Sequence
atgc intronic sequence ATGC exonic sequencegtacttgttttccttcatttcttttgcttgtcaaatattcaatatttaattatcacaagggtgtgcaatgaacattatgtttcttatgttattgctcataaactattctcacgcatggtcacatgcaaataaagGTATAACCCTGTGGTTTGGGGCGTTCCAAAAGGAAGCTATGCAAGTAACCCAGATGGTCCAAGTCGTATCATTGAGTACCGGCTGATGGTGCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G158043_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os04g08270.1 (Oryza sativa), 3'ss of exon 2
gtacttgttttccttcatttcttttgcttgtcaaatattcaatatttaattatcacaagggtgtgcaatgaacattatgtttcttatgttattgctcataaactattctcacgcatggtcacatgcaaa-taaagGTATAACCCTGTGGTTTGGGGCGTTCCAAAAGGAAGCTATGCAAGTAACCCAGATGGTCCAAGTCGTATCATTGAGTACCGGCTGATGGTGCAG
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-------gtattcttccttgctcttttctttcaaacattacacatactaatgcatcttggtggtcttttcaaagtaaagtttgttatgttcttgcctgtaaattattctcacg----gtcatatgcacactaaagGTATGACCCTGTACTCTGGGGGGTTCCAAAAGGAAGCTATGCAAGTAACCCAGATGGTCCTAGTCGTATTATTGAATACCGACAGATGGTTCAG
upper sequence: GRMZM2G158043_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA10G34080.1 (Glycine max), 3'ss of exon 10
gtacttgttttccttcatttcttttgcttgtcaaatattcaatatttaattatcacaagggtgtgcaatgaacattatgtttcttatgttattgctcataaactattctcacgcatggtcacatgcaaataaagGTATAACCCTGTGGTTTGGGGCGTTCCAAAAGGAAGCTATGCAAGTAACCCAGATGGTCCAAGTCGTATCATTGAGTACCGGCTGATGGTGCAG
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-------------------------------------gtatgctcttgaatggcacattgattgacaatccaaac---attttttatgtta--------agtttgcttttttatatg-ttgtcttcaa---aagGTACAACCCTGTTCTTTGGGGCGTTCCTAAAGGCAGCTATGCAAGTAATCCAAACGGTCCATACCGTACAATTGAGTTCCGAAAGATGGTTATG
upper sequence: GRMZM2G158043_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT5G04360.1 (Arabidopsis thaliana), 3'ss of exon 10
gtacttgttttccttcatttcttttgcttgtcaaatattcaatatttaattatcacaagggtgtgcaatgaacattatgtttcttatgttattgctcataaactattctcacgcatggtcacatgcaa-ataaagGTATAACCCTGTGGTTTGGGGCGTTCCAAAAGGAAGCTATGCAAGTAACCCAGATGGTCCAAGTCGTATCATTGAGTACCGGCTGATGGTGCAG
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---------------------------------------------------------gtagtttgttttacacaagttacttcattcttcataatgaatcaatcaccttcatcacaagttttatgttttgtgaagGTATAATCCTGTGCTCTGGGGAGTCCCAAAAGGAAGCTATGCTAGTGATCCGACTGGTCCATGCCGCATAATTGAATTTAGAAAAATGGTTCAG
upper sequence: GRMZM2G158043_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv13s0019g05160.t01 (Vitis vinifera), 3'ss of exon 10
gtacttgttttccttcatttcttttgcttgtcaaatattcaatatttaattatcacaagggtgtgcaatgaacattatgtttcttatgttattgctcataaactattctcacgcatggtcacatgcaaataaagGTATAACCCTGTGGTTTGGGGCGTTCCAAAAGGAAGCTATGCAAGTAACCCAGATGGTCCAAGTCGTATCATTGAGTACCGGCTGATGGTGCAG
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---------------------------------------gtatgatagaatacc-catatatgt-caatttgaattat---ttttatgtttttaataaatttgcatttgctaattatatcatttgttaacaaagGTACAATCCTGTTCTCTGGGGGGTTCCTAAAGGAAGCTATGCAAGTAACCCTAATAGTCCATGCCGTACACTTGAGTTTAGAAAGATGGTGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcttatgttattgctcataaactattctcacgcatggtcacatgcaaataaagGTATAACCCTGTGGTTTGGGGCGTTCCAAAAGGAAGCTATGCAAGTAACCCAGATGGTCCAAGTCGTATCATTGAGTACCGGCTGATGGTGCAG
ttctcac putative branch site (score: 2)
ataaactatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttgttttccttcatttcttttgcttgtcaaatattcaatatttaattatcacaagggtgtgcaatgaacattatgtttcttatgttattgctcataaactattctcacgcatggtcacatgcaaataaagGTATAACCCTGTGGTTTGGGGCGTTCCAAAAGGAAGCTATGCAAGTAACCCAGATGGTCCAAGTCGTATCATTGAGTACCGGCTGATGGTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT