Sequence
atgc intronic sequence ATGC exonic sequencegtaatgtatctgtgttgcattctcctgtttgtcacagacaatatagttgagatcctggagtcctagaatactactggcttactttacttatcgtacgtgttaattttgcagGAAATTGACTTGAAGAATCACAAATGGGGGCATTACTTCATATGCGC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G06580.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G06580.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G03990.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------------------gtaatgtatctgtgttgcattctcctgtttgtcacagacaatatagttgagatcctggagtcctagaatactactggcttactttacttatcgtacgtgttaattttgcagGAAATTGACTTGAAGAATCACAAATGGGGGCATTACTTCATATGCGC
| | | ||| | ||| | | ||| | | | | | | ||||| || | | | || | | || | | | ||||| | |||||||||| ||||||||||| ||||||||||| ||||| || ||||| |
gtggatcctccaatccttttttgttttaaatactactgtataacaatgaagaccgttttcagaaatgtgtgtttaatatttttttctttatgattcattttgtcaataagatcgtgctatgttttgttggtaatttgatctgatattctttggttgtgtttttcatgcagGAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATATGTGG
upper sequence: AT3G06580.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G36610.1 (Glycine max), 3'ss of exon 2
----------------------------------gtaatgtatctgtgttg--cattctc---ctgtttgtcacagacaatatagttgagatcc----tggagtcctagaatactactggctt-actttactta--tcgtacgtgttaattttgcagGAAATTGACTTGAAGAATCACAAATGGGGGCATTACTTCATATGCGC
||| | | || | | || || ||| ||| | | | || || ||| | || || | | | || | |||| || | | ||||| | |||||||||| ||||||||||| ||||||||||| ||||| || || || |
gtggatcctccaatccttttctgtttcaaatattgtataacaacaatgaagaccgttttcagaatgtgtgtttaatattctttatttatgattcattttgtcaatctgttttgttggtaatttgattttattttctttggttgtgtttttcatgcagGAAATCGACTTGAAGAACCACAAATGGGGACATTATTTTATTTGTGG
upper sequence: AT3G06580.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv05s0077g00690.t01 (Vitis vinifera), 3'ss of exon 2
-gtaatgtatctgtgttgcattctcctgtttgtcacagacaatatagttgagatcctggagtcctagaatactactggcttactttacttatcgtacgtgttaattttgcagGAAATTGACTTGAAGAATCACAAATGGGGGCATTACTTCATATGCGC
| || | | | | | || ||||| | || | || | | || || ||| ||| | | || | | || || ||||||||||||| || ||||||||||||||||| ||||| ||||| ||||
aacttaggctcagggacttaatgtgctctttgtaattttcatttctatttatgacaaggcagtgtaaaatg--------ttaaatcatttggcattgttgcta----tgcagGAAATTGATTTAAAGAATCACAAATGGGGTCATTATTTCATTTGCGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggagtcctagaatactactggcttactttacttatcgtacgtgttaattttgcagGAAATTGACTTGAAGAATCACAAATGGGGGCATTACTTCATATGCGC
tgttaat putative branch site (score: 3)
tgttaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgtatctgtgttgcattctcctgtttgtcacagacaatatagttgagatcctggagtcctagaatactactggcttactttacttatcgtacgtgttaattttgcagGAAATTGACTTGAAGAATCACAAATGGGGGCATTACTTCATATGCGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA