Sequence
atgc intronic sequence ATGC exonic sequencegtttggttacacatatttctgataattgatgtggctttgtcgcacatattctagatgattgcttatgctgcttagatttaagGTTTTAGCTGGAGATGTTGATCCTGCTATTCGCACACATGCTGCCTTCTTCAGCGTCTGGAAAAAGTATGGTTTTACCCCTGAAGGTTTTAATCTTGCTA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G173868_T04 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 11
gtttgg-ttacacatatttctgataattgatgtggctttgtcgcacatattctagatgattgcttatgctgcttagatttaagGTTTTAGCTGGAGATGTTGATCCTGCTATTCGCACACATGCTGCCTTCTTCAGCGTCTGGAAAAAGTATGGTTTTACCCCTGAAGGTTTTAATCTTGCTA
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gtttggattactcgtatatcagagataaaaaaaaa---tgatgcacacattctagatgatttcttattctgcttagatttaagGTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTCAGTGTATGGAAAAAATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTA
upper sequence: GRMZM2G173868_T04 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA10G32320.1 (Glycine max), 3'ss of exon 10
----------------gtttggttacacatatttctgataattga-tgtggctttgtcgca----catattctagatgattgcttatgctgcttagatttaagGTTTTAGCTGGAGATGTTGATCCTGCTATTCGCACACATGCTGCCTTCTTCAGCGTCTGGAAAAAGTATGGTTTTACCCCTGAAGGTTTTAATCTTGCTA
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gttttcattttcctagtttttaatata-atagtatttttagctgactctggataaataataatatcatggtggggataattg--taacatgtattttttcaagGTTTTAGCTGGAGATATCAATCCCGCAATTCGCACCCATGCTGCCTTCTTGAGTGTCTGGAGAAGATATGGTTTTACTCCTGAGGGCTTTAATCTTGCTA
upper sequence: GRMZM2G173868_T04 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA20G35290.1 (Glycine max), 3'ss of exon 6
-gtttggttacacatatttctgata-attgatgt--------ggctttg--tcgcacatattctag-atgattgcttatgctgcttagattt--aagGTTTTAGCTGGAGATGTTGATCCTGCTATTCGCACACATGCTGCCTTCTTCAGCGTCTGGAAAAAGTATGGTTTTACCCCTGAAGGTTTTAATCTTGCTA-------
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gttttcatttttcttgtttttgatataatggtatttttagttgactctggataaataatatcatggtggggctaattgtaatgtgtatttttgcaatgttttagCTGGAGATATCAATCCTGCAATTCGCACTCATGCTGCCTTCTTGAGTGTCTGGAGAAGATATGGTTTTACCCCTGAGAGCTTTAATCTTGCTAGTCTCAG
upper sequence: GRMZM2G173868_T04 (Zea mays), 3'ss of exon 11
lower sequence: AT5G43710.1 (Arabidopsis thaliana), 3'ss of exon 11
-----gtttggttacacatatttctga-taattgatgtggctttgtcgcacatattctag-atgatt----gcttatgctgcttagatttaagGTTTTAGCTGGAGATGTTGATCCTGCTATTCGCACACATGCTGCCTTCTTCAGCGTCTGGAAAAAGTATGGTTTTACCCCTGAAGGTTTTAATCTTGCTA
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gtaaatagtgattctacgtttgaccaaattgttaatatatttcaggctggaaaatttaactatgattttgtatctatgtttctctctcaaaagGTTTTAGCTGGAGACGTTGATCCAGCAATAAGAACTCACACTGCCTTCTTTAGCGTCTGGAAACGATATGGTTTCACCCCTGAGGGTTTTAATCTTGCTA
upper sequence: GRMZM2G173868_T04 (Zea mays), 3'ss of exon 11
lower sequence: Vv05s0020g04650.t01 (Vitis vinifera), 3'ss of exon 12
gtttggttacacatatttctgataattgatgtggctttgtcgcacatattctagatgattgcttatgctgcttagatttaagGTTTTAGCTGGAGATGTTGATCCTGCTATTCGCACACATGCTGCCTTCTTCAGCGTCTGGAAAAAGTATGGTTTTACCCCTGAAGGTTTTAATCTTGCTA
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---gtattttatctattatttatatattata-aattttgcattgtcgattaatcaaaaccgattat--cactttgg---aagGTTCTAGCTGGAGACATTGACCCTGCTATTCGAACGCATACTGCCTTTTTTAGTGTTTGGAAAAGATATGGCTTCACCCCAGAGGGTTTTAATCTTGCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatgtggctttgtcgcacatattctagatgattgcttatgctgcttagatttaagGTTTTAGCTGGAGATGTTGATCCTGCTATTCGCACACATGCTGCCTTCTTCAGCGTCTGGAAAAAGTATGGTTTTACCCCTGAAGGTTTTAATCTTGCTA
aattgat putative branch site (score: 4)
ttagatttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttggttacacatatttctgataattgatgtggctttgtcgcacatattctagatgattgcttatgctgcttagatttaagGTTTTAGCTGGAGATGTTGATCCTGCTATTCGCACACATGCTGCCTTCTTCAGCGTCTGGAAAAAGTATGGTTTTACCCCTGAAGGTTTTAATCTTGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG