Sequence
atgc intronic sequence ATGC exonic sequencegtatgtctactttatctttatagtaaatctgtaatcattttctcatgtaaatgctgtgtgaaaggcatctgatgtggtttctgttgtccaaataaaatcttacagAGGCAAAGACCACTATTGATTGTTTCTGAAGATGTGGAAAGTGATGCTCTTGCAACTCTTATCCTTAACAAGCTCCGTGCCGGAATTAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G23990.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 8
gtatgtctactttatctttatagtaaatctgtaatcattttctcatgtaaatgctgtgtgaaaggcatctgatgtggtttctgttgtccaaataaaatcttacagAGGCAAAGACCACTATTGATTGTTTCTGAAGATGTGGAAAGTGATGCTCTTGCAACTCTTATCCTTAACAAGCTCCGTGCCGGAATTAAG
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----------------------gtgag-cagtg-ccattcacttttgcatttgacttttaaaa--taattgatat--ttgctgacacctacata----tctccagAGACAAAGACCTTTATTGATTATTGCCGAGGATGTGGAAAGTGATGCACTTGCAACTCTTATTCTAAATAAGCTTCGGGCCGGAATTAAG
upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 8
gtatgtctactttatctttatagtaaatctgtaatcattttctcatgtaaatgctgtgtgaaaggcatctgatgtggtttctgttgtccaaataaaatcttacagAGGCAAAGACCACTATTGATTGTTTCTGAAGATGTGGAAAGTGATGCTCTTGCAACTCTTATCCTTAACAAGCTCCGTGCCGGAATTAAG
| | | | | | | | | || | || | |||| | | ||| | | || | ||||| |||||| | |||||||| || | || ||||||||||||||||| |||||||||||||| || || ||||| || || |||||||||
--------------------------gtgagcagtggcatccacttttgcatttgacttctaaaataattgatattgg--ctgacacctactta----tctccagAGACAAAGATCTTTATTGATTATTGCCGAGGATGTGGAAAGTGATGCACTTGCAACTCTTATTCTAAATAAGCTTCGGGCTGGAATTAAG
upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 8
gtatgtctactttatctttatagtaaatctgtaatcattttctcatgtaaatgctgtgtgaaaggcatctgatgtggtttctgttgtccaaataaaatcttacagAGGCAAAGACCACTATTGATTGTTTCTGAAGATGTGGAAAGTGATGCTCTTGCAACTCTTATCCTTAACAAGCTCCGTGCCGGAATTAAG
| ||| | ||| ||| | || | || | | || || | || | | | | ||||| ||||| || || ||||||| |||| ||||||||||||||||| |||||||||||||| || || || || ||||| ||||| |||
-------------------gtgagcaatgc-cattcactttattttgcactgactttttaaa---tattggtatcggctaacacttctttattgc-------cagAGACAAAGGCCTTTACTGATTGTCGCTGAGGATGTGGAAAGTGATGCCCTTGCAACTCTTATTCTAAATAAACTTCGTGCTGGAATCAAG
upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 8
gtatgtctactttatctttatagtaaatctgtaatcattttctcatgtaaatgctgtgtgaaaggcatctgatgtggtttctgttgtccaaataaaatctta----cagAGGCAAAGACCACTATTGATTGTTTCTGAAGATGTGGAAAGTGATGCTCTTGCAACTCTTATCCTTAACAAGCTCCGTGCCGGAATTAAG
|| | || | || || | | | | | | | ||| | | || | ||| | || | ||| ||||| |||||| | |||||||||| | || ||||||||||||||||| |||||||||||||| || || || || ||||| ||||| |||
------------------------------gtgagcaatgtc--attcacttcattttccattgacttcttaaata-ttggtattggctaa-cacttctttattgccagAGACAAAGATCTTTATTGATTGTCGCCGAGGATGTGGAAAGTGATGCCCTTGCAACTCTTATTCTAAATAAACTTCGTGCTGGAATCAAG
upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 8
gtatgtctactttatctttatagtaaatctgtaatcattttctcatgtaaatgctgtgtgaaaggcatctgatgtggtttctgttgtccaaataaaatcttacagAGGCAAAGACCACTATTGATTGTTTCTGAAGATGTGGAAAGTGATGCTCTTGCAACTCTTATCCTTAACAAGCTCCGTGCCGGAATTAAG
|| ||| ||| | ||| | | || || | | | | ||||| | | ||| | | | | |||| || || || || |||||||| |||||||||||||||| || || || || |||||||| || || ||||| ||||| ||||| |||
-----------------gta-agtgggtctttggtcaat--cggattcaattagatctttacatgcatcaagtttagttgactacattgttcttgccttattcagACTCAGAGGCCTTTACTGATTGTTGCTGAAGATGTGGAAAGCGAAGCACTGGCCACTCTTATTCTAAATAAGCTTCGTGCTGGAATCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgctgtgtgaaaggcatctgatgtggtttctgttgtccaaataaaatcttacagAGGCAAAGACCACTATTGATTGTTTCTGAAGATGTGGAAAGTGATGCTCTTGCAACTCTTATCCTTAACAAGCTCCGTGCCGGAATTAAG
atctgat putative branch site (score: 4)
aaataaaatcttaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtctactttatctttatagtaaatctgtaatcattttctcatgtaaatgctgtgtgaaaggcatctgatgtggtttctgttgtccaaataaaatcttacagAGGCAAAGACCACTATTGATTGTTTCTGAAGATGTGGAAAGTGATGCTCTTGCAACTCTTATCCTTAACAAGCTCCGTGCCGGAATTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT