Sequence
atgc intronic sequence ATGC exonic sequencegttagtgcttgctctattcaattgtgtcatcagaaatttatcaaattcgaaactttaggattttaaagtttgagttttttcaggttactttgatgttttagctcatgtgttggaattgatcttgtgtcagGGAAGATAGCTGTGATTGGAGGATGTCGTGAATACACAGGAGCTCCATACTTCGCTGCCATTTCAGCTTTGAAAATC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G19150.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G19150.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM5G840928_T03 (Zea mays), 3'ss of exon 1
gttagtgcttgctctattcaattgtgtcatcagaaatttatcaaattcgaaactttaggattttaaagtttgagttttttcaggttactttgatgttttagctcatgtgttggaattgatcttgtg-tcagGGAAGATAGCTGTGATTGGAGGATGTCGTGAATACACAGGAGCTCCATACTTCGCTGCCATTTCAGCTTTGAAAATC-----------------------
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----------------ttttattttgttaa-------ttgctgaatcttaattttgctgtgtgtcaaatgaaacttctgtta--tta-ttgaaagtt---gcttatgttatgta--tgattatgtcctcagGGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATTTTGCCGCTATCTCTGCCTTGAAAGTTGTCAGTATCATCTAGAACTTTCA
upper sequence: AT5G19150.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM5G840928_T01 (Zea mays), 3'ss of exon 1
gttagtgcttgctctattcaattgtgtcatcagaaatttatcaaattcgaaactttaggattttaaagtttgagttttttcaggttactttgatgttttagctcatgtgttggaattgatcttgtg-tcagGGAAGATAGCTGTGATTGGAGGATGTCGTGAATACACAGGAGCTCCATACTTCGCTGCCATTTCAGCTTTGAAAATC
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----------------ttttattttgtta------attgctgaatcttaattttgctgtgtgtcaaa---tgaaacttctgttatta-ttgaaagtt---gcttatgttatgta--tgattatgtcctcagGGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATTTTGCCGCTATCTCTGCCTTGAAAGTT
upper sequence: AT5G19150.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA17G01960.1 (Glycine max), 3'ss of exon 2
gttagtgcttgctctattcaattgtgtcatcagaaatttatcaaattcgaaactt--taggattttaaagtttgagttttttcaggttactttgatgttttagctcatgtgttggaattgatcttgtgtcagGGAAGATAGCTGTGATTGGAGGATGTCGTGAATACACAGGAGCTCCATACTTCGCTGCCATTTCAGCTTTGAAAATC
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-----------------------------------gtataacataattgcaactctctatgatccttttatttaagaaaaga-agaaacctctaatgtttcc-ttcacttat--------gtttcaaatcagGAAATATAGCTGTTATTGGAGGTTGCCGTGAATACACAGGTGCTCCATATTTTGCTGCAATTTCAGCCTTAAAAATT
upper sequence: AT5G19150.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G38750.1 (Glycine max), 3'ss of exon 2
gttagtgcttgctctattcaattgtgtcatcagaaatttatcaaattcgaaactttaggattttaaagtttgagttttttcaggttactttgatgttttagctcatgtgttggaattgatcttgtgtcagGGAAGATAGCTGTGATTGGAGGATGTCGTGAATACACAGGAGCTCCATACTTCGCTGCCATTTCAGCTTTGAAAATC
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-----------------------------------gtataacatatgatcctttcttttatttttgggctcaagataaagaagaaacgtctaatgtttcc-ttcacttat--------gttttaaatcagGAAATATAGCTGTTATTGGAGGTTGCCGTGAATACACAGGTGCTCCATATTTTTCTGCAATTTCGGCCTTAAAAATT
upper sequence: AT5G19150.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv05s0020g02800.t01 (Vitis vinifera), 3'ss of exon 1
gttagtgcttgctctattcaattgtgtcatcagaaatttatcaaattcgaaactttaggattttaaagtttgagttttttcaggttactttgatgttttagctcatgtgttggaattgatcttgtgtcagGGAAGATAGCTGTGATTGGAGGATGTCGTGAATACACAGGAGCTCCATACTTCGCTGCCATTTCAGCTTTGAAAATC
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----------------------tacagaattaaga--ttgtccaccgtgatctgtttgttttct---gtacaaataagtata---tagttctctgttatgaatccccactaagtactatttgttactcagGAAAAATAGCTGTTATTGGCGGCTGTCGTGAATATACAGGTGCCCCATACTTCTCTGCTATCTCAGCTTTAAAAATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttcaggttactttgatgttttagctcatgtgttggaattgatcttgtgtcagGGAAGATAGCTGTGATTGGAGGATGTCGTGAATACACAGGAGCTCCATACTTCGCTGCCATTTCAGCTTTGAAAATC
aattgat putative branch site (score: 4)
atgtttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtgcttgctctattcaattgtgtcatcagaaatttatcaaattcgaaactttaggattttaaagtttgagttttttcaggttactttgatgttttagctcatgtgttggaattgatcttgtgtcagGGAAGATAGCTGTGATTGGAGGATGTCGTGAATACACAGGAGCTCCATACTTCGCTGCCATTTCAGCTTTGAAAATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT