Sequence
atgc intronic sequence ATGC exonic sequencegtaaattcacagtgctagagtgtttttctagttaagtataaaatctgtctagtgatgtaaattcaaaagcataaatcatgtgaagttatcatatagacctttatcctctgaattatctgtgccaggtttttctagagttagtactgttttgttcttaggcctcactctttcatcttttgatctttactatagAGGTTCACTCGTCTGGGAGGAAAGCTTCCTAAGGGTGTGTTGCTTGTCGGTCCTCCTGGGACAGGAAAAACTATGCTTGCTAGAGCTATTGCTGGAGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G26140.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G26140.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G463032_T01 (Zea mays), 3'ss of exon 4
gtaaattcacagtgctagagtgtttttctagttaagtataaaatctgtctagtgatgtaaattcaaaagcataaatcatgtgaagttatcatatagacctttat-cctctgaattatctgtgccaggtttttctagagttagtactgttttgttcttaggcctcactctttcatcttttgatctttactatagAGGTTCACTCGTCTGGGAGGAAAGCTTCCTAAGGGTGTGTTGCTTGTCGGTCCTCCTGGGACAGGAAAAACTATGCTTGCTAGAGCTATTGCTGGAGAAG
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------------------------------------------------------------------------------------accatcaaatatgattgtgtgccgtcgtaacacacgggc---atcgtactagtcttatta-tatgtttttataag-----atgctcacaaactgtgctcttattttcagCGCTTCACATGTCTTGGTGGAAAACTTCCTAAAGGTGTCTTGCTTGTGGGCCCTCCTGGCACTGGGAAAACCATGCTAGCTAGGGCTATTGCTGGTGAAG
upper sequence: AT2G26140.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G096764_T01 (Zea mays), 3'ss of exon 5
gtaaattcacagtgctagagtgtttttctagttaagtataaaatctgtctagtgatgtaaattcaaaagcataaatcatgtgaagttatcatatagacctttatcctctgaattatctgtgccaggtttttctagagttagtactgttttgttcttaggcctcactctttcatcttttgatctttactatagAGGTTCACTCGTCTGGGAGGAAAGCTTCCTAAGGGTGTGTTGCTTGTCGGTCCTCCTGGGACAGGAAAAACTATGCTTGCTAGAGCTATTGCTGGAGAAG
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-----------------------------------------------------------------------------------tgcttttatgaagctcatc-tcgtcttgacaacacctgg-aggtacct-------tatttttcattttgtctttcgtatgatgctcacaaactgtgctcttgttttcagCGCTTCACACGTCTTGGTGGAAAACTTCCGAAAGGAGTCTTGCTTGTTGGTCCTCCTGGCACTGGGAAAACCATGCTAGCTAGGGCTATTGCTGGTGAAG
upper sequence: AT2G26140.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G451483_T01 (Zea mays), 3'ss of exon 6
gtaaattcacagtgctagagtgtttttctagttaagtataaaatctgtctagtgatgtaaattcaaaagcataaatcatgtgaagttatcatatagacctttatcctctgaattatctgtgccaggtttttctagagttagtactgttttgttcttaggcctcactctttcatcttttgatctttactatagAGGTTCACTCGTCTGGGAGGAAAGCTTCCTAAGGGTGTGTTGCTTGTCGGTCCTCCTGGGACAGGAAAAACTATGCTTGCTAGAGCTATTGCTGGAGAAG
| | | | | | | | | || | || || | | | | | |||| | |||||| ||| ||||| |||| |||| | | | || | || || | || || |||||||||||||| ||||| ||||| || || || ||||| || |||||||||||||| || || ||||| ||||| ||||
----------------------------------------------------------------------ttgcgctttttagggaca-cgtcaaagtgctcatttt-tgggttgtatattc---atgtttcaaatattagta------------tagtactcaca--ttcacctttcattgtgccc---agCGTTTTACATGCCTTGGTGGAAAGCTTCCTAAAGGTGTTTTGCTGGTGGGACCACCTGGAACTGGAAAAACTATGCTGGCAAGGGCTATAGCTGGGGAAG
upper sequence: AT2G26140.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA14G10960.1 (Glycine max), 3'ss of exon 3
gtaaattcacagtgctagagtgtttttctagttaagtataaaatctgtctagtgatgtaaattcaaaagcataaatcatgtgaagttatcatatagacctttatcctctgaattatctgtgccaggtttttctagagttagtactgttttgttcttaggcctcactctttcatcttttgatctttactatagAGGTTCACTCGTCTGGGAGGAAAGCTTCCTAAGGGTGTGTTGCTTGTCGGTCCTCCTGGGACAGGAAAAACTATGCTTGCTAGAGCTATTGCTGGAGAAG
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---------------------------------------------------------------------------ttttgtta---cattttatatgcttctttcct---gactgcatatactggcttgtactt-------ttccttatcatctttg----taattgtatgactttttttcccttgtgacagCGCTTTACTCGTCTTGGTGGTAAGCTTCCAAAAGGAGTTTTGCTTGTTGGTCCACCTGGCACTGGAAAAACTATGTTAGCAAGAGCTATTGCTGGAGAGG
upper sequence: AT2G26140.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA14G10950.1 (Glycine max), 3'ss of exon 5
gtaaattcacagtgctagagtgtttttctagttaagtataaaatctgtctagtgatgtaaattcaaaagcataaatcatgtgaagttatcatatagacctttatcctctgaattatctgtgccaggtttttctagagttagtactgttttgttcttaggcctcactctttcatcttttgatctttactatagAGGTTCACTCGTCTGGGAGGAAAGCTTCCTAAGGGTGTGTTGCTTGTCGGTCCTCCTGGGACAGGAAAAACTATGCTTGCTAGAGCTATTGCTGGAGAAG
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---------------------------------------------------------------------------ctttgtta---cattttatatgcttctttcct---gactgcatatagtggcttgtactt-------ttccttatcatctttg----taattgtatgactttttttcccttgtgacagCGCTTTACTCGTCTTGGTGGTAAGCTTCCAAAAGGAGTTTTGCTTGTTGGTCCACCTGGCACTGGAAAAACTATGTTAGCAAGAGCTATTGCTGGAGAGG
upper sequence: AT2G26140.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G34610.1 (Glycine max), 3'ss of exon 3
gtaaattcacagtgctagagtgtttttctagttaagtataaaatctgtctagtgatgtaaattcaaaagcataaatcatgtgaagttatcatatagacctttatcctctgaattatctgtgccaggtttttctagagttagtactgttttgttcttaggcct-cactctttcatcttttgatctttactatagAGGTTCACTCGTCTGGGAGGAAAGCTTCCTAAGGGTGTGTTGCTTGTCGGTCCTCCTGGGACAGGAAAAACTATGCTTGCTAGAGCTATTGCTGGAGAAG
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----------------------------------------------------------------------------------acttttttgttacgttttttattcttt------cctg-accgcgtatact---ggcttgtact-tttccttatcatctttgtaattttatgacttttttcccttgtgacagCGCTTTACTCGTCTTGGTGGTAAGCTTCCGAAAGGAGTTTTACTTGTTGGTCCACCTGGCACTGGGAAAACAATGTTAGCTAGAGCTATTGCTGGAGAGG
upper sequence: AT2G26140.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv04s0008g01170.t01 (Vitis vinifera), 3'ss of exon 5
gtaaattcacagtgctagagtgtttttctagttaagtataaaatctgtctagtgatgtaaattcaaaagcataaatcatgtgaagttatcatatagacctttatcctctgaattatctgtgccaggtttttctagagttagtactgttttgttcttaggcctcactctttcatcttttgatctttactatagAGGTTCACTCGTCTGGGAGGAAAGCTTCCTAAGGGTGTGTTGCTTGTCGGTCCTCCTGGGACAGGAAAAACTATGCTTGCTAGAGCTATTGCTGGAGAAG
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---------------------------------------------------------------------aaaaacttccatgaaattaaaatgtaaaccctgaagccct-----atct---ctag------ttagagtt-gta----tatctgaataggtttc-ttattttatgtttc---ccttgttacagCGCTTCACTCGTCTAGGTGGCAAACTTCCAAAGGGTGTTTTGCTTGTTGGTCCACCTGGCACCGGCAAGACCATGTTGGCAAGAGCTATCGCTGGAGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagtactgttttgttcttaggcctcactctttcatcttttgatctttactatagAGGTTCACTCGTCTGGGAGGAAAGCTTCCTAAGGGTGTGTTGCTTGTCGGTCCTCCTGGGACAGGAAAAACTATGCTTGCTAGAGCTATTGCTGGAGAAG
ctctttcatcttttga CT-rich tract
tttactata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaattcacagtgctagagtgtttttctagttaagtataaaatctgtctagtgatgtaaattcaaaagcataaatcatgtgaagttatcatatagacctttatcctctgaattatctgtgccaggtttttctagagttagtactgttttgttcttaggcctcactctttcatcttttgatctttactatagAGGTTCACTCGTCTGGGAGGAAAGCTTCCTAAGGGTGTGTTGCTTGTCGGTCCTCCTGGGACAGGAAAAACTATGCTTGCTAGAGCTATTGCTGGAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA