Sequence
atgc intronic sequence ATGC exonic sequence...ctctgttagatctcctatcttggtttattggtggattcttcatatttcattatcttgtttacgttgtaatgtgattggtttggggatgaaacttatgcagGGTCTAATGAAAAACCATGAAGAGATAGTAGAATACTTCAAAACCCGAGGCGTGTCTGCTATTTTCCTCTTTAGAAGAAACCTCTTGCGCCGGATGATTT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G15730.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G15730.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g57550.2 (Oryza sativa), 3'ss of exon 3
ctctgttagatctcctat-cttggtttattggtggattcttcatatttcattatcttgtttacgttgtaa--tgtgattggtttggggatgaaacttatgcagGGTCTAATGAAAAACCATGAAGAGATAGTAGAATACTTCAAAACCCGAGGCGTGTCTGCTATTTTCCTCTTTAGAAGAAAC-CTCTTGCGCCGGATGATTT
| | | | || | || | | | || | | | || | | || |||| || | ||| |||| | | | || || || |||||||||| || || | ||||||||| |||| ||||||||||| ||||||||||||| || ||||| || |||||||| |||| || ||| |
-tttctcaatcctgcgattcaaaggggcctagtttactgcacctactctgacacctattttaatttattttctgttattgttatcttggtgtaaatt--gcagGGTCTAGTGCAACATCATGAAGAGGTAGTTGAATACTTCAACCGAAGAGGCGTGTCTGCAATCTTCCTTTTAAGAAGAAATACTCTCCAGCGTTATGTCT-
upper sequence: AT2G15730.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G142507_T01 (Zea mays), 3'ss of exon 3
--ctctgttagatctcctatcttggtttattggtgga---ttcttcatatttcattatcttgtttacgttgtaatgtgattggtttggggatgaaacttatgcagGGTCTAATGAAAAACCATGAAGAGATAGTAGAATACTTCAAAACCCGAGGCGTGTCTGCTATTTTCCTCTTTAGAAGAAACCTCTTGCGCCGGATGATTT
| | | | | | || | ||| | | |||| || | | |||| |||| | || || || || | | | ||||| |||| ||||||||||||| ||||| |||||||||| ||||||||||| | || || || || ||||| || | |||||||| || | || || | |
ctttgtatcacgattgtttgtgcggctaatttccaaagatatattcagcttccttgatctgttttatctagtgatatgcttattctag---tgaaaattat--agGGTCTAATGAAGCACCATCAAGAGATAGTTGAATACTTCAACCGAAGGGGTGTTTCCGCAATTTTTCTACTAAGAAGAAATCTTCTTCGGCGTTACGTCT
upper sequence: AT2G15730.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G142507_T02 (Zea mays), 3'ss of exon 4
--------------ctctgttagatctcctatcttggtttattggtggat---tcttcatatttcattatcttgtttacgttgtaatgtgattggtttggggatgaaacttatgcagGGTCTAATGAAAAACCATGAAGAGATAGTAGAATACTTCAAAACCCGAGGCGTGTCTGCTATTTTCCTCTTTAGAAGAAACCTCTTGCGCCGGATGATTT
| | | | | | || | ||| | | |||| || | | |||| |||| | || || || || | | | ||||| |||| ||||||||||||| ||||| |||||||||| ||||||||||| | || || || || ||||| || | |||||||| || | |
catagaactattctttgtatcacgattgtttgtgcggctaatttccaaagatatattcagcttccttgatctgttttatctagtgatatgcttattctag- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcattatcttgtttacgttgtaatgtgattggtttggggatgaaacttatgcagGGTCTAATGAAAAACCATGAAGAGATAGTAGAATACTTCAAAACCCGAGGCGTGTCTGCTATTTTCCTCTTTAGAAGAAACCTCTTGCGCCGGATGATTT
aaacttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctctgttagatctcctatcttggtttattggtggattcttcatatttcattatcttgtttacgttgtaatgtgattggtttggggatgaaacttatgcagGGTCTAATGAAAAACCATGAAGAGATAGTAGAATACTTCAAAACCCGAGGCGTGTCTGCTATTTTCCTCTTTAGAAGAAACCTCTTGCGCCGGATGATTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - -atctcct
- - - - - - - - - - -ggtttat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtttgg