Sequence
atgc intronic sequence ATGC exonic sequencegttacacttactttattatctattggctccttcatatcttcatataatgtctccttcttgcacctaattgtatatgaaccaaaaacagAATGATTTGGTTCACGGTTGGGGTCTTGACTTTGCACTGAGAAGATGTGTTGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G24570.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G24570.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 11
--------------------gttacacttacttta----------ttatctattggctccttcatatcttcatataatgtctccttcttgcaccta-----attgtatatgaacca------aaaacagAATGATTTGGTTCACGGTTGGGGTCTTGACTTTGCACTGAGAAGATGTGTTGAG
|| | || ||||| || ||| | | | || || | | | ||| |||| || ||| | || |||| | |||||||| ||||| ||||| ||||||||||| ||||| || |||||||||||||||
gttgactgattaatcctgaagtcctaattgctttaaaagatgcccttgactagttgttttttatgatgcatccttgacaagttctttaagcacttagtaaaattatggttgtaccacttgacattgcagAATGACTTGGTCCACGGGTGGGGTCTTGATTTTGCTCTTAGAAGATGTGTTGAG
upper sequence: AT1G24570.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA08G14040.1 (Glycine max), 3'ss of exon 11
------------------gttacacttactttattatctattggctccttcatatcttcatataatgtctcctt-----cttgcacctaattgtatatgaacca--------aaaacagAATGATTTGGTTCACGGTTGGGGTCTTGACTTTGCACTGAGAAGATGTGTTGAG
|| ||| | || || | | || || ||| || ||| || || || ||||| | || ||| | |||||||||||||| || || ||||| ||||| ||||| || |||| ||||||||||
gttaaatgttttctctttattctttttaaatatccattggttagttgtttaatgtctgtttaagcgcactcgttaaagtctaacaattaattatgattgttccattctgggcatttcagAATGATTTGGTCCATGGCTGGGGCCTTGATTTTGCTCTTAGAAAATGTGTTGAG
upper sequence: AT1G24570.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA11G37770.1 (Glycine max), 3'ss of exon 11
gtt-acactta--ctttattatctattggctccttcatatcttcat-ataatgtctccttcttgcacct-----aattgtatatgaaccaa-----aaacagAATGATTTGGTTCACGGTTGGGGTCTTGACTTTGCACTGAGAAGATGTGTTGAG
||| || ||| | | | ||| | | | | || | | | |||| | | ||| |||| | |||| | || |||| | |||||||| ||||| || || ||||||||||| ||||| || |||| ||||||||||
gttgactgttaatcctaaagtcctaattgttttaaaagatgtccttgataagttgttctttaagcacttggtaaaattatgattgtaccacttgacatgcagAATGACTTGGTCCATGGGTGGGGTCTTGATTTTGCTCTTAGAAAATGTGTTGAG
upper sequence: AT1G24570.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA05G30830.1 (Glycine max), 3'ss of exon 11
---------------gttacacttactttattatctattggctccttcatatct--tcatataat-gtctccttcttgcacctaattgtatatgaacca--------aaaacagAATGATTTGGTTCACGGTTGGGGTCTTGACTTTGCACTGAGAAGATGTGTTGAG
||| ||| || | |||| ||||| | || || ||| | || | | || ||| || ||||| | || | || | |||||||||||||| || || ||||| ||||| ||||| || |||| ||||||||||
gttaaatgtttactctttattcttttttaaatatccattggttgtttaatgtctgtttatgcactcgttagagtctaacaattaattatgattgtaacattctgggcatttcagAATGATTTGGTCCATGGCTGGGGCCTTGATTTTGCTCTTAGAAAATGTGTTGAG
upper sequence: AT1G24570.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 11
-----gttacacttactttattatctattggctccttcatatcttcatataatgtctccttcttgcacctaattgtatatgaaccaaaa--acagAATGATTTGGTTCACGGTTGGGGTCTTGACTTTGCACTGAGAAGATGTGTTGAG
|| || | || | || | | || | || || | | | | | | ||| || | | || |||||||| |||| || |||||||||||||||||||| || ||||||||||| |||
gtatatatatcctcaaatttagaattagtaagttctcagttgctccagttgacctgttactatcaagtttaagtgcctttctgtgggaattgcagAATGACCTGGTACATGGTTGGGGTCTTGACTTTGCTCTCAGAAGATGTGTAGAG
upper sequence: AT1G24570.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv00s0187g00030.t01 (Vitis vinifera), 3'ss of exon 6
-----gttacacttactttattatctattggctccttcatatcttcatataatgtctccttcttgcacctaattgtatatgaaccaaaa--acagAATGATTTGGTTCACGGTTGGGGTCTTGACTTTGCACTGAGAAGATGTGTTGAG
|| || | || | || | | || | || || | | | | | | ||| ||| | | || |||||||| ||| || |||||||||||||||||||| || ||||||||||| |||
gtatatctatcctcaaatttagaattagtaagttctcagttgctccaattgacctgttactatcaagtttaagtgtctttctgtgggaattgcagAATGACCTGGCACATGGTTGGGGTCTTGACTTTGCTCTTAGAAGATGTGTAGAG
upper sequence: AT1G24570.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv13s0106g00570.t01 (Vitis vinifera), 3'ss of exon 2
-----gttacacttactttattatctattggctccttcatatcttcatataatgtctccttcttgcacctaattgtatatgaaccaaaa--acagAATGATTTGGTTCACGGTTGGGGTCTTGACTTTGCACTGAGAAGATGTGTTGAG
|| || | || | || | | || | || || | | | | | | ||| || | | | || ||||||||| |||| || |||||||||||| ||||||| || ||||||||||| |||
gtatatatatcctcaaatttagaattagtaagttctcagttgctccagttgacctgttactatcaagtttaagtgcctttctatgggaattacagAATGACCTGGTACATGGTTGGGGTCTTAACTTTGCTCTTAGAAGATGTGTAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatcttcatataatgtctccttcttgcacctaattgtatatgaaccaaaaacagAATGATTTGGTTCACGGTTGGGGTCTTGACTTTGCACTGAGAAGATGTGTTGAG
acctaat putative branch site (score: 3)
taattgtatatgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttacacttactttattatctattggctccttcatatcttcatataatgtctccttcttgcacctaattgtatatgaaccaaaaacagAATGATTTGGTTCACGGTTGGGGTCTTGACTTTGCACTGAGAAGATGTGTTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG