Sequence
atgc intronic sequence ATGC exonic sequencegtaatttctcattgtttctactgaatttaagctgataactttacggtggagaaagctaaaatttttttcctctcactgtttgtctcctatagGAGGTTTGTACTCAGGAGGAAGTGCTCAAATGATAGAGAGTTCACTCAACGTTCATGGAGATGAGATTTTGTATGTTGGTGACCACATCTACACTGATGT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G48960.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G48960.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA17G04580.1 (Glycine max), 3'ss of exon 11
--gtaatttctcatt---gtttctactga----atttaagctgataactttacggtggagaaagctaaaatttttttcctctcactgtttgtctcctatagGAGGTTTGTACTCAGGAGGAAGTGCTCAAATGATAGAGAGTTCACTCAACGTTCATGGAGATGAGATTTTGTATGTTGGTGACCACATCTACACTGATGT
||| | | |||| |||| | | || | ||| |||| | || || || | || | || ||| || |||| |||||||||||||| |||||||| |||||| | || | ||| || | ||||||||||||| || ||||||||||| ||||| || |||||||||||
caaccattcaccgtgttagttttcactgtggataactgggccgctaattttaatacttatcaa-ttatgatcatggcactttatcttaccctcttctgtagGTGGTTTGTACTCAGGGGGAAGTGCACAAATGGTTGAAAATTCCCTAGATATTCATGGAGATGAAATATTGTATGTTGGCGACCATATTTACACTGATGT
upper sequence: AT5G48960.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA13G17950.1 (Glycine max), 3'ss of exon 11
-gtaatttctca---ttgtttctactg----aatttaagctgataactttacggtggagaaagctaaaatttttttcctctcactgtttgtctcctatagGAGGTTTGTACTCAGGAGGAAGTGCTCAAATGATAGAGAGTTCACTCAACGTTCATGGAGATGAGATTTTGTATGTTGGTGACCACATCTACACTGATGT
||| || | |||| |||| | | ||| | ||| |||| | || | | | | | | | ||| || ||| ||||||||||| || |||||||| |||||| | || | ||| || | ||||||||||||| || ||||||||||| ||||| || |||||||||||
aaccattcaccacgttagttttcactgccgataactgagccgctaattttaatacttatgaattacgatcatgatactttaccttaaccctcttctgcagGTGGTTTGTACTCGGGGGGAAGTGCACAAATGGTTGAAAATTCCCTAGATATTCATGGAGATGAAATATTGTATGTTGGCGACCATATTTACACTGATGT
upper sequence: AT5G48960.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA15G21240.1 (Glycine max), 3'ss of exon 10
---------gtaatttctcattgtttctactgaatttaagctgataactttacggtggagaaagctaaaatttttttcctctcactgtttgtctcctatagGAGGTTTGTACTCAGGAGGAAGTGCTCAAATGATAGAGAGTTCACTCAACGTTCATGGAGATGAGATTTTGTATGTTGGTGACCACATCTACACTGATGT
|||| | | | | | | | | | ||| | | | | || ||| || | ||| | || ||| |||||||||||||| || ||||| || ||| | || ||||| || || | |||||||||||||| ||||| |||| ||||| || |||||||||||
gaatatattacggaaatgaattgactttgcaatgtgttacatt-tgaagttatttttaaaatgatttaactttgttatactttacttaccatactctgcagGTGGTTTGTACTCAGGGGGGAGTGCGCAGATGGTTGAAAGTTCCCTAAATATACATGGAGATGAGATACTGTATATTGGAGACCATATTTACACTGATGT
upper sequence: AT5G48960.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv05s0020g00880.t01 (Vitis vinifera), 3'ss of exon 11
gtaatttc------tcattgtttctactgaatttaagctgataactttacggtggagaaagctaaaatttttttcctctcactgtt----tgtctcctatagGAGGTTTGTACTCAGGAGGAAGTGCTCAAATGATAGAGAGTTCACTCAACGTTCATGGAGATGAGATTTTGTATGTTGGTGACCACATCTACACTGATGT
| |||| ||| | ||| | ||| | | | | || | || || || |||| | ||| || | | | | ||| || || ||||||||||| |||||||| ||||| || | ||| || || | ||||||||||||||||||||||| ||||||||||| | || |||||
-tgttttccggagatcacttaatctgcaaaatgttaaataa-aattgtaaactgtcatggttcaactattttgtgtattcatccttcttatattttttgcagGGGGCTTATACTCAGGAGGGAGTGCTCAGATGATTGAAAATTCCCTTAAAATCCATGGAGATGAGATTTTGTATGTCGGTGACCACATTCATACAGATGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actttacggtggagaaagctaaaatttttttcctctcactgtttgtctcctatagGAGGTTTGTACTCAGGAGGAAGTGCTCAAATGATAGAGAGTTCACTCAACGTTCATGGAGATGAGATTTTGTATGTTGGTGACCACATCTACACTGATGT
tttttttcctctcact CT-rich tract
aaagctaaaatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatttctcattgtttctactgaatttaagctgataactttacggtggagaaagctaaaatttttttcctctcactgtttgtctcctatagGAGGTTTGTACTCAGGAGGAAGTGCTCAAATGATAGAGAGTTCACTCAACGTTCATGGAGATGAGATTTTGTATGTTGGTGACCACATCTACACTGATGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG