Sequence
atgc intronic sequence ATGC exonic sequencegtaattttgtcataagcttattcataatataaactgaaaattgtgtggccttaatagaaagaaagcacatatgctttgacattatctccagTTGCAATGAGTCTTGAGGAGTTAATACCATCAAACTATGGGAAGTCACGTTTCTACGCAATCGCCATTAGAAGTGCATTAGCCATCTCTACTCTGCTCGT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G54830.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G54830.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA20G32260.1 (Glycine max), 3'ss of exon 9
-------------------------gtaattt--------tgtcataagcttattcataatataaactgaaaattgtgtggccttaatagaaagaaagcacatatgctttgacattatctccagTTGCAATGAGTCTTGAGGAGTTAATACCATCAAACTATGGGAAGTCACGTTTCTACGCAATCGCCATTAGAAGTGCATTAGCCATCTCTACTCTGCTCGT
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tctttgaacaggttttttatgtcatgtcatttctcttgcatttctaaagtactcttacactgtgagcaaagaaagatgtt-ttttacttaattagcttcacGTATGCGTTGACTATATCCCCAGTGGCAATGAGTCTGGAGGAGTTGATACCATCAAACCATGCCAAGTCTTATCTATATTCCATCTTCATCAGAACAGGG-----------------------
upper sequence: AT3G54830.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA10G35280.2 (Glycine max), 3'ss of exon 8
-------------------------gtaattt--------tgtcataagcttattcataatataaactgaaaattgtgtggccttaatagaaagaaagcacatatgctttgacattatctccagTTGCAATGAGTCTTGAGGAGTTAATACCATCAAACTATGGGAAGTCACGTTTCTACGCAATCGCCATTAGAAGTGCATTAGCCATCTCTACTCTGCTCGT
|| |||| | || ||| || | | | | | | | || ||| || | | | ||| ||||| ||||| |||||||||| ||||||||||| |||||||| ||||| |||||| ||| ||||| | | || | ||| ||| |||| |
tgttatatcaattttagtcccacatgtcatttctcttgcatttctaaagtacttttacactgtgagcaaagaaagatgtt-ttgtacttaactagcatcacGTATGCATTGACTATATCTCCAGTGGCAATGAGTCTGGAGGAGTTGATACCGTCAAACCATGCCAAGTCTTATCTATATTCCATCTTCATCAGAACAGGG----------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaattgtgtggccttaatagaaagaaagcacatatgctttgacattatctccagTTGCAATGAGTCTTGAGGAGTTAATACCATCAAACTATGGGAAGTCACGTTTCTACGCAATCGCCATTAGAAGTGCATTAGCCATCTCTACTCTGCTCGT
ctttgac putative branch site (score: 4)
ttatctcc CT-rich tract
ttaatagaaagaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattttgtcataagcttattcataatataaactgaaaattgtgtggccttaatagaaagaaagcacatatgctttgacattatctccagTTGCAATGAGTCTTGAGGAGTTAATACCATCAAACTATGGGAAGTCACGTTTCTACGCAATCGCCATTAGAAGTGCATTAGCCATCTCTACTCTGCTCGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT