Sequence
atgc intronic sequence ATGC exonic sequencegtaaaatctttctcaatcactatgccttttcgacttaacgtctcataaaaataattttatacaagacacactgcagtttcttgttctaaattcgtacttttagtggtagtacttgtggtggttgctttcgttgttggtatatgtcgacgttaatgtcctccgtaacattttctatgttctatgttttacagATTGATCGAGTTAACCTCGAAATTGAATCTGCTGAACGTGAATATGATCTAAACCGAGCTGCTGAGCTGAAGTATGGAACACTTTTGTCCCTCCAACGCC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G25140.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G25140.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G060561_T01 (Zea mays), 3'ss of exon 5
gtaaaatctttctcaatcactatgccttttcgacttaacgtctcataaaaataattttatacaagacacactgcagtttcttgttctaaattcgtactttta-gtggtagtacttgtggtggttgctttcgttgttggtatatgtcgacgttaatgtcctccg--taacattttctatgttctatgttttacagATTGATCGAGTTAACCTCGAAATTGAATCTGCTGAACGTGAATATGATCTAAACCGAGCTGCTGAGCTGAAGTATGGAACACTTTTGTCCCTCCAACGCC
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----------------------------------------------------------------------------------------------tgctgcagcacagcaacagccagagccagctatctgatcaggctgatttccccccctcggtgccatatgggttctaattcttgtcttttatcttgtttagACTGACAGAGTGAACCTGGAGATTGAAGCTGCTGAGAGAGAATATGATTTGAATCGTGCTGCTGAACTGAAGTATGGAACACTTTTATCACTTCAGAAAC
upper sequence: AT2G25140.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA04G06610.1 (Glycine max), 3'ss of exon 8
gtaaaatctttctcaatcactatgccttttcgacttaacgtctcataaaaataattttatacaagacacactgcagtttcttgttctaaattcgtacttttagtggtagtacttgtggtggttgctttcgttgttggtatatgtcgacgttaatgtcctccgtaacattttctatgttctatgttt-tacagATTGATCGAGTTAACCTCGAAATTGAATCTGCTGAACGTGAATATGATCTAAACCGAGCTGCTGAGCTGAAGTATGGAACACTTTTGTCCCTCCAACGCC
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------------------------------------------------------------------------gtaatgtttagttt---gtgtgttgtcattgccatagttcctcttccccctcccctcccctcccctcc---cctcccccaaagaattct---acgccttacatgttataaacatatgtagATTGATAGAGTCAACCTAGAGATGGAAGCTGCTGAGCGTGATTATGACCTGAACCGTGCTGCTGAGCTTAAGTATGGAACTTTGATGTCCCTTCAGCGCC
upper sequence: AT2G25140.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA06G06690.1 (Glycine max), 3'ss of exon 4
gtaaaatctttctcaatcactatgccttttcgacttaacgtctcataaaaataattttatacaagacacactgcagtttcttgttctaaattcgtacttttagtggtagtacttgtggtggttgctttcgttgttggtatatgtcgacgttaatgtcctccgtaacattttctatgttctatgttttacagATTGATCGAGTTAACCTCGAAATTGAATCTGCTGAACGTGAATATGATCTAAACCGAGCTGCTGAGCTGAAGTATGGAACACTTTTGTCCCTCCAACGCC
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-------------------------------------------------------------------------------gtaatgtttagtttgtgtgtt-----gtcatgaccatagttcttctcccctttctctccctccctcccccaaagtctgcgacttaa-atgttataaacacg----tgtatagATTGATAGAGTCAACCTAGAGATGGAAGCTGCTGAGCGTGATTATGACCTGAACCGTGCTGCCGAGCTTAAGTATGGAACTTTGATGTCCCTTCAGCGCC
upper sequence: AT2G25140.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv04s0008g05870.t01 (Vitis vinifera), 3'ss of exon 8
gtaaaatctttctcaatcactatgccttttcgacttaacgtctcataaaaataattttatacaagacacactgcagtttcttgttctaaattcgtacttttagtggtagtacttgtggtggttgctttcgttgttggtatatgtcgacgttaatgtcctccgtaacattttctatgttctatgttttacagATTGATCGAGTTAACCTCGAAATTGAATCTGCTGAACGTGAATATGATCTAAACCGAGCTGCTGAGCTGAAGTATGGAACACTTTTGTCCCTCCAACGCC
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-------------------------------------------------------------------------------------gtaaattcttctttttgtttgtttt-ctttaaatggtaaaattcgattatgttaaat---catcctgacatctcttaattcattggct-tgaaaaac-tcttacagATTGACAGGGTGAACCTGGAGATGGAATCTGCTGAACGTGAATATAATTTAAATCGTGCTGCTGAGCTCAAATATGGAACCTTAATTTCTCTTCAGCGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtatatgtcgacgttaatgtcctccgtaacattttctatgttctatgttttacagATTGATCGAGTTAACCTCGAAATTGAATCTGCTGAACGTGAATATGATCTAAACCGAGCTGCTGAGCTGAAGTATGGAACACTTTTGTCCCTCCAACGCC
ccgtaac putative branch site (score: 3)
taacatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaatctttctcaatcactatgccttttcgacttaacgtctcataaaaataattttatacaagacacactgcagtttcttgttctaaattcgtacttttagtggtagtacttgtggtggttgctttcgttgttggtatatgtcgacgttaatgtcctccgtaacattttctatgttctatgttttacagATTGATCGAGTTAACCTCGAAATTGAATCTGCTGAACGTGAATATGATCTAAACCGAGCTGCTGAGCTGAAGTATGGAACACTTTTGTCCCTCCAACGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG