Sequence
atgc intronic sequence ATGC exonic sequencegtaagctcataccccctagcatctcgttaattcctacctgttcaaaataaaaaactgaattgccttgaagtagttaaccattgtttgactcccttttctttctgcagTTACTGTGAATGCTTTGCTGCTGGGGTTTATTGCATAGAGCCATGTTCATGTATAGATTGCTTCAACAAACCTATCCATGAAGAAACTGTTTTGGCTACC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G22780.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G22780.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G00920.1 (Glycine max), 3'ss of exon 7
gtaagctcataccccctagcatctcgttaattcctacctgttcaaaataaaaaactgaattgccttgaagtagttaaccattgtttgactcccttttctttctgcagTTACTGTGAATGCTTTGCTGCTGGGGTTTATTGCATAGAGCCATGTTCATGTATAGATTGCTTCAACAAACCTATCCATGAAGAAACTGTTTTGGCTACC
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---tgtttttattcaatgcaagct--ttggaaccaaaaaagggaaagaaaatgacctcactgtatttgaata--tacttattttatttttctttctttttgtatcagTTATTGTGAGTGCTTTGCTGCTGGTGTCTACTGCATAGAACCCTGCTCCTGTCAGGATTGCTTCAACAAACCTATTCATGAAGACACTGTTCTTCAAACT
upper sequence: AT3G22780.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G44670.2 (Glycine max), 3'ss of exon 5
gtaagctcataccccctagcatctcgttaattcctacctgttcaaaataaaaaactgaattgccttgaagtagttaaccattgtttgactcccttttctttctgcagTTACTGTGAATGCTTTGCTGCTGGGGTTTATTGCATAGAGCCATGTTCATGTATAGATTGCTTCAACAAACCTATCCATGAAGAAACTGTTTTGGCTACC
| ||||| || || | | |||| | | ||| | ||| || | | || || ||| || ||| | | | |||||| || || |||||||||||||| || || |||||||| || || || ||| |||||||||||||||||||| |||||||| |||||| | ||
gaaagctt-tagaaccaaaaaagggaaaggaaatgacctcactgtatttgaaattagccttgttttacacttatt-----ttctttttcttttctttttgtat-cagTTATTGCGAGTGCTTTGCTGCTGGTGTCTACTGCATAGAACCCTGCTCCTGTCAGGATTGCTTCAACAAACCTATTCATGAAGACACTGTTCTTCAAACT
upper sequence: AT3G22780.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G39080.1 (Glycine max), 3'ss of exon 11
gtaagctcataccccctagcatctcgttaattcctacctgttca---aaataaaaaactgaattgccttgaagtagttaaccattgtttgactcccttttctttctgcagTTACTGTGAATGCTTTGCTGCTGGGGTTTATTGCATAGAGCCATGTTCATGTATAGATTGCTTCAACAAACCTATCCATGAAGAAACTGTTTTGGCTACC
| | | | || || | | | ||| || ||| ||| | | | | || | || || | | | || ||| |||||| ||||| |||||||||||||| || || |||||||| || ||| |||| ||||||||||| |||||||| |||| || |||||| | ||
--------aatcttctcaatttccttcagctttgtgcatattctcttgcatgaaagcttgagaagaaataaggc--tttattatctttctaattaatcttttttaaccagTTATTGTGAGTGCTTTGCTGCTGGAGTCTACTGCATAGAACCTTGTGCATGCCATGATTGCTTCAATAAACCTATTCATGTTGAGACTGTTCTTCAAACT
upper sequence: AT3G22780.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G28740.1 (Glycine max), 3'ss of exon 10
gtaagctcataccccctagcatctcgt-taattcctacctgttcaaaataaaaaactgaattgccttgaagtagttaaccattgtttgactcccttttctttctgcagTTACTGTGAATGCTTTGCTGCTGGGGTTTATTGCATAGAGCCATGTTCATGTATAGATTGCTTCAACAAACCTATCCATGAAGAAACTGTTTTGGCTACC
|| || ||| | | ||||| | | | || | ||| ||| | | | || | || ||| | | | || || | |||||| ||||| |||||||||||||| || || |||||||| || ||| |||| ||||||||||| |||||||| |||| || |||||| | ||
-cttctcaatttccttcagctttgtgcataatttgttctcataca---tgaaatcttgagaataaataaggc--tttattatctttttaattaatctttttac--cagTTATTGTGAGTGCTTTGCTGCTGGAGTCTACTGCATAGAACCTTGTGCATGCCGCGATTGCTTCAATAAACCTATTCATGTTGAGACTGTTCTTCAAACT
upper sequence: AT3G22780.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv05s0020g03880.t01 (Vitis vinifera), 3'ss of exon 6
gtaagctcataccccctagcatctcgttaattcctacctgttcaaaataaaaa---actgaattgccttgaagtagttaaccattgtttgactccct---tttctttctgcagTTACTGTGAATGCTTTGCTGCTGGGGTTTATTGCATAGAGCCATGTTCATGTATAGATTGCTTCAACAAACCTATCCATGAAGAAACTGTTTTGGCTACC
| | | |||| || | | ||| || ||| | | ||| |||| | | || |||||| | ||||| ||||||||||||||||||||||||||||| || || || |||||||||||||||| ||| ||||| ||||||||||| |||||||| |||||| | || ||
-----------tgtctttgaatct--ttgaggggggcaaaggaaaattagaaatttattttatttccttctgttttgttcttatgatttgaccttttaagcttcttcatgcagTTACTGTGAATGCTTTGCTGCTGGTGTCTACTGTGTAGAGCCATGTTCATGCCAAGAATGCTTTAACAAACCTATTCATGAAGATACTGTTCTTGCAACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aactgaattgccttgaagtagttaaccattgtttgactcccttttctttctgcagTTACTGTGAATGCTTTGCTGCTGGGGTTTATTGCATAGAGCCATGTTCATGTATAGATTGCTTCAACAAACCTATCCATGAAGAAACTGTTTTGGCTACC
ttgtttgactcccttt CT-rich tract
ttttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagctcataccccctagcatctcgttaattcctacctgttcaaaataaaaaactgaattgccttgaagtagttaaccattgtttgactcccttttctttctgcagTTACTGTGAATGCTTTGCTGCTGGGGTTTATTGCATAGAGCCATGTTCATGTATAGATTGCTTCAACAAACCTATCCATGAAGAAACTGTTTTGGCTACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA