Sequence
atgc intronic sequence ATGC exonic sequencegtaaacaaaacaaaataatggaatattaaaatagacctttaattgaattggttattgaccgtatttggtgggtttggccatgcgtggaatgcagGAGGCTAGGGGCAGACAGGTTCTTCACAAGCAATTTCAACGAGGAGACATACACAAAGAAGGGACTTGAATGGGTGAACACCACGGAGAGTCTGAAAGAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0066g01670.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os12g26290.6 (Oryza sativa), 3'ss of exon 11
----gtaaacaaaacaaaataatggaatattaaaatag-acctttaattga--attggttattgaccgtatttggtgggtttggccatgcgtggaatgcagGAGGCTAGGGGCAGACAGGTTCTTCACAAGCAATTTCAACGAGGAGACATACACAAAGAAGGGACTTGAATGGGTGAACACCACGGAGAGTCTGAAAGAT
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tgttaccagaaaaaaaaagaagtcaaatgtggaagtactaattatagatgataaccactcagttaagatatgaatattaatttaacatctctaaaa-acagGAGGCTCGAAGCAGATCGATTTTTTACAAGCAATTTCAATGAGGAAACATACACCAAGAAGGGGATGCAATGGGTCAAAACAACAGAAGGCCTACGAGAT
upper sequence: Vv14s0066g01670.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G312997_T01 (Zea mays), 3'ss of exon 9
----gtaaacaaaacaaaataatggaatattaaaatag-acctttaattga--attggttattgaccgtatttggtgggtttggccatgcgtggaatgcagGAGGCTAGGGGCAGACAGGTTCTTCACAAGCAATTTCAACGAGGAGACATACACAAAGAAGGGACTTGAATGGGTGAACACCACGGAGAGTCTGAAAGAT
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gaatgttaccagcaaaaagaagtcaaatgtggaagtactagtttgagatgataaccactaagttaagatatgaatattaatttaacatctctataa-acagGAGACTGGAAGCAGATCGATTTTTTACAAGCAATTTCAATGAGAAAACATACACAAAGAAGGGGATGCAATGGGTCAAAACAACTGAAGGCCTACGGGAT
upper sequence: Vv14s0066g01670.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA13G04410.1 (Glycine max), 3'ss of exon 9
gtaaacaaaacaaaataatggaatattaaaa--tagacctttaattgaattggtt-attgaccgtatt----tggtgggtttggccatgcgtggaat-gcagGAGGCTAGGGGCAGACAGGTTCTTCACAAGCAATTTCAACGAGGAGACATACACAAAGAAGGGACTTGAATGGGTGAACACCACGGAGAGTCTGAAAGAT
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--tcttaattctgaatgatatagcctaagatctttgagcttttgtgaagtgattttgtaaggcaaattatagtaatgaataagaacttttgcacatttgcagGAGGTTAAAAGCTGACAGGTTCTTCACAAGCAACTTTAACGAAGAGACATATACCAAGAAGGGACTGGAATGGGTGAACACAACTGAGAGTCTGAAAGAT
upper sequence: Vv14s0066g01670.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA19G01470.1 (Glycine max), 3'ss of exon 9
--------------gtaaacaaaacaaaataatggaatattaaaatagacctttaattgaattggttattgaccgtatttggtgggtttggccatgcgtggaatgcagGAGGCTAGGGGCAGACAGGTTCTTCACAAGCAATTTCAACGAGGAGACATACACAAAGAAGGGACTTGAATGGGTGAACACCACGGAGAGTCTGAAAGAT
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acatattgggtgtgacatatagcctaagatctttgagcttttgtgaaggattttg--taaagcaaattatagtaatgaataataagttttgcc---catt---tgcagGAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATATACCAAGAAAGGACTGGAATGGGTGAATACAACTGAGAGCCTAAAGGAT
upper sequence: Vv14s0066g01670.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA19G01480.1 (Glycine max), 3'ss of exon 9
---gtaaacaaaacaaaata-atggaatatta-aaatagacctttaattgaattggttattgaccgtatttggtgggtttggccatgcgtggaat--gcagGAGGCTAGGGGCAGACAGGTTCTTCACAAGCAATTTCAACGAGGAGACATACACAAAGAAGGGACTTGAATGGGTGAACACCACGGAGAGTCTGAAAGAT
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tctctaaaagatgcattggacatgttatatcccaaccatataattattcttaatgaaaatt-atagtaatagatgtaaacctctattaattaattttacagGAGGCTAGAAGCTGACAGATTCTTCACTAGTAATTTTAATGAGGATGCGTATACCAAGAAAGGACTAGAATGGGTGAACACAACTGAGAGCTTGAAGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taattgaattggttattgaccgtatttggtgggtttggccatgcgtggaatgcagGAGGCTAGGGGCAGACAGGTTCTTCACAAGCAATTTCAACGAGGAGACATACACAAAGAAGGGACTTGAATGGGTGAACACCACGGAGAGTCTGAAAGAT
tattgac putative branch site (score: 2)
ttattga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaacaaaacaaaataatggaatattaaaatagacctttaattgaattggttattgaccgtatttggtgggtttggccatgcgtggaatgcagGAGGCTAGGGGCAGACAGGTTCTTCACAAGCAATTTCAACGAGGAGACATACACAAAGAAGGGACTTGAATGGGTGAACACCACGGAGAGTCTGAAAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG