Sequence
atgc intronic sequence ATGC exonic sequencegttttcattttcctagtttttaatataatagtatttttagctgactctggataaataataatatcatggtggggataattgtaacatgtattttttcaagGTTTTAGCTGGAGATATCAATCCCGCAATTCGCACCCATGCTGCCTTCTTGAGTGTCTGGAGAAGATATGGTTTTACTCCTGAGGGCTTTAATCTTGCTA
Basic information
species | Glycine max |
transcript | GLYMA10G32320.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G32320.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 11
gttttcattttcctagtttttaatataatagtatttttagctgactctggataaataataatatcatggtggggataattgtaacatgtattttttcaagGTTTTAGCTGGAGATATCAATCCCGCAATTCGCACCCATGCTGCCTTCTTGAGTGTCTGGAGAAGATATGGTTTTACTCCTGAGGGCTTTAATCTTGCTA
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-----------------gtttggattactcgtatatcaga---gataaaaaaaaatgatgcacacattctagatgatttcttattctgcttagatttaagGTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTCAGTGTATGGAAAAAATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTA
upper sequence: GLYMA10G32320.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G173868_T04 (Zea mays), 3'ss of exon 11
gttttcattttcctagtttttaatata-atagtatttttagctgactctggataaataataatatcatggtggggataattg--taacatgtattttttcaagGTTTTAGCTGGAGATATCAATCCCGCAATTCGCACCCATGCTGCCTTCTTGAGTGTCTGGAGAAGATATGGTTTTACTCCTGAGGGCTTTAATCTTGCTA
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----------------gtttggttacacatatttctgataattga-tgtggctttgtcgca----catattctagatgattgcttatgctgcttagatttaagGTTTTAGCTGGAGATGTTGATCCTGCTATTCGCACACATGCTGCCTTCTTCAGCGTCTGGAAAAAGTATGGTTTTACCCCTGAAGGTTTTAATCTTGCTA
upper sequence: GLYMA10G32320.1 (Glycine max), 3'ss of exon 10
lower sequence: AT5G43710.1 (Arabidopsis thaliana), 3'ss of exon 11
gttttcattttcctagtttttaatataatagtatttttagctgactctggataaataataatatcatggtggggataattgtaacatgtattttttcaagGTTTTAGCTGGAGATATCAATCCCGCAATTCGCACCCATGCTGCCTTCTTGAGTGTCTGGAGAAGATATGGTTTTACTCCTGAGGGCTTTAATCTTGCTA
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gtaaatagtgattctacgtttgaccaaattgttaatatatttcaggctgga-aaatttaactatgattttg----tatctatgt--ttctctctcaaaagGTTTTAGCTGGAGACGTTGATCCAGCAATAAGAACTCACACTGCCTTCTTTAGCGTCTGGAAACGATATGGTTTCACCCCTGAGGGTTTTAATCTTGCTA
upper sequence: GLYMA10G32320.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv05s0020g04650.t01 (Vitis vinifera), 3'ss of exon 12
gttttcattttcctagtttttaatataatagtatttttagctgactctggataaataataa-tatcatggtggggat-aattgtaaca---tgtattttttcaagGTTTTAGCTGGAGATATCAATCCCGCAATTCGCACCCATGCTGCCTTCTTGAGTGTCTGGAGAAGATATGGTTTTACTCCTGAGGGCTTTAATCTTGCTA
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------------------------------gtatttt--atctattatttatatattataaattttgcattgtcgattaatcaaaaccgattatcactttggaagGTTCTAGCTGGAGACATTGACCCTGCTATTCGAACGCATACTGCCTTTTTTAGTGTTTGGAAAAGATATGGCTTCACCCCAGAGGGTTTTAATCTTGCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctggataaataataatatcatggtggggataattgtaacatgtattttttcaagGTTTTAGCTGGAGATATCAATCCCGCAATTCGCACCCATGCTGCCTTCTTGAGTGTCTGGAGAAGATATGGTTTTACTCCTGAGGGCTTTAATCTTGCTA
ttgtaac putative branch site (score: 2)
tattttttc putative PPT
ataattgtaacatgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttcattttcctagtttttaatataatagtatttttagctgactctggataaataataatatcatggtggggataattgtaacatgtattttttcaagGTTTTAGCTGGAGATATCAATCCCGCAATTCGCACCCATGCTGCCTTCTTGAGTGTCTGGAGAAGATATGGTTTTACTCCTGAGGGCTTTAATCTTGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA