Sequence
atgc intronic sequence ATGC exonic sequencegtaactcatattcatgctagccaaaggtggaaatttacttacatgtggattggagaccttgggttatactttttctcatttcttttcttttattcttacaatgaaatgttgtaacaacatgttaggatctaattgcaaggtatgagacttgagttcattatttgtctatcagttgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAGAGTGAAGACTTTGTTGCCACCTGCGTTTCACCCAAAGGAGAATGGATTTATTTTGTTGGTGAAGACA
Basic information
species | Glycine max |
transcript | GLYMA02G18000.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G18000.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g21940.1 (Oryza sativa), 3'ss of exon 12
gtaactcatattcatgctagccaaaggtggaaatttacttacatgtggattggagaccttgggttatactttttctcatttcttttctttt-attcttacaatgaaatgttgtaacaacatgttaggatctaattgcaaggtatgagacttgagttcattatttgtctatcagttgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAGAGTGAAGACTTTGTTGCCACCTGCGTTTCACCCAAAGGAGAATGGATTTATTTTGTTGGTGAAGACA
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----------------------------------------------------------------------------cataaagtggctattgagcatcgaagtgcattgctttttt--cattttgatggttatttatgaattctattatggttattc-ttgactggaaacttgtt-acagGTTGTAAAAAGTTTTTCATCTGGTAAACGGGAAGGGGGAGATTTCCTTGCAGCTTCCGTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACA
upper sequence: GLYMA02G18000.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G037683_T01 (Zea mays), 3'ss of exon 12
gtaactcatattcatgctagccaaaggtggaaatttacttacatgtggattggagaccttgggttatactttttctcatttcttttcttttattcttacaatgaaatgttgtaacaacatgttagg-atctaattgcaaggtatgagacttgagt-tcattat-ttgtctatcagttgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAGAGTGAAGACTTTGTTGCCACCTGCGTTTCACCCAAAGGAGAATGGATTTATTTTGTTGGTGAAGACA
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---------------------------------------------------------------------------------tttaacaaaggctgtagaagataagcaaggcgaggatatctcagccatttaactgttatttctagtgcttggttatgattgccttgaaaatttgttt-cagGTTGTGAAGAGTTTCTCATCAGGTAAGCGAGAAGGGGGAGATTTTGTTGCAGCTTCAGTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACA
upper sequence: GLYMA02G18000.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 13
gtaactcatattcatgctagccaaaggtggaaatttacttacatgtggattggagaccttgggttatactttttctcatttcttttcttttattcttacaatgaaatgttgtaacaacatgttaggatcta-attgcaaggtatgagacttgagttcattatttgtctatcagttgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAGAGTGAAGACTTTGTTGCCACCTGCGTTTCACCCAAAGGAGAATGGATTTATTTTGTTGGTGAAGACA
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----------------------------------------------------------------------------ggtgcgtaaccaaggggaactacgatcaga-atggttgtgatttctaaatgtttgtgatgcaggttacttatcaaaaaaaaaaaaaatgtttgtga---tgcagGTTGTGAAGAGCTTCTCTTCTGGTAAAAGAGAAGGTGGAGATTTTGTTGCAGCCTGTGTCTCACCCAAAGGAGAATGGATTTATTGTGTTGGTGAAGACA
upper sequence: GLYMA02G18000.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ30597 (Selaginella moellendorffii), 3'ss of exon 11
gtaactcatattcatgctagccaaaggtggaaatttacttacatgtggattggagaccttgggttatactttttctcatttcttttcttttattcttacaatgaaatgttgtaacaacatgttaggatctaattgcaaggtatgagacttgagttcattatttgtctatcagttgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAGAGTGAAGACTTTGTTGCCACCTGCGTTTCACCCAAAGGAGAATGGATTTATTTTGTTGGTGAAGACA
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------------------------------------------------------------------------------------------------------------------------gtgcatttctcctttc---ctttgtgcctgatttttcccttccggctttgcattggcagGTTGTCAAGAGCTTCTCGTCTGGCAAAAGAGAGGGTGGCGATTTCGTCGCGGCCTGCGTCTCGCCAAAAGGAGACTGGATTTATTGCGTTGGAGAAGACA
upper sequence: GLYMA02G18000.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ15973 (Selaginella moellendorffii), 3'ss of exon 11
gtaactcatattcatgctagccaaaggtggaaatttacttacatgtggattggagaccttgggttatactttttctcatttcttttcttttattcttacaatgaaatgttgtaacaacatgttaggatctaattgcaaggtatgagacttgagttcattatttgtctatcagttgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAGAGTGAAGACTTTGTTGCCACCTGCGTTTCACCCAAAGGAGAATGGATTTATTTTGTTGGTGAAGACA
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------------------------------------------------------------------------------------------------------------------------gtgcatttctcctttt---ctttgtgcctgatttttcccttccggctttgcattggcagGTTGTCAAGAGCTTCTCGTCTGGCAAAAGAGAGGGTGGCGATTTCGTCGCGGCCTGCGTCTCGCCAAAAGGAGACTGGATTTATTGCGTTGGAGAAGACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggatctaattgcaaggtatgagacttgagttcattatttgtctatcagttgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAGAGTGAAGACTTTGTTGCCACCTGCGTTTCACCCAAAGGAGAATGGATTTATTTTGTTGGTGAAGACA
atctaat putative branch site (score: 3)
ttcattattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaactcatattcatgctagccaaaggtggaaatttacttacatgtggattggagaccttgggttatactttttctcatttcttttcttttattcttacaatgaaatgttgtaacaacatgttaggatctaattgcaaggtatgagacttgagttcattatttgtctatcagttgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAGAGTGAAGACTTTGTTGCCACCTGCGTTTCACCCAAAGGAGAATGGATTTATTTTGTTGGTGAAGACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA