Sequence
atgc intronic sequence ATGC exonic sequence...accatgttgagataattgaaaaagaaagtctgataaattgtgggaatttcctgaattattttccttgatgaaattttgagaaagtggattctaaatccagAGAAATGTGGGAGACATCAATGGAAGGTCTCAAAAGCTTGATTCGTAGGACAACACCATCCTCCTTTGCATACATATGTGAGAAGAATGGGAGGTTCTTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv11s0052g00140.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os04g51690.1 (Oryza sativa), 3'ss of exon 9
-----------------------accatgttgagataattgaaaaagaaagtctgataaattgtgggaatttcctgaattattttccttgatgaaattttgagaaagtggattctaaatccagAGAAATGTGGGAGACATCAATGGAAGGTCTCAAAAGCTTGATTCGTAGGACAACACCATCCTCCTTTGCATACATATGTGAGAAGAATGGGAGGTTCTTG
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gtttgagcctataagcctcacttttcaccttttcatattcccttcactgatttcttttactggaaattccatacagtttcatttagcatgttgataact-gtttatatgatttttga--ctagACAAATGTGGGAGACATCAATGGAAGGCCTACTAAGCTTGACCAAAAAAACTACACCCTCTAATTACTACTACATTTGCGAGAAGAATGGTGGTTCATTG
upper sequence: Vv11s0052g00140.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G130889_T03 (Zea mays), 3'ss of exon 5
-------accatgttgagataattgaaaaa-gaaagtctgat----aaattgtgggaatttcctgaa---ttattttccttgatgaaattttgagaaag----------tggattctaaatccagAGAAATGTGGGAGACATCAATGGAAGGTCTCAAAAGCTTGATTCGTAGGACAACACCATCCTCCTTTGCATACATATGTGAGAAGAATGGGAGGTTCTTG
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gtttgggactattatcagactattgtcacttgtcagcctggcttcagaatgttaagtagccattgcaatttcaatttattcaattcaacatggataacaattccatttatgttttttcgtttcagACAAATGTGGGAGACATCAATGGAAGGTCTATTAAGTTTAACCAAGAAAACTACACCATCTAATTACTACTACATTTGTGAAAAGAATGGTGGCTCGTTG
upper sequence: Vv11s0052g00140.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G128914_T03 (Zea mays), 3'ss of exon 9
accatgttgagataattgaaaaagaaagtctgataaattgtgggaatttcctgaattattttccttgatg-aaattttgagaaagtg---gattctaaatccagAGAAATGTGGGAGACATCAATGGAAGGTCTCAAAAGCTTGATTCGTAGGACAACACCATCCTCCTTTGCATACATATGTGAGAAGAATGGGAGGTTCTTG
||| || |||| || | | | | | | |||||| | | || | | | || | | | ||| |||||||||||||||||||||||||||| ||| || | | || |||||||| | ||||| ||||| |||||||| | | |||
----gtttgggactattgtcaacctggtttcacaatgctaagtaggcattgcaatttatttgattcaacatggataacaattccattcatgtttttcattttagACAAATGTGGGAGACATCAATGGAAGGTCTATTAAGTTTAACAAAGAAAACTACACCATCTAATTACTACTACATTTGTGAAAAGAATGGTGGCTCATTG
upper sequence: Vv11s0052g00140.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA13G00470.1 (Glycine max), 3'ss of exon 10
accatgttgagataattgaaaaagaaagtctgata-aattgtgggaatttc--ctgaattattttccttgatgaaattt---tgagaaagtggattctaaatccagAGAAATGTGGGAGACATCAATGGAAGGTCTCAAAAGCTTGATTCGTAGGACAACACCATCCTCCTTTGCATACATATGTGAGAAGAATGGGAGGTTCTTG
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------gcaaatccctttacagtacttctctgatatgaaagttcaaactttgaattaagcatatatttggaacatatttaaatgtgcgaacaaatggtgcatccagGGAAATGTGGGAGAAATCAATGAAAGGTCTTCAAAGCTTGATTTGGAG---------------------------------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttcctgaattattttccttgatgaaattttgagaaagtggattctaaatccagAGAAATGTGGGAGACATCAATGGAAGGTCTCAAAAGCTTGATTCGTAGGACAACACCATCCTCCTTTGCATACATATGTGAGAAGAATGGGAGGTTCTTG
ttctaaa putative branch site (score: 2)
tgaattatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
accatgttgagataattgaaaaagaaagtctgataaattgtgggaatttcctgaattattttccttgatgaaattttgagaaagtggattctaaatccagAGAAATGTGGGAGACATCAATGGAAGGTCTCAAAAGCTTGATTCGTAGGACAACACCATCCTCCTTTGCATACATATGTGAGAAGAATGGGAGGTTCTTG
-ccatgtt
- - - - - - -aattgaa
- - - - - - - - - - aaagaaa
- - - - - - - - - - - - - - - - - - -ttgtggg
- - - - - - - - - - - - - - - - - - - - - - - -ttcctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagaaag