Sequence
atgc intronic sequence ATGC exonic sequencegtgagttttaatctcaagttttttttaccagatattagtgtttgaaacaaaagcttgtgatcatcacaaccaatcaaaaaatctttttgatattgatttttttcttttcatactgcttatgaagtcttaaaccgcagattatattattttttgttggaattaaatgtcatgttgtttgttttttcctctttttagGCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAAAGAATTTTTGAGGAAACTTTGCATAGGAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G07350.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G07350.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G136296_T02 (Zea mays), 3'ss of exon 2
gtgagttttaatctcaagttttttttaccagatattagtgtttgaaacaaaagcttgtgatcatcacaaccaatcaaaaaatctttttgatattgatttttttcttttcatactgcttatgaagtcttaaaccgcagattatattattttttgttggaattaaatgtcatgttgtttgttttttcct--ctttttagGCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAAAGAATTTTTGAGGAAACTTTGCATAGGAAAG
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---------------------------------------------------------------------------------------------tggaactatttactgagtatcaattgtagcttcttga-caattgacattcttctcatttctctagttttcatttt---tcgcttgtttattcatggtgctatagGCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG
upper sequence: AT5G07350.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G38010.1 (Glycine max), 3'ss of exon 2
gtgagttttaatctcaagttttttttaccagatattagtgtttgaaacaaaagcttgtgatcatcacaaccaatcaaaaaatctttttgatattgatttttttcttttcatactgcttatgaagtcttaaaccgcagattatattattttttgttggaattaaatgtcatgttgtttgttttttcc--tctttttagGCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAAAGAATTTTTGAGGAAACTTTGCATAGGAAAG
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-------------------------------------------------------------------------------gtacttttagttatttgactttttttcattggattaattaatcaattaaataatttaaggctctgtgttaattgct-----ttagtgttgttttttttttttttgcgaattattgtagGCGCGTAGAGGTGGTGTGGACGAGCCTTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG
upper sequence: AT5G07350.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G17050.4 (Glycine max), 3'ss of exon 2
gtgagttttaatctcaagttttttttaccagatattagtgtttgaaacaaaagcttgtgatcatcacaaccaatcaaaaaatctttttgatattgatttttttcttttcatactgcttatgaagtcttaaaccgcagattatattattttttgttgg--aattaaatgtcatgttgtttgttttttcc---tctttttagGCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAAAGAATTTTTGAGGAAACTTTGCATAGGAAAG
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--------------------------------------------------------------------------------------gtagttttagttatttgactttttttcattggattaattaatcaattaaataatttaaagctttgtgttaattgctttagtgttttttttttttttttttgcgaattgtggtagGCGCGTAGAGGTGGTGTGGACGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG
upper sequence: AT5G07350.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0068g00720.t01 (Vitis vinifera), 3'ss of exon 1
gtgagttttaatctcaagttttttttaccagatattagtgtttgaaacaaaagcttgtgatcatcacaaccaatcaaaaaatctttttgatattgatttttttcttttcatactgctta--tgaagtcttaaaccgcagattatattattttttgttggaattaaatgtcatgttgtttgttttttcctctttttagGCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAAAGAATTTTTGAGGAAACTTTGCATAGGAAAG
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-------------------------------------------------------------------------------------------tttggcattactaataccacactttttaaatgaattctc------tatattccatactcttattctgtaccctgacctgatttttttgaatatctattgactatagGCCCGTAGAGGTGGTATTGATGAACCATTTGCATGGGATAGTAGAGAGTATTTGAGGAAACTCTGCATAGGAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atattattttttgttggaattaaatgtcatgttgtttgttttttcctctttttagGCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAAAGAATTTTTGAGGAAACTTTGCATAGGAAAG
tcatgttgtttgtttt CT-rich tract
attttttgtt 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
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gtgagttttaatctcaagttttttttaccagatattagtgtttgaaacaaaagcttgtgatcatcacaaccaatcaaaaaatctttttgatattgatttttttcttttcatactgcttatgaagtcttaaaccgcagattatattattttttgttggaattaaatgtcatgttgtttgttttttcctctttttagGCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAAAGAATTTTTGAGGAAACTTTGCATAGGAAAG
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