Sequence
atgc intronic sequence ATGC exonic sequencegtaattgtgagtttctttatcctttagaatgtaaaagtttaggtttttaattgcttgtgtttgtgtgtgttgatttggatacagTATGTTGTGGTGGATTACCTTTGGTATAGAAAGAAAGTTGAAGGAGCTTATGTGGATTCTCTTGGGTTTGATGTGATTGATGAATGGGGAAGATTGCATC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G26380.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G26380.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G37760.2 (Glycine max), 3'ss of exon 2
--gtaattg-tgagtttctttatcctttaga--atgtaaaagtt--taggtttttaattgcttgtgtttgtgt--gtgttgatttgga----tacagTATGTTGTGGTGGATTACCTTTGGTATAGAAAGAAAGTTGAAGGAGCTTATGTGGATTCTCTTGGGTTTGATGTGATTGATGAATGGGGAAGATTGCATC
|| || |||| | || | | || | | ||||| ||| ||| ||| | | || || || | | |||||||||| ||||||||||| |||||||||| |||||| || || |||||| |||||||| || ||||||||||||||||||||||| || || ||
gtatagtttctgaggaaccatagctaatggatgagtttgaagttagtagtactttcattagatatagacatgataaccttccttcaaacccttgtagTATGTTGTAGTGGATTACCTCTGGTATAGAAGGAAAGTAGAGGGCGCTTATCATGATTCTCTCGGATTTGATGTGATTGATGAATGGGGGAGGATGGTTC
upper sequence: AT3G26380.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G30770.1 (Glycine max), 3'ss of exon 3
-----gtaattgtgagtttctttatcctttaga--atgtaaaagtttaggtttttaattgcttgtgtttgtgtgtgttgatttggat--------acagTATGTTGTGGTGGATTACCTTTGGTATAGAAAGAAAGTTGAAGGAGCTTATGTGGATTCTCTTGGGTTTGATGTGATTGATGAATGGGGAAGATTGCATC
| | || | | || | | | || || ||| || | | | ||| || | | || ||| || ||| ||| |||||||||||||| |||||||| |||||||| || |||||| ||||||||||| ||||| |||||||||||||||||||| ||| |
gtatagatactgcaaagaacaataacttatggatgatttaactgtgttagcagtgctttggttagatatagactgatttctttccatcaactcttgtagTTTGTCGTGGTGGATTACCTCTGGTATAGGAAGAAAGTCACGGGTGCTTATCCTGATTCTCTTGGATTTGACGTGATTGATGAATGGGGAAGGATGCTCC
upper sequence: AT3G26380.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G13960.1 (Glycine max), 3'ss of exon 2
---------------------gtaattgtgagtttctttatcctttagaatgtaaaagtttaggtttttaattgcttgtgtttgtgtgtgttgatttggatacagTATGTTGTGGTGGATTACCTTTGGTATAGAAAGAAAGTTGAAGGAGCTTATGTGGATTCTCTTGGGTTTGATGTGATTGATGAATGGGGAAGATTGCATC
||| | | | |||||| | | | | || |||| || | || ||| | | | | | | ||| ||| |||||||||||||| |||||||| |||||||| | || ||||| ||||||||||| ||||| ||||| |||||||||||||| || |
gtatagatactgcaaagaacaataacttatggatgatttatctgtgttagc---agtgctttggttagatatggactg-atttctttccatcaactct--tgtagTTTGTCGTGGTGGATTACCTCTGGTATAGGAAGAAAGTCAAGGGTGCTTACCCTGATTCTCTTGGATTTGACGTGATCGATGAATGGGGAAGGATGATCC
upper sequence: AT3G26380.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G43530.1 (Glycine max), 3'ss of exon 1
-------gtaatt-gtgagtttct--ttatcctttagaatgtaaaagtttaggtttttaa-ttgcttgtgtttgtgtgtgttgatttgg---atacagTATGTTGTGGTGGATTACCTTTGGTATAGAAAGAAAGTTGAAGGAGCTTATGTGGATTCTCTTGGGTTTGATGTGATTGATGAATGGGGAAGATTGCATC------
|| || || | || || | | | ||| | | | || ||| ||| | | | | | | | || || ||||||| | | ||||||||||| |||||||| || | | || | || |||||||||| |||||| |||||||| ||||||||||| ||| |
gtattgtatatttcatgcactcctacttttgaatcacaattcatatgaatatgttagtaaataaatagaaataacatatttcccttgaaaccatgcagTATGCTATTGTGGATTACCTCTGGTATAG---GAGTCTCAAGGGTG---ATAGCAATTCTCTTGGTTTTGATATGATTGATAAATGGGGAAGAATGCTCCCTGACC
upper sequence: AT3G26380.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv01s0137g00630.t01 (Vitis vinifera), 3'ss of exon 2
-----gtaattgtgagtttctttatcctttagaatgtaaaag-----------tttaggttt-----ttaattgcttgtgtttgtgtgtgttgatttggatacagTATGTTGTGGTGGATTACCTTTGGTATAGAAAGAAAGTTGAAGGAGCTTATGTGGATTCTCTTGGGTTTGATGTGATTGATGAATGGGGAAGATTGCATC
|| | | || | | | | || || | ||| ||| |||| | | | | | | | | ||| | |||||||||||| | ||||||||||||||||||| || || || || ||||| |||||| | || |||||||||||||| ||||||| || || ||
gtacaaccatctggtacatgttcttatatcaataggtgaagggacgacttctctttgaatttgaggcttaactaactttcctcatttcgttgtaattgcttgcagTATGTTGTGATTGATTACCTTTGGTATAGAAGAAAGGTGGAGGGTGCTTACACTGATTCTTTAGGATTTGATGTGATTGACAAATGGGGGAGGATGGCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtaaaagtttaggtttttaattgcttgtgtttgtgtgtgttgatttggatacagTATGTTGTGGTGGATTACCTTTGGTATAGAAAGAAAGTTGAAGGAGCTTATGTGGATTCTCTTGGGTTTGATGTGATTGATGAATGGGGAAGATTGCATC
tttaggtttttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattgtgagtttctttatcctttagaatgtaaaagtttaggtttttaattgcttgtgtttgtgtgtgttgatttggatacagTATGTTGTGGTGGATTACCTTTGGTATAGAAAGAAAGTTGAAGGAGCTTATGTGGATTCTCTTGGGTTTGATGTGATTGATGAATGGGGAAGATTGCATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA