Sequence
atgc intronic sequence ATGC exonic sequencegtttgtcaatacataagcttgtttttactagaaaacaaaacataaacaagtttaaggtgtttatttggcctgttccaagttaaacataacatccttttaagttataaatatttatactaggaaataggaattttgatttattaagcatgtcaatatagtgatatgtgaatatctgatctacactattctaacagGCGAGAATTTTGCAATGATGTCTGGCACAAGCATGGCTGCACCTCATGTTGCTGGTCTTGCTGCACTAATTAAGCAACAGTTTCCCAATTTTAGTCCTGC
Basic information
species | Glycine max |
transcript | GLYMA05G30460.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G30460.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g56320.1 (Oryza sativa), 3'ss of exon 8
gtttgtcaatacataagcttgtttttactagaaaacaaaacataaacaagtttaaggtgtttatttggcctgttccaagttaaacataacatccttttaagttataaatatttatactaggaaataggaattttgatttattaagcatgtcaatatagtgat-atgtgaatatctgatctacactattctaacagGCGAGAATTTTGCAATGATGTCTGGCACAAGCATGGCTGCACCTCATGTTGCTGGTCTTGCTGCACTAATTAAGCAACAGTTTCCCAATTTTAGTCCTGC
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--------------------------------------------------------------------------ccaaccta----taacatcttct--attaataaatttgcttat------ataataatttt--tttcttacatagattaattgaataattatgttgtt-tttgacttactgtct------agGTGAAAGTTTTGCAATAATTTCCGGTACAAGTATGGCTGCACCACACGTTGCTGGGCTTGCTGCTCTAGTCAAGCAGAAGTTCCCTTATTTTAGCCCTGC
upper sequence: GLYMA05G30460.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM5G837606_T01 (Zea mays), 3'ss of exon 2
gtttgtcaatacataagcttgtttttactagaaaacaaaacataaacaagtttaaggtgtttatttggcctgttccaagttaaacataacatccttttaagttataaatatttatactaggaaataggaattttgatttattaagcatgtcaatatagtgatatgtgaatatctgatctacactattctaacagGCGAGAATTTTGCAATGATGTCTGGCACAAGCATGGCTGCACCTCATGTTGCTGGTCTTGCTGCACTAATTAAGCAACAGTTTCCCAATTTTAGTCCTGC
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-----------------------------------------------------------------------------------ttgcaatattcagttttctcaaacaaaattgtctttgca--ttagagtccagcactac--agattttcctttcactgata---gaatctgtga---aaact-cccttgtagGTGAAAGTTTCGCGATGCTCTCTGGCACAAGTATGGCTGCACCCCATGTTGCTGGCCTGGCTGCTCTAATCAAGCAGAAGTTTCCTTCTTTTAGCCCAGC
upper sequence: GLYMA05G30460.1 (Glycine max), 3'ss of exon 9
lower sequence: AT4G20430.2 (Arabidopsis thaliana), 3'ss of exon 9
gtttgtcaatacataagcttgtttttactagaaaacaaaacataaacaagtttaaggtgtttatttggcctgttccaagttaaacataacatccttttaagttataaatatttatactaggaaataggaattttgat-ttattaagcatgtcaatatagtgatatgtgaatatctgatctacactattctaacagGCGAGAATTTTGCAATGATGTCTGGCACAAGCATGGCTGCACCTCATGTTGCTGGTCTTGCTGCACTAATTAAGCAACAGTTTCCCAATTTTAGTCCTGC
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-------------------------------------------------------------------------------------------------------------------------gtatacaaagcatgacattgatatagttgatgacattcccatttaaactgttgtgttccttttgctcattttagGAGAAAGTTTTGCGATGATGTCTGGTACGAGTATGGCTGCTCCTCATGTAGCTGGTGTGGCTGCATTGGTCAAGCAGAAATTCAGAAAGTTTAGTCCTTC
upper sequence: GLYMA05G30460.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv10s0092g00170.t01 (Vitis vinifera), 3'ss of exon 8
gtttgtcaatacataagcttgtttttactagaaaacaaaacataaacaagtttaaggtgtttatttggcctgttccaagttaaacataacatccttttaagttataaatatttatactaggaaataggaattttgattt-attaagcatgtcaatatagtgatatgt-gaatatctgatctacactattctaacagGCGAGAATTTTGCAATGATGTCTGGCACAAGCATGGCTGCACCTCATGTTGCTGGTCTTGCTGCACTAATTAAGCAACAGTTTCCCAATTTTAGTCCTGC
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------------------------------------------------------------------------------------------gtatacacaaacta-aaaagtgcaatgtgggtggcacacctttccatgtgatctaccactacattcaaaacatggattggctaattaacttatga-attatttcagGAGAGAACTTTGCAATGATGTCTGGGACAAGCATGGCTGCTCCTCATGTTTCTGGGCTTGCAGCATTGATTAAGCAGAAGTTTCCCAAGTTCAGTCCGTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attaagcatgtcaatatagtgatatgtgaatatctgatctacactattctaacagGCGAGAATTTTGCAATGATGTCTGGCACAAGCATGGCTGCACCTCATGTTGCTGGTCTTGCTGCACTAATTAAGCAACAGTTTCCCAATTTTAGTCCTGC
atctgat putative branch site (score: 4)
ctattct putative PPT
tcaatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtcaatacataagcttgtttttactagaaaacaaaacataaacaagtttaaggtgtttatttggcctgttccaagttaaacataacatccttttaagttataaatatttatactaggaaataggaattttgatttattaagcatgtcaatatagtgatatgtgaatatctgatctacactattctaacagGCGAGAATTTTGCAATGATGTCTGGCACAAGCATGGCTGCACCTCATGTTGCTGGTCTTGCTGCACTAATTAAGCAACAGTTTCCCAATTTTAGTCCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA