Sequence
atgc intronic sequence ATGC exonic sequencegtataggcgcttaacattgccacttgttggacttcagtgcttataagcaagtttgggaaatcattaaatttgattgttatttttaatggctcagGGAACTGTTGTGGAGGGTACTATACAGCAGTTATTTGAAGGGCACCATATGAACTATATTGAATGCATTAATGTGGACTATAAATCAACAAGAAAGGAAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 6
gtataggcgcttaacattgccacttgttggacttcagtgcttataagcaagtttgggaaatcattaaatttgattgttatttttaatggctcagGGAACTGTTGTGGAGGGTACTATACAGCAGTTATTTGAAGGGCACCATATGAACTATATTGAATGCATTAATGTGGACTATAAATCAACAAGAAAGGAAT
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--------gttggacatttatttttgttatatgtaaga--taataaatagtgtt------tcatcaatgt--acaactactctct-cgattcagGGAACTACTGTGGAAGGGACAATTCAACAGCTATTTGAAGGTCATCATATGAATTATATTGAGTGCATTAATGTTGACTACAAATCTACAAGGAAAGAAT
upper sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 6
gtataggcgcttaacattgccacttgttggacttcagtgcttataagcaagtttgggaaatcattaaatttgattgtta--tttttaatggctcagGGAACTGTTGTGGAGGGTACTATACAGCAGTTATTTGAAGGGCACCATATGAACTATATTGAATGCATTAATGTGGACTATAAATCAACAAGAAAGGAAT
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--------------------------gtgaatatta----taacaaacat-tttattatatgtctacgatttgttattaactttgcgttgacccagGAAACTGTTGTGGAAGGAACAATTGAACAATTATTTGAAGGCCACCACATAAACTATATCGAGTGCATTAATGTTGATTATAAATCTAACAGAAAAGAAT
upper sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 6
gtataggcgcttaacattgccacttgttggacttcagtgcttataagcaagtttgggaaatcattaaatttgattgttatttttaatggctcagGGAACTGTTGTGGAGGGTACTATACAGCAGTTATTTGAAGGGCACCATATGAACTATATTGAATGCATTAATGTGGACTATAAATCAACAAGAAAGGAAT
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---------------------------gtgaatatgacaataatgaattatcattacaccaatttactttttattaacttttctttctacacagGGAACTGTTGTGGAAGGAACAATTGAACAATTATTCGAAGGCCACCACATTAATTACATTGAGTGCATTAACGTGGACTATAAATCTAACAGAAAAGAAT
upper sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G23680.1 (Glycine max), 3'ss of exon 2
-------------gtataggcgcttaacattgccacttgttggacttcagtgcttataa----gcaagtttgggaaatcattaaat-ttgattgtta---tttttaatggctcagGGAACTGTTGTGGAGGGTACTATACAGCAGTTATTTGAAGGGCACCATATGAACTATATTGAATGCATTAATGTGGACTATAAATCAACAAGAAAGGAAT
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gtactggtttttcatgatggctcttattgtcttcttaaaatagcttttactctagatacttgtgtatttttatgatgtcttgaaagattatttgttggggtttcatcttggccagGGAACTGTTGTGGAAGGCACTATACAGCAATTGTTTGAAGGACACCATATGAACTATATTGAATGCATAAATGTGGATTATAAATCAACAAGGAAAGAAT
upper sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 6
gtataggcgcttaacattgccacttgttggacttcagtgcttataagcaagtttgggaaatcattaaatttgattgttatttttaatggct----cagGGAACTGTTGTGGAGGGTACTATACAGCAGTTATTTGAAGGGCACCATATGAACTATATTGAATGCATTAATGTGGACTATAAATCAACAAGAAAGGAAT
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gtatggataaat--ctctgttagctatgtcttctcggttttcaagagta-gctgggtacattatgtttactggtgggaatccttctgtgcttttacagGGAACTGCTGTCGAGGGCACAATCCAGCAACTGTTCGAAGGGCATCACATGAACTACATAGAGTGCATCAATGTTGATTATAAATCAACACGGAAAGAGT
upper sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ14291 (Selaginella moellendorffii), 3'ss of exon 4
gtataggcgcttaacattgccacttgttggacttcagtgcttataagcaagtttgggaaatcattaaatttgattgttatttttaatggctcagGGAACTGTTGTGGAGGGTACTATACAGCAGTTATTTGAAGGGCACCATATGAACTATATTGAATGCATTAATGTGGACTATAAATCAACAAGAAAGGAAT
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-----------------------------gtttactgctattttcttcacgtt----aaatgttt---tctaacaccaagctccacta---cagAGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAAT
upper sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ18164 (Selaginella moellendorffii), 3'ss of exon 4
gtataggcgcttaacattgccacttgttggacttcagtgcttataagcaagtttgggaaatcattaaatttgattgttatttttaatggctcagGGAACTGTTGTGGAGGGTACTATACAGCAGTTATTTGAAGGGCACCATATGAACTATATTGAATGCATTAATGTGGACTATAAATCAACAAGAAAGGAAT
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-----------------------------gtttactgctattttcttcacgtt----aaatgttt---tctaacaccaagctccacta---cagAGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCACCATATGAATTATATTGAATGCATCAATGTGGACTACAAGTCCACTCGAAAGGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttataagcaagtttgggaaatcattaaatttgattgttatttttaatggctcagGGAACTGTTGTGGAGGGTACTATACAGCAGTTATTTGAAGGGCACCATATGAACTATATTGAATGCATTAATGTGGACTATAAATCAACAAGAAAGGAAT
ttttaat putative branch site (score: 3)
aaatcattaaatttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataggcgcttaacattgccacttgttggacttcagtgcttataagcaagtttgggaaatcattaaatttgattgttatttttaatggctcagGGAACTGTTGTGGAGGGTACTATACAGCAGTTATTTGAAGGGCACCATATGAACTATATTGAATGCATTAATGTGGACTATAAATCAACAAGAAAGGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA