Sequence
atgc intronic sequence ATGC exonic sequencegtaagtattttttgccggcaccacctggcacaagaatcctgccaaatttatgagttccactattaatacataattataactagtaaccaaattttaataatgcaaagtgacaaatgttttataaaaacatggaatgctccagGTAAAAGCTGATGTGGAGACACAAGGAGAATTTGTTGAGTCTCTAGCAAATGAGGTCCGAGCAGCAAGCTTTGTAAATATTGATGATGTTGTTGCATTTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G396927_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g01439.2 (Oryza sativa), 3'ss of exon 3
gtaagtattttttgccggcaccacctggcacaagaatcctgccaaatttatgagttccactattaatacataattataactagtaaccaaattttaataatgcaaagtgacaaatgttttataaaaacatggaat-gctccagGTAAAAGCTGATGTGGAGACACAAGGAGAATTTGTTGAGTCTCTAGCAAATGAGGTCCGAGCAGCAAGCTTTGTAAATATTGATGATGTTGTTGCATTTG
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gtaagttattcaagatgatgcttcctttcagaaatatat----atactaccgaattccc---ttagtccatta--gtaatt--caggtagatt---attatgaggactgact--ttttatataaaaaaatggatttgtttcagGTCAAAGCGGATGTGGAGACACAAGGAGACTTTGTCGAGTCTCTAGCAAATGAGGTCCGAGCAGCAAGTTTTGTAAATATCGACGATGTTGTTGCATTTG
upper sequence: GRMZM2G396927_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g01449.1 (Oryza sativa), 3'ss of exon 4
gtaagtattttttgccggcaccacctggcacaagaatcctgccaaatttatgagttccactattaatacataattataactagtaaccaaattttaataatgcaaagtgacaaatgttttataaaaacatggaat-gctccagGTAAAAGCTGATGTGGAGACACAAGGAGAATTTGTTGAGTCTCTAGCAAATGAGGTCCGAGCAGCAAGCTTTGTAAATATTGATGATGTTGTTGCATTTG
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gtaagttattcaagatgatgctacctttcagaaatat------atactactgaattcctttagt------------ccactgctaattcaggtagattattatgaggacttactttttatataaaaaaatggatttgtttcagGTCAAAGTGGATGTGGAGACACAAGGAGACTTTGTTGAGTCTCTAGCAAATGAGGTCCGAGCAGCTAGTTTTGTAAATATCGACGACGTTGTTGCATTTG
upper sequence: GRMZM2G396927_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT3G25690.2 (Arabidopsis thaliana), 3'ss of exon 5
gtaagtattttttgccggcaccacctggcacaagaatcctgccaaatttatgagttc-cactattaatacataattataactagtaaccaaattttaataatgcaaagtgacaaatgttttataaaaacatggaatgctccagGTAAAAGCTGATGTGGAGACACAAGGAGAATTTGTTGAGTCTCTAGCAAATGAGGTCCGAGCAGCAAGCTTTGTAAATATTGATGATGTTGTTGCATTTG
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-------------------------------------------------gtaagttcacactttcaat--ataatgttaaat-gcaattggatttgaa----acaaagaatcaattgttt-----aaacttga----ttacagGTAAAAGCGGATGTGGAGACACAAGGGGACTTTGTACAGTCGTTAGCAACTGAAGTCCGAGCTTCTTCTTTCACCGACATAGAAGATCTCTTGGCGTTCG
upper sequence: GRMZM2G396927_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S2_699V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaagtattttttgccg--gcaccacctggcacaag-------aatcctgccaaa----tttatgagttccactattaatacataattataactagtaacc------aaattttaataa--tgcaaagtgacaaatgt--tttataaaaacatggaatg---------ctccagGTAAAAGCTGATGTGGAGACACAAGGAGAATTTGTTGAGTCTCTAGCAAATGAGGTCCGAGCAGCAAGCTTTGTAAATATTGATGATGTTGTTGCATTTG
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gtaagtgtctctcagaattggaagacctcgtgcaaattgacgaaatgcctggaaacggctttttgaaccctcatattcattctcatctctttcacgaagtctgtaatagacggcagcaacttgtatgattataactgtagctaacgacgctgagaaatggtttggcaactgcagATCAAAGCGGATGTTGAGACACAAGGAGAATTTGTGGAGTCTCTGGCAGCTGAAGTTCGTGCAGCCTCTTTCAGTAATATTGAAGAAGTCGTGGAGTTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caaattttaataatgcaaagtgacaaatgttttataaaaacatggaatgctccagGTAAAAGCTGATGTGGAGACACAAGGAGAATTTGTTGAGTCTCTAGCAAATGAGGTCCGAGCAGCAAGCTTTGTAAATATTGATGATGTTGTTGCATTTG
ttttaat putative branch site (score: 3)
acaaatgttttataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtattttttgccggcaccacctggcacaagaatcctgccaaatttatgagttccactattaatacataattataactagtaaccaaattttaataatgcaaagtgacaaatgttttataaaaacatggaatgctccagGTAAAAGCTGATGTGGAGACACAAGGAGAATTTGTTGAGTCTCTAGCAAATGAGGTCCGAGCAGCAAGCTTTGTAAATATTGATGATGTTGTTGCATTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT