatgcacattgattctcaagctctgctagttccacctattcaataatgcagtagctactgcttaaacgttgttaagttacaataaaaactgtataatgacaagcttttctgttggtccagGTGTTTTTTAAGGATGTAGCTGGTTG----TGATGAAGCTAAGCAAGAAATAATGGAGTTTGTGCATTTCCTTAAGAATCCCAAGAAGTATGAAGAGTTAGGAG---------------
upper sequence: Vv08s0007g00560.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os01g62500.1 (Oryza sativa), 3'ss of exon 5
----------------------------------------gtcagccatgg----catttcatttacttcagat---tatctcacagattt-tggtctatgaagaaagaa---atggtattcaaactaagttcttcagcaaggataattgcttttgaatttttatgtggcaatccaggtatatttcaaggatgtagCTGGCTGGCTGTGATGAGGCAAAGCAAGAAATCATGGAGTTTGTGCACTTCCTCAAGAAGCCAAAGAAATATGAGGAGTTGGGAGCAAAAATTCCAAAAG
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gttagtttttatttgctatttccatctcttgctattttgaacaaaacatgaaattcatatccttttttgtaaatgtttgttctgtagctttattcaccattgacaaagaacatacaataacatattcatataattctactgaagtaac--cttgt---ttcttgtgtgcta---cagGTGTTCTTTAAGGATGTAGCTGGCTG----TGATGAAGCCAAACAAGAAATTATGGAATTTGTTCATTTCCTGAAAAATCCCAAGAAATATGAAGAACTGGGAG---------------
upper sequence: Vv08s0007g00560.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G038401_T01 (Zea mays), 3'ss of exon 5
gtcagccatggcatttcatttacttcagattatctcacagattttggtctatgaagaaagaaatggtattcaaactaagttcttcagcaaggataattgcttttgaatttttatgtggcaatccaggtatatttcaaggatgtagCTGGCTGGCTGTGATGAGGCAAAGCAAGAAATCATGGAGTTTGTGCACTTCCTCAAGAAGCCAAAGAAATATGAGGAGTTGGGAGCAAAAATTCCAAAAG
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-------------------ttgttgtagcttcatttgcccttttc------ttaagaaacaaagcatact-acatgaaattcgaagatttgtcttttcatcaatgtctacttttctgctggtccagGTGTTTTTTAAGGATGTAGCCGGTTG----TGACGAAGCAAAACAAGAAATAATGGAGTTTGTGCATTTCCTTAAAAACCCTAAGAAGTATGAAGATTTGGGAG---------------
upper sequence: Vv08s0007g00560.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT2G29080.1 (Arabidopsis thaliana), 3'ss of exon 5
gtcagccatggcatttcatttacttcagattatctcacagattttggtctatgaagaaagaaatggtattcaaactaagttcttcagcaaggataa--ttgcttttgaatttttatgtggcaatccaggtatatttcaaggatgtagCTGGCTGGCTGTGATGAGGCAAAGCAAGAAATCATGGAGTTTGTGCACTTCCTCAAGAAGCCAAAGAAATATGAGGAGTTGGGAGCAAAAATTCCAAAAG
|| | || || | | || || || | | || | | |||| || |||||| |||| | | |||| | |||||||||||||| ||||| || ||| ||||| || |||||||| ||||||||||| || ||||| ||||| |||||||| ||||| || ||||| |
----------------------------------------gttagagacttagagttttgcctttgtttttaa--tgatccgtttggaatttataaacttacttttgttgttttcttcg-----ccagATTTATTTCAAGGATGTTGCTGGATG----TGACGAGGCTAAACAAGAAATTATGGAGTTTGTACATTTCCTTAAGAACCCAAAGAAGTATGAAGATTTGGGTG---------------
upper sequence: Vv08s0007g00560.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G07510.1 (Arabidopsis thaliana), 3'ss of exon 5
gtcagccatggcatttcatttacttcagattatctcacagattttggtctatgaagaaagaaatggtattcaaactaagttcttcag--caaggataattgcttttgaatttttatgtggcaatccaggtatatttcaaggatgtagCTGGCTGGCTGTGATGAGGCAAAGCAAGAAATCATGGAGTTTGTGCACTTCCTCAAGAAGCCAAAGAAATATGAGGAGTTGGGAGCAAAAATTCCAAAAG
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----------------------------gtcagcatttcaatcagggtggagaagttgaattaccatcttcatttccaattcatgatgctattgagatttactactgatctattttgttttttgccagATATATTTTAAAGATGTTGCGGGATG----CGAGGAGGCTAAACAAGAAATTATGGAATTTGTGCATTTCCTTCAGAACCCAAAGAAATATGAAGATTTGGGAG--------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggataattgcttttgaatttttatgtggcaatccaggtatatttcaaggatgtagCTGGCTGGCTGTGATGAGGCAAAGCAAGAAATCATGGAGTTTGTGCACTTCCTCAAGAAGCCAAAGAAATATGAGGAGTTGGGAGCAAAAATTCCAAAAG
ttttgaatttttatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagccatggcatttcatttacttcagattatctcacagattttggtctatgaagaaagaaatggtattcaaactaagttcttcagcaaggataattgcttttgaatttttatgtggcaatccaggtatatttcaaggatgtagCTGGCTGGCTGTGATGAGGCAAAGCAAGAAATCATGGAGTTTGTGCACTTCCTCAAGAAGCCAAAGAAATATGAGGAGTTGGGAGCAAAAATTCCAAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA