Sequence
atgc intronic sequence ATGC exonic sequencegtaaattatctgtccctgatagactatgatagaaataatcttttaaactttaaagagagattttggtgtagccattactcaagtttgttgtcactagtctgttggcctagtggtaacattcgctttgcattaaaaaaaatcttgatgcctgacttcatgaatgaagtattttcatttcctacagATTGGCTGGCTCAATGCAATTAGAGAGTGGCAAGAAGAGTTTGTTGGCAACATGAGTTCTAGGGAATTTGTCGACACTATTACAAGAGATCTGCTGGGCA
Basic information
species | Glycine max |
transcript | GLYMA03G37450.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G37450.1 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os03g22160.1 (Oryza sativa), 3'ss of exon 16
gtaaattatctgtccctgatagactatgatagaaataatcttttaaactttaaagagagattttggtgtagccattactcaagtttgttgtcactagtctgttggcctagtggtaacattcgct-ttgcattaaaaaaaatcttgatgcctgacttcatgaatgaagtattttcatttcctacagATTGGCTGGCTCAATGCAATTAGAGAGTGGCAAGAAGAGTTTGTTGGCAACATGAGTTCTAGGGAATTTGTCGACACTATTACAAGAGATCTGCTGGGCA
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----------------------------------------------------------------------gctgtgaaataagttagtacgcttta-tattttagaacggagg-agtatttattatcacattt-------ccttaagaaagaactcca------aagacttctcatctttgatagATTGGTTGGCTCAATGCAATCCGTGAATGGCAAGAAGAGTTTGTTGGTAACATGAGTTCTAGGGAATTTGTTGATACTATCACCCGAGATCTTCTGGGAA
upper sequence: GLYMA03G37450.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G353147_T01 (Zea mays), 3'ss of exon 15
gtaaattatctgtccctgatagactatgatagaaataatcttttaaactttaaagagagattttggtgtagcca--ttactcaagtttgttgtcactagtctgttggcctagtggtaacattcgctttgcattaaaaaaaatcttgatgcctgacttcatgaatgaagtattttcatttcctacagATTGGCTGGCTCAATGCAATTAGAGAGTGGCAAGAAGAGTTTGTTGGCAACATGAGTTCTAGGGAATTTGTCGACACTATTACAAGAGATCTGCTGGGCA
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---------------------------------------------------------gtactatactttatctaatctaatcatacgaatgcttttaagctttatag--tatttctgctttacatattgtactgcagtgggtttgagaattt--tttttttaatagcatac---catctttcatagATTGGTTGGCTCAATGCAATCCGCGAGTGGCAAGAAGAGTTTGTTGGTAATATGAGTTCTAGGGAATTTGTTGATACTATCACCCGAGATCTTCTAGGAA
upper sequence: GLYMA03G37450.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G416698_T01 (Zea mays), 3'ss of exon 9
gtaaattatctgtccctgatagactatgatagaaataatcttttaaactttaaagagagattttggtgtagccattactcaagtttgttgtcacta-gtctgttggcctagtggtaacattcgctttgcattaaaaaaaatcttgatgcctgacttcatgaatgaagtattt-tcatttcctacagATTGGCTGGCTCAATGCAATTAGAGAGTGGCAAGAAGAGTTTGTTGGCAACATGAGTTCTAGGGAATTTGTCGACACTATTACAAGAGATCTGCTGGGCA
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----------------------------------------------------------------gtactatacattatctaatccaatcatactgatgcctttaaagctaacagta----ctgctttaaatagtgtaccacaatag-gtttgagaaaaaaaattaatagcataccatctttcatagATTGGTTGGCTCAATGCAATCCGCGAGTGGCAAGAAAAGTTTGTTGGTAATATGAGTTCTAGGG------------------------------------
upper sequence: GLYMA03G37450.1 (Glycine max), 3'ss of exon 18
lower sequence: Vv07s0005g00770.t01 (Vitis vinifera), 3'ss of exon 16
gtaaattatctgtccctgatagactatgatagaaataatcttttaaactttaaagagagattttggtgtagccattactcaagtttgttgtcactagtctgttggcctagtggtaacattcgctttgcattaaaaaaaatcttgatgcctgacttcatgaatgaagtattttcatttcctacagATTGGCTGGCTCAATGCAATTAGAGAGTGGCAAGAAGAGTTTGTTGGCAACATGAGTTCTAGGGAATTTGTCGACACTATTACAAGAGATCTGCTGGGCA
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--------------------------------------------------------------------------gtacttca-tctgttgtc-----cttcctgaatta-tgatagtcaacagtcttccttgaagggatttcgaataaatcattcaa------agttcattctttttgctccagATTAGCTGGCTCAATGCAATCAGAGAGTGGCAAGAGGAGTTTGTCGGAAACATGACCTCCAGGGAATTTGTAGACACTGTCACTAAAGATCTGTTAGGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaaaaaaaatcttgatgcctgacttcatgaatgaagtattttcatttcctacagATTGGCTGGCTCAATGCAATTAGAGAGTGGCAAGAAGAGTTTGTTGGCAACATGAGTTCTAGGGAATTTGTCGACACTATTACAAGAGATCTGCTGGGCA
gcctgac putative branch site (score: 3)
tattttcatttcct putative PPT
aagtattttcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaattatctgtccctgatagactatgatagaaataatcttttaaactttaaagagagattttggtgtagccattactcaagtttgttgtcactagtctgttggcctagtggtaacattcgctttgcattaaaaaaaatcttgatgcctgacttcatgaatgaagtattttcatttcctacagATTGGCTGGCTCAATGCAATTAGAGAGTGGCAAGAAGAGTTTGTTGGCAACATGAGTTCTAGGGAATTTGTCGACACTATTACAAGAGATCTGCTGGGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC