Sequence
atgc intronic sequence ATGC exonic sequencegtaagtcttatctttgtttcattacatgttgttatttaatcatttaaggctactaggtcttttcaatctaactttttctttctttccttttttgcagATGGGACTGATGAAAAAGCACCCTTCGATTGTTCCCTTCATGGTATACATCGCTAACGAGGAGAAACACTTGGAACGGTTTGCTGTCCGAGCCAAGTACA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G45090.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G45090.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G123544_T01 (Zea mays), 3'ss of exon 4
--------------------gtaagtcttatctttgtttcattacatgttgttatttaatcatttaaggctactaggtcttttcaatctaactttttctttctttccttttttgcagATGGGACTGATGAAAAAGCACCCTTCGATTGTTCCCTTCATGGTATACATCGCTAACGAGGAGAAACACTTGGAACGGTTTGCTGTCCGAGCCAAGTACA
| || | || || || | ||| | || ||| | ||| | || | | ||| | ||| | | ||||||||| | ||||| ||||| ||||| || | || ||||||||||||||| | ||||||||||||||| |||||||||||||||| || || |||||||
gtacgtatcagtcaagaaacgaaaatgagattgttcgtttagcctatgcttttttttttttttttttg-----cagatggcactga-ctatacgctacttctactgttgaccgacagATGGGATTAATGAAGAAGCATCCTTCCATAATACCATTCATGGTATACATCACAAACGAGGAGAAACACATGGAACGGTTTGCTGTGCGTGCGAAGTACA
upper sequence: AT3G45090.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S15_107V6.1 (Physcomitrella patens), 3'ss of exon 6
gtaagtcttatctttgtttcattacatgttgttattta----atcattta-aggctactaggtcttttcaatctaactttttctttctttccttttttgcagATGGGACTGATGAAAAAGCACCCTTCGATTGTTCCCTTCATGGTATACATCGCTAACGAGGAGAAACACTTGGAACGGTTTGCTGTCCGAGCCAAGTACA
|||| ||||| || | ||| || | ||| | | | ||| ||| | || | | || | | | | ||| ||||||||||||||||||| ||||| || ||||| | || |||||| |||||||||||||||| || ||| |||| ||||||| || || || |||||||
--aagttacttctttacctcgtagtcctccgtttttcatggtgtcactgatatgctgctaagagttcgaagatgattcttatttgagtctaaatttctgcagATGGGACTGATGAAGAAGCATCCATCGATCATACCGTTCATGATATACATCGCTAACGAAAGCAAGCACATGGAGAGGTTTGCAGTTCGTGCAAAGTACA
upper sequence: AT3G45090.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ30825 (Selaginella moellendorffii), 3'ss of exon 3
gtaagtcttatctttgtttcattacatgttgttatttaatcatttaaggctactaggtcttttcaatc-taactttttctttctttcctttt--ttgcagATGGGACTGATGAAAAAGCACCCTTCGATTGTTCCCTTCATGGTATACATCGCTAACGAGGAGAAACACTTGGAACGGTTTGCTGTCCGAGCCAAGTACA
|| | | | || || | || | || | | | ||||| || |||| | ||| | || | | | || |||||||| || |||| ||||| |||||||| | || || ||| | || || | |||||||||||||||||||| || ||||| ||||||||||||||||
---------------gtaacgtggctcgtgcttttagaaaaacttctctttcttgttttttttctctcctaacgtgctctcttttcctgtgtgtttccagATGGGCCTCATGAGGAAGCATCCTTCGATCATCCCGTTTATGATTTATATTTCCAACGAGGAGAAACACTTGGAGCGCTTTGCGGTCCGAGCCAAGTACA
upper sequence: AT3G45090.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ22815 (Selaginella moellendorffii), 3'ss of exon 4
gtaagtcttatctttgtttcattacatgttgttatttaatcatttaaggctactaggtcttttcaatctaactttttctttctttcctttt--ttgcagATGGGACTGATGAAAAAGCACCCTTCGATTGTTCCCTTCATGGTATACATCGCTAACGAGGAGAAACACTTGGAACGGTTTGCTGTCCGAGCCAAGTACA
| | || | ||| || | | | | | | || | ||||| | ||| | || | | | || |||||||| || |||| ||||| |||||||| | || || ||| | || || | |||||||||||||||||||| || ||||| ||||||||||||||||
-------------gtaacgtggctcgtgcttttagaaaaacttctcttttttttcttttttcttctcctaacgtgctctcttttcctgtgtgtttccagATGGGCCTCATGAGGAAGCATCCTTCGATCATCCCGTTTATGATTTATATTTCCAACGAGGAGAAACACTTGGAGCGCTTTGCGGTCCGAGCCAAGTACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttaaggctactaggtcttttcaatctaactttttctttctttccttttttgcagATGGGACTGATGAAAAAGCACCCTTCGATTGTTCCCTTCATGGTATACATCGCTAACGAGGAGAAACACTTGGAACGGTTTGCTGTCCGAGCCAAGTACA
atctaac putative branch site (score: 2)
tcttttcaatctaact CT-rich tract
taacttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtcttatctttgtttcattacatgttgttatttaatcatttaaggctactaggtcttttcaatctaactttttctttctttccttttttgcagATGGGACTGATGAAAAAGCACCCTTCGATTGTTCCCTTCATGGTATACATCGCTAACGAGGAGAAACACTTGGAACGGTTTGCTGTCCGAGCCAAGTACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA