Sequence
atgc intronic sequence ATGC exonic sequencegtaagcctattttctttctttctccttttattatggtgaaattccttcatattcagcatgctagaaaaagttacaaatcttctatttgttaaatagagaaacaattcttctttccttataaaggcctgcaatatttggaatggttgtggtgtgtatacagGGGCTAGACACAATGGTGGGTGAACATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCACGAATCC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv10s0003g02540.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os02g21750.1 (Oryza sativa), 3'ss of exon 1
gtaagcctattttctttctttctccttttattatggtgaaattccttcatattcagcatgctagaaa-aagttacaaatcttctatttgttaaatagagaaacaattcttctttccttataaaggcctgcaatatttggaatggttgtggtgtgtatacagGGGCTAGACACAATGGTGGGTGAACATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCACGAATCC
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-----------------gtacactcatctattcaaac--aacccctctctttctgcccttttagctttgacttatggattctgcgatctctttttagc-atttatttcatcttaatttg--gggcccatgaatcatgatcataagtgataactattttcagGGACTAGATACAATGGTTGGTGAGCATGGCACACAGCTATCTGGTGGACAGAAACAAAGAATTGCAATTGCAAGAGCAATTTTGAAGGACCCTAGGATAC
upper sequence: Vv10s0003g02540.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os05g47490.1 (Oryza sativa), 3'ss of exon 7
gtaagcctattttctttctttctccttttattatggtgaaattccttcatattcagcatgctagaaaaagttacaaat-cttctatttgttaaatagagaaacaattcttctttccttataaaggcctgcaatatttggaatggttgtggtgtgtatacagGGGCTAGACACAATGGTGGGTGAACATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCACGAATCC
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-----------------------------------------------------------gtatgaaagacacagaaatgcttcaacctgt------gcgatttttttatcgtattgttatttgacaactaactaacta-accatctcttctgttttctcagGGCCTGGACACAATGGTTGGTGAACATGGAGCTCAGCTATCTGGAGGGCAAAAGCAAAGAATTGCTATCGCAAGAGCGATCCTTAAAAATCCCAAAATCT
upper sequence: Vv10s0003g02540.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os01g50080.1 (Oryza sativa), 3'ss of exon 4
gtaagcctattttctttctttctccttttattatggtgaaattccttcatattcagcatgctagaaaaagttacaaatcttctatttgttaaatagagaaacaattcttctttccttataaaggcctgcaatatttggaatggttgtggtgtgtatacagGGGCTAGACACAATGGTGGGTGAACATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCACGAATCC
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-----------------------------------------------------------------gtagttcctagatacgccatttgtttccaacagtaccatatatactagtgt-attagaattaactatccctt---ttatcttcacatg-atatagGCATATGACACAATGGTGGGTCAACATGGTGCTCAGCTTTCTGGGGGACAAAAGCAAAGGATTGCCATTGCAAGAGCTATCCTTAAAAATCCAAAAGTCC
upper sequence: Vv10s0003g02540.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os01g50100.1 (Oryza sativa), 3'ss of exon 7
gtaagcctattttctttctttctccttttattatggtgaaattccttcatattcagcatgctagaaaaagttacaaatcttctatttgttaaatagagaaacaattcttctttccttataaaggcctgcaatatttggaatggttgtggtgtgtatacagGGGCTA-GACACAATGGTGGGTGAACATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCACGAATCC
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-------------------------------------------------------gtaagaaaggaaaaactg-aatgctccaagttctcaaatt------taattgtatattaatgaaataatcagctaacaat-------gttttcatgt-cataccagGGTTATGATACTTTAGTTGGCCAGCGCGGTACTCAGCTCTCTGGAGGACAAAAACAGAGAATTGCAATTGCAAGAGCCATCCTCAAAGATCCAAAAATCC
upper sequence: Vv10s0003g02540.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os05g47500.1 (Oryza sativa), 3'ss of exon 6
gtaagcctattttctttctttctccttttattatggtgaaattccttcatattcagcatgctagaaaaagttacaaatcttctatttgttaaatagagaaacaattcttctttccttataaaggcctgcaatatttggaatggttgtggtgtgtatacagGGGCTAGACACAATGGTGGGTGAACATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCACGAATCC
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----------------------------------------------------------------------gtacacacataacactatctgttcataccaaca--cacacctcatgtatgaagaacta----atcttgtattcacatgattt-----cagGGTTACGATACATTAGTTGGACAGCGTGGCGCTCAGCTTTCAGGGGGGCAGAAGCAAAGGATAGCAATTGCCAGAGCCATACTTAAAAACCCCAAAATCC
upper sequence: Vv10s0003g02540.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G412276_T01 (Zea mays), 3'ss of exon 5
gtaagcctattttctttctttctccttttattatggtgaaattccttcatattcagcatgctagaaaaagttacaaatcttctatttgttaaatagagaaacaattcttctttccttataaaggcctgcaatatttggaatggttgtggtgtgtatacagGGGCTAGACACAATGGTGGGTGAACATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCACGAATCC
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---------------------------------------------gtataactcaatgaactattacgtccgtaatgctatttatttattatatagatgc-taattttctgccactcccattgttaatcagtacatc------ttgtgaaacatccgcagGGTCTTGACACAATGGTGGGGGAACATGGAACTCAGCTGTCTGGAGGGCAGAAACAGAGAATAGCAATTGCTAGAGCAATCATAAAGAACCCTAAGATCT
upper sequence: Vv10s0003g02540.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G086730_T01 (Zea mays), 3'ss of exon 6
gtaagcctattttctttctttctccttttattatggtgaaattccttcatattcagcatgctagaaaaagttacaaatcttctatttgttaaatagagaaacaattcttctttccttataaaggcctgcaatatttggaatggttgtggtgtgtatacagGGGCTAGACACAATGGTGGGTGAACATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCACGAATCC
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----------------------------------------------------------------------gtacatataaactaatg--cggtcataatattaaccttttttttttgccacagatt---attaaccagtatattttgtgaacat-tacagGGTCTTGACACATTGGTTGGGGAACGTGGAACTCAACTGTCTGGAGGACAGAAGCAGAGAATAGCAATTGCTAGAGCAATCGTAAAGAACCCTAGGATCT
upper sequence: Vv10s0003g02540.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G014089_T01 (Zea mays), 3'ss of exon 6
gtaagcctattttctttctttctccttttattatggtgaaattccttcatattcagcatgctagaaaaagttacaaatcttctatttgttaaatagagaaacaattcttctttccttataaaggcctgcaatatttggaatggttgtggtgtgtatacagGGGCTAGACACAATGGTGGGTGAACATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCACGAATCC
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------------------------------gtatggaagaatctccccctctt--------ttaaaaaaaatatatatttccaataatttc--ttggcaacttatgctaatgagcaactgaaaacattttttttcttgactgacaaac-------cacagGGCTATGATACTATGGTTGGGCAGCGTGGCACGCAGCTCTCTGGAGGACAGAAGCAAAGGATCGCGATTGCAAGAGCCATCCTTAAAGACCCCAAGATAC
upper sequence: Vv10s0003g02540.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA15G09680.1 (Glycine max), 3'ss of exon 4
gtaagcctattttctttctttctccttttattatggtgaaattccttcatattcagcatgctagaaaaagttacaaatcttctatttgttaaatagagaaacaattcttctttccttataaaggcctgcaatatttggaatggttgtggtgtgtatacagGGGCTAGACACAATGGTGGGTGAACATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCACGAATCC
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------------------------------------------------gtgtttaat-tccaaaatccaaactcttaccttacgctagc-aactattgcttcaggttgctttcttttatcaagt-------tagttagtgtgttt-tattctgtttgtagGGCCTTGAGACAATGGCAGGCCAGAATGGGACTCAACTTTCTGGTGGGCAAAAGCAAAGAATTGCAATTGCAAGGGCAATTTTGAAGAACCCAAGAATCC
upper sequence: Vv10s0003g02540.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA13G29380.1 (Glycine max), 3'ss of exon 6
gtaagcctattttctttctttctccttttattatggtgaaattccttcatattcagcatgctagaaaaagttacaaatcttctatttgttaaatagagaaacaattcttctttccttataaaggcctgcaatatttggaatggttgtggtgtgtatacagGGGCTAGACACAATGGTGGGTGAACATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCACGAATCC
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---------------------------------gtatgacattcttttacaca-actgaaccaaaccaagttttatgt-ttctctctctt-----------------ttttttctttaagattatttgaagttaataaaattgtattattctgtttgtagGGAATTGACACAATGGTTGGAGGGCATGGAACTCAACTTTCTGGTGGGCAAAAACAAAGAATAGCAATTGCAAGGGCAATTTTGAAGAACCCAAGAATCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttctttccttataaaggcctgcaatatttggaatggttgtggtgtgtatacagGGGCTAGACACAATGGTGGGTGAACATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCACGAATCC
ttataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcctattttctttctttctccttttattatggtgaaattccttcatattcagcatgctagaaaaagttacaaatcttctatttgttaaatagagaaacaattcttctttccttataaaggcctgcaatatttggaatggttgtggtgtgtatacagGGGCTAGACACAATGGTGGGTGAACATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCACGAATCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC