Sequence
atgc intronic sequence ATGC exonic sequence...ttctatactggtcccagaacataaattctatagttcacattttttcatttgttattaggtcttttgtggttactgtttggctgccttgaaaattttatagGATACAATGGCCAGAAGAACTACAGATCCAGAAGAAGAGCTCCGTTGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTGAACAGCCTTGCTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv03s0038g00540.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 18
-ttctat--actggtcccagaacataaattctatagttcacattttttcatttgttattaggtcttttgtggttactgtttggctgccttgaaaattttatagGATACAATGGCCAGAAGAACTACAGATCCAGAAGAAGAGCTCCGTTGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTGAACAGCCTTGCTG
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ctcatatcaacctgttccactttcccacggccatgattat--tttttgaatgtgtcaaacacaaattttgaattgcc-tgtgacacaattactctcccttaagGATACGATGGCCCGGAAGCCTGCTGATCCTGAAGAAGAACTTCGGTGGATGTCTCAAGAAGTTCGTGGTTATGTAGAGGCTGTTTTGAACAGTTTGGCAG
upper sequence: Vv03s0038g00540.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os08g32920.1 (Oryza sativa), 3'ss of exon 18
----------------------ttctatactggtcccagaacataaattctatagttcacattttttcatttgttattaggtcttttgtggttactgtttggctgccttgaaaattttatagGATACAATGGCCAGAAGAACTACAGATCCAGAAGAAGAGCTCCGTTGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTGAACAGCCTTGCTG
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gtaagtcagaatccttcttttattcttcaaaaagttcatcgtgaaaagattttgaaaatcatcttctagagtagaaaggattaattagtatatcgtttttgtaatcctttcctatttt-cagGACACGATGCTTAGAAAGCCAGTAGATCCTGAGGAAGAGCTTAAATGGATATCTCAAGAAGTCCGTGGGTATGTGGAAGCTGTTCTCAGCAGTCTTGCGG
upper sequence: Vv03s0038g00540.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 18
-----ttctatactggtcccagaacataaattctatagttcacattttttcatttgttattaggtcttttgtggttactgtttggctgccttgaaaattttatagGATACAATGGCCAGAAGAACTACAGATCCAGAAGAAGAGCTCCGTTGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTGAACAGCCTTGCTG
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atgttccttaagataaacatgttgtattgttgttgttggcatgagttacttactt-ccatttgacctttca--attgacatctgat--ccctgcacttttcaaagGATACTATGGCACGGAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAG
upper sequence: Vv03s0038g00540.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM5G870253_T01 (Zea mays), 3'ss of exon 2
ttctatactggtcccagaacataa-attctatagttcacattttttcatttgttattaggtcttttgtggttactgtttggctgccttgaaaattttatagGATACAATGGCCAGAAGAACTACAGATCCAGAAGAAGAGCTCCGTTGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTGAACAGCCTTGCTG
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ttttatcttacctaaaggctaaagcatgttttcatttaaatgtatccaaacacaagatcacttattttactcttcattctacaactcttttctgttta-agGATACAATGGCTCGGAGGCCTGCTGATCCTGAAGAAGAACTTCGATGGATGTCTCAAGAAGTCCGTGGTTATGTTGAAGCTGTTTTGAACAGTTTGGCTG
upper sequence: Vv03s0038g00540.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM5G811223_T01 (Zea mays), 3'ss of exon 6
-----------------------------------------------------------------------------ttctatact-ggtcccagaacataaattcta--tagttcacat-tttttcatttgttatta--------ggtcttttgtggtt-----actgtttggctgccttgaaaatttt--atagGATACAATGGCCAGAAGAACTACAGATCCAGAAGAAGAGCTCCGTTGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTGAACAGCCTTGCTG
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gtaagttctaggttaatacataattgaattgcatttctagctttccttttgtagttttgctttactcaattaaatcttgatttattagggatcatcatgtaatttcaggttcccttgtatgttttggatgtgccaatataaatactgctccattaaaatacacaaactaaacatctgatcatacacttttcgaaagGATGCTATGGCGCGGAGACCAGCTGATCCTGAAGAAGAACTTAGATGGATGTCTCAAGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAG
upper sequence: Vv03s0038g00540.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 18
---------------------------------------------------------------------------------------------ttctata----ctggtcccagaacataaattctatagttcacattttttcatttgttattaggtcttttgtggttactgtttggctgccttgaaaattttatagGATACAATGGCCAGAAGAACTACAGATCCAGAAGAAGAGCTCCGTTGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTGAACAGCCTTGCTG
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gtaagttctagattaatacataattgtattgcatttctagctttcttttgtcgttttgctctactcaactaaatcatgatttattaaggatcatcatgtaatttcaggtccccttgtatattttggatgtgccaatataaatatttttccattaaaatacaca-aactaacatctgaccatac--atttttcaaaagGATACTATGGCACGTAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCTCAAGAAGTTCGTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catttgttattaggtcttttgtggttactgtttggctgccttgaaaattttatagGATACAATGGCCAGAAGAACTACAGATCCAGAAGAAGAGCTCCGTTGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTGAACAGCCTTGCTG
ttgaaaattttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttctatactggtcccagaacataaattctatagttcacattttttcatttgttattaggtcttttgtggttactgtttggctgccttgaaaattttatagGATACAATGGCCAGAAGAACTACAGATCCAGAAGAAGAGCTCCGTTGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTGAACAGCCTTGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - atactgg
- - - - - -tcccaga
- - - - - - - - - acataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgcct