Sequence
atgc intronic sequence ATGC exonic sequencegtagttttatatcctagtacttgtgtacagaagagggtcaaaaagaagaatgctatgagcaaaatatgcttactgtaactccttatgttttgacattattgctagCCTCAAGCAAAAGAAAAAGGCGAGAAGGAAGGATTTAAAGTTAGTGTTGTCAAGACAAGTTTCAAGGCTAACACAAAGGCCCTAGCTGAAAATGAAGGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G16950.2 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 11
gtagttt---tatatcctagtacttgtgtacagaagagggtcaaaaagaagaatgctatgagcaaaatatgcttactgtaactccttatgttttgacattattgctagCCTCAAGCAAAAGAAAAAGGCGAGAAGGAAGGATTTAAAGTTAGTGTTGTCAAGACAAGTTTCAAGGCTAACACAAAGGCCCTAGCTGAAAATGAAGGAG
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gtattttatccatgctaaagcaactcttcatctactgtgctttaggacagtaaccacattcttaata-attcgtaaattaagttccta-------gtaaaatttacagCCACAAGCGAGAGAAAAGGCTGATAAGGAAGGATTTGAGATAAGTGTTGTTAAGACCAGCTTCAAGGCAAACACGAAGGCTCTGGCTGAGAATGAAGGAG
upper sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 11
-------------------------------------------------------------gtagttttatatc--ctagtac-ttgtgtacagaagagggtcaaaaa--------gaagaatgctatg-------agcaaaatatgcttactgtaactccttatgttttgacattattgctagCCTCAAGCAAAAGAAAAAGGCGAGAAGGAAGGATTTAAAGTTAGTGTTGTCAAGACAAGTTTCAAGGCTAACACAAAGGCCCTAGCTGAAAATGAAGGAG
||| ||| | ||||||| | | | || | | ||| || | |||| || |||||| | ||| | |||| || | | || |||| || || | || || | || |||||||||||| || | |||||||| ||||| ||||| |||||||||||||||||||| || || ||||||||||
gtaagtgagataccattctccaatattacattctctgttcaacatagttgaaatctgcttggtaaagttaatttgactagtacactttcttaagtataaaatcacaacttgtttccaactcttgctttgcttggctagcaaaccaatctt--tacgactctaatcattgttcctgcttttgcagCCACAGGCTAGGGAGAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTAAAGACCAGTTTTAAGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAG
upper sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 6
gtagttttatatcctagtacttgtgtacagaagagggtcaaaaagaagaatgctatgagcaaaatatgcttactgtaactccttatgttttgacattattgct--agCCTCAAGCAAAAGAAAAAGGCGAGAAGGAAGGATTTAAAGTTAGTGTTGTCAAGACAAGTTTCAAGGCTAACACAAAGGCCCTAGCTGAAAATGAAGGAG
|| | || ||| || | | | | || | | | | || | | | | | ||||| | ||||||| | |||||||||||| || |||| || ||||| || ||| |||| ||||||| ||| |||||||| || ||||||||||||||| |||||||||| ||||| |
------ttctgatctgttacccccttatattatatatatattaaaattactcat-tgtccctcactcatatgaactcatggattatgatcaaacattatatatgcagCCTCAAGCAAGGGAGAAAGCTGAAAAGGAGGGTTTTGAAGTAAGTGTTGCCAAAACAAGTTTTAAAGCTAACACAAAGGCCTTAGCTGAAAACGAAGGGG
upper sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 11
gtagttttatatcctagtac-ttgtgtacagaagagggtcaaaaagaagaatgctatgagcaaaatatgcttactgtaactccttatgttttgaca--ttattgctagCCTCAAGCAAAAGAAAAAGGCGAGAAGGAAGGATTTAAAGTTAGTGTTGTCAAGACAAGTTTCAAGGCTAACACAAAGGCCCTAGCTGAAAATGAAGGAG
| | ||| || || | || | || | | | | || | | || || | |||| ||||| | ||| |||| |||||||||||| || |||| || ||||| || ||| |||| ||||||| ||| |||||||| || ||||||||||||||| |||||||||| ||||| |
-tcaccccctttccccttatattatttatataataaaattactgcttgttgtcct-tcactcgtatgaactca-tgta-----ttatgataaaacatattatatgcagCCTCAAGCAAGGGAGAAAGCTGAAAAGGAGGGTTTTGAAGTAAGTGTTGCCAAAACAAGTTTTAAAGCTAACACAAAGGCCTTAGCTGAAAACGAAGGGG
upper sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA07G37050.1 (Glycine max), 3'ss of exon 11
gtagttttatatcctagtacttgtgtacagaagagggtcaaaaagaagaatgctatgagcaaaatatgcttactgtaactccttatgttttgacatta---ttgctagCCTCAAGCAAAAGAAAAAGGCGAGAAGGAAGGATTTAAAGTTAGTGTTGTCAAGACAAGTTTCAAGGCTAACACAAAGGCCCTAGCTGAAAATGAAGGAG
| ||| || | | | || | | ||| || | | ||| | | | | | || | | |||| | |||||||||||| || ||||| || || || || ||| |||| ||||||| ||| |||||||| || |||||||||||||| ||||| ||||| |||||||
-----tccatactcttttccct---tatattatttatacaataaaattactgcctctcattcttcacttgaattctcatgtgttgcgatcaaacataaaatcctgcagCCTCAAGCAAGGGAGAAAGGTGAAAAAGAGGGGTTTGAAGTAAGTGTTGCCAAAACAAGTTTTAAAGCTAACACAAAGGCTCTAGCAGAAAACGAAGGAG
upper sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 11
------------------------------------------------------------------------------------------gtagttttatatcctagtacttgtgtacagaagagggtcaaaaagaagaatgctatgagcaaaatatgcttactgtaactccttatgttttgac-------attattgctagCCTCAAGCAAAAGAAAAAGGCGAGAAGGAAGGATTTAAAGTTAGTGTTGTCAAGACAAGTTTCAAGGCTAACACAAAGGCCCTAGCTGAAAATGAAGGAG
| | || | | | | | || | | | | | | | | | ||| | || | || | ||| |||| ||| | || |||||||||||| | ||||| || || || || ||| |||| ||||||| ||| |||||||| || |||||||||||||| ||||| ||||| |||||||
gtatatcataattttattttgtttgatgtgtcattcactgcaacaatttacaatgaatgagttctcttttatgtgtggttaactttctctccattcttcttttcca-tcctcttttccttatattatttatacattaaaat-ttctgcctcttgtccttcacttgaattctcttgtgttgtgatcaaacttaaaatctgcagCCTCAAGCAAGGGTGAAAGGTGAAAAAGAGGGGTTTGAAGTAAGTGTTGCCAAAACAAGTTTTAAAGCTAACACAAAGGCTCTAGCAGAAAACGAAGGAG
upper sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 11
----------------------------gtagttttatatcctagt----acttgtgtacagaagagggtcaaaaagaagaatgctatg-agcaaaatatgcttact--gtaactccttatgttttgacattat-tgctagCCTCAAGCAAAAGAAAAAGGCGAGAAGGAAGGATTTAAAGTTAGTGTTGTCAAGACAAGTTTCAAGGCTAACACAAAGGCCCTAGCTGAAAATGAAGGAG
||| ||| | | | || | | | | || | ||| ||| ||| ||| || || | | || | || ||| | || |||| ||||||| || | || ||||| || || || ||||||||||||| |||||| || ||||| || ||||| ||||| || ||||| |||||||| |
gtatagcaatccttttgtttcacaatttactttttaataacttgatttgaacctctttgtaatgtagctcttgtgactggaaagcttcacagcctaatccatttttcaggtgaaagttaatttctttttattctctggcagCCACAAGCAAGAGCACTGGGAGAGAAAGAGGGTTTCAAAGTTAGTGTTGCCAAGACTAGCTTCAAAGCCAACACTAAGGCTCTCGCTGAGAATGAAGGCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctatgagcaaaatatgcttactgtaactccttatgttttgacattattgctagCCTCAAGCAAAAGAAAAAGGCGAGAAGGAAGGATTTAAAGTTAGTGTTGTCAAGACAAGTTTCAAGGCTAACACAAAGGCCCTAGCTGAAAATGAAGGAG
ttatgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagttttatatcctagtacttgtgtacagaagagggtcaaaaagaagaatgctatgagcaaaatatgcttactgtaactccttatgttttgacattattgctagCCTCAAGCAAAAGAAAAAGGCGAGAAGGAAGGATTTAAAGTTAGTGTTGTCAAGACAAGTTTCAAGGCTAACACAAAGGCCCTAGCTGAAAATGAAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG