Sequence
atgc intronic sequence ATGC exonic sequencegtaaaatagtaatcacatggactttcttggatttgtatgatagaagaataagttaagtgatctaattaaagtttttacatcttggttaaagGTTGGAGCTCAAACTGAGACAGAGCTCAAAGAAAAGAAGCTGAGAGTGGAAGATGCTCTTAATGCTACAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G13470.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G18760.1 (Glycine max), 3'ss of exon 8
gtaaaatagtaatcacatggactttcttggatttgtatgatagaagaataagttaagtgatctaattaaagtttttacatcttggttaaagGTTGGAGCTCAAACTGAGACAGAGCTCAAAGAAAAGAAGCTGAGAGTGGAAGATGCTCTTAATGCTACAAAG
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gtaacagactcactgaaatg-tggtaatatattagtttggtactctg-caaggtatatcaacttggggcaatttttgtacata---tatagGTTGGCGCACAAACTGAGACAGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAG
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 8
gtaaaatagtaatcacatggactttcttggatttgtatgatagaagaataagttaagtgatctaattaaagtttttacatcttggttaaagGTTGGAGCTCAAACTGAGACAGAGCTCAAAGAAAAGAAGCTGAGAGTGGAAGATGCTCTTAATGCTACAAAG
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--gtaacag-actcactgaaatggtaatatgttagtttggtacgccgttgggtatatcaacttgggcaatttttgtacatgt-----gtagGTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAG
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 9
gtaaaatagtaatcacatggactt---tcttggatttgtatgatagaagaataagttaagtgatctaattaaagtttttacatcttggttaaagGTTGGAGCTCAAACTGAGACAGAGCTCAAAGAAAAGAAGCTGAGAGTGGAAGATGCTCTTAATGCTACAAAG
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gtaaattcttagttagtccagttaaaatttataaatgatttcatcattgcaggtgcttagt-atctattaattattcattgaactt--ttgaagGTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAG
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ33580 (Selaginella moellendorffii), 3'ss of exon 8
gtaaaatagtaatcacatggactttcttggatttgtatgatagaagaataagttaagtgatctaattaaagtttttacatcttggttaaagGTTGGAGCTCAAACTGAGACAGAGCTCAAAGAAAAGAAGCTGAGAGTGGAAGATGCTCTTAATGCTACAAAG
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--------------------------gtaagtttattttgcag-----tatttttagcagcacatctttaacttctctgta--aattgaagGTTGGTGCACAAACTGAGACAGAATTAAAAGAAAAGAAGTTAAGAGTGGAAGATGCTTTGAATGCGACGAAG
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ36935 (Selaginella moellendorffii), 3'ss of exon 8
gtaaaatagtaatcacatggactttcttggatttgtatgatagaagaataagttaagtgatctaattaaagtttttacatcttggttaaagGTTGGAGCTCAAACTGAGACAGAGCTCAAAGAAAAGAAGCTGAGAGTGGAAGATGCTCTTAATGCTACAAAG
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--------------------------gtaagtttattttgcagtatttttagc--agc-acatcgttaacttttctgta----aattgaagGTTGGTGCACAAACTGAGACAGAACTAAAAGAAAAGAAGTTAAGAGTGGAAGATGCTTTGAATGCAACGAAG
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ32217 (Selaginella moellendorffii), 3'ss of exon 8
gtaaaatagtaatcacatggactttcttggatttgtatgatagaagaataagttaagtgatctaattaaagtttttacatcttggttaa---agGTTGGAGCTCAAACTGAGACAGAGCTCAAAGAAAAGAAGCTGAGAGTGGAAGATGCTCTTAATGCTACAAAG
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----------------------------------gtaagacatcgctttttttgccgtttccggaaaaaattcttctgacattgattcgcgcagGTGGGAGCTCAAACGGAAACCGAGCTGAAAGAGAAGAAGCTTAGAGTGGAGGACGCTCTAAATGCAACAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgatagaagaataagttaagtgatctaattaaagtttttacatcttggttaaagGTTGGAGCTCAAACTGAGACAGAGCTCAAAGAAAAGAAGCTGAGAGTGGAAGATGCTCTTAATGCTACAAAG
atctaat putative branch site (score: 3)
atctaattaaagtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaatagtaatcacatggactttcttggatttgtatgatagaagaataagttaagtgatctaattaaagtttttacatcttggttaaagGTTGGAGCTCAAACTGAGACAGAGCTCAAAGAAAAGAAGCTGAGAGTGGAAGATGCTCTTAATGCTACAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG