Sequence
atgc intronic sequence ATGC exonic sequencegtggctttaacaggtttactgtggttgttttctgtaattatcgtaggaagagtcagtttatttgcgattatcagttggtgacataagatggggaacggatattgcatctgcttatattctttttctttatctgccttcagAGTTGTAGGCGGACTTCTTAGTGCGTATGATCTTTCTGGGGACAAAATGTTCCTTGAAAAGGCTAAGGATATTGCAGACAGATTATTGCCTGCATGGAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G51590.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G51590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G23730.1 (Glycine max), 3'ss of exon 5
gtggctttaacaggtttac--tgtggttgtt-ttctgtaattatcgtaggaagagtcagtttatttgcgattatcagttggtgacataagatggggaacggatattgcatctgcttatattctttttctttatctgccttcagAGTTGTAGGCGGACTTCTTAGTGCGTATGATCTTTCTGGGGACAAAATGTTCCTTGAAAAGGCTAAGGATATTGCAGACAGATTATTGCCTGCATGGAAT
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gttactttataaggtttactttgcagttgaagttccttccccat--ttacaaaagttatatt-tttgagctcatgtgttag-actactgattgtttttttaat----cattctttttgttggtcgatttccaccaaaatccagAGTAGTAGGTGGCCTTCTTAGTGCATATGATCTTTCAGGGGACAAAGTATTCCTCGACAAAGCAATAGAAATTGCAGACAGATTACTGCCTGCATGGAAT
upper sequence: AT1G51590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G02290.1 (Glycine max), 3'ss of exon 4
gtggctttaacaggtttac--tgtggttgttttctgtaattatcgtaggaagagtcagtttatttgcgattatcagttggtgacataagatggggaacggatattgcatctgcttatattctttttctttatctgccttcagAGTTGTAGGCGGACTTCTTAGTGCGTATGATCTTTCTGGGGACAAAATGTTCCTTGAAAAGGCTAAGGATATTGCAGACAGATTATTGCCTGCATGGAAT
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gttactttataaagtttactttgcagttgaagtccct--tccccatttacaaaattatatt-tttgagctcatgtgttag--acaactgatattgtttttttaatctttttctttgt-tggtcgatttccaccaaaatccagAGTAGTAGGTGGTCTTCTTAGTGCATATGATCTTTCAGGGGACAAAGTTTTCCTCAACAAAGCAATAGAAATTGCAGACAGATTATTGCCTGCATGGAAT
upper sequence: AT1G51590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv09s0054g00370.t01 (Vitis vinifera), 3'ss of exon 5
gtggctttaacaggtttactgtg---gttgttt--tctgtaatta---tcgtaggaagagtcagttt--atttgcgattatcagttggtgacataagatg-----gggaacgga-tattgcatct---gcttat---------attctttttc---tttatctgcctt----------------cagAGTTGTAGGCGGACTTCTTAGTGCGTATGATCTTTCTGGGGACAAAATGTTCCTTGAAAAGGCTAAGGATATTGCAGACAGATTATTGCCTGCATGGAAT
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gttgcattataaggtttaatatgtagattgtttaatttgtcctttctcttgttcggaagaccagttatgggttatgatgaccttgcaatctctaaagatgaacttgggattgaaatcttgcatttttgacttatcatttttggatttttttttaattttattttattttattctttttgaaatccagAGTTGTGGGTGGACTACTTAGTGCATATGATCTCTCAGAGGACAAACTTTTCCTTGAAAAAGCTAGAGATATTGCAGATAGGTTGCTGCCTGCCTGGAAT
upper sequence: AT1G51590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv11s0052g00140.t01 (Vitis vinifera), 3'ss of exon 5
gtggctttaacaggtttactgtggttgttttctgtaattatcgtaggaagagtcagtttatttgcgattatcagtt--------ggtgacataagatggggaacggatattgcatctgct----tatattctttttctttatctgcctt-----cagAGTTGTAGGCGGACTTCTTAGTGCGTATGATCTTTCTGGGGACAAAATGTTCCTTGAAAAGGCTAAGGATATTGCAGACAGATTATTGCCTGCATGGAAT
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gttgcattataaggtttcatcttatttatttatttaataat--aagtttctttttttttctttggggacagaggtcctctctgggatggttgagaggaagaagcgtatgacatgtccactgctttttatcctttttgtatacttatgttgaatgcagAGTTTTAGGTGGACTTCTTAGTGCATATGATCTTTCCGGTGACAAAGTCTTCCTTGAAAAGGCTCAAGATATTGCAGATAGATTGCTGCCTGCTTGGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agatggggaacggatattgcatctgcttatattctttttctttatctgccttcagAGTTGTAGGCGGACTTCTTAGTGCGTATGATCTTTCTGGGGACAAAATGTTCCTTGAAAAGGCTAAGGATATTGCAGACAGATTATTGCCTGCATGGAAT
cttatattctttttct CT-rich tract
ttatattctttttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtggctttaacaggtttactgtggttgttttctgtaattatcgtaggaagagtcagtttatttgcgattatcagttggtgacataagatggggaacggatattgcatctgcttatattctttttctttatctgccttcagAGTTGTAGGCGGACTTCTTAGTGCGTATGATCTTTCTGGGGACAAAATGTTCCTTGAAAAGGCTAAGGATATTGCAGACAGATTATTGCCTGCATGGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA