Sequence
atgc intronic sequence ATGC exonic sequence...tcttccattctcctagatgacatgatttcacatatcatgatcttaattatcactcagctcgtctgactaaagtaaacatgctttttcatgtgtcttgcagGTGGTCTTTGCTTGAAAAGTATAGCTGCAAAGCTTCAAAACTTCATCTCAAGCCCCGGAGATTCAAACTATTTATAGAGGCCTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G36960.3 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G36960.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g13790.1 (Oryza sativa), 3'ss of exon 4
tcttccattctcctagatgacatgatttcacatatcatgatctta-attatcactcagctcgtctgactaaagtaaacatgctttttcatgtgtcttgcagGTGGTCTTTGCTTGAAAAGTATAGCTGCAAAGCTTCAAAACTTCATCTCAAGCCCCGGAGATTCAAACTATTTATAGAGGCCTTG
| | | || || ||| || || | || | | | | | | | | || || | || || | || | |||||||||||| |||||||||| | |||||||| || |||||||| ||||| ||||| |||||||||||| || |||| || |||
taccgtttgttgcttattgtcattgcttttgatttgatcctatgatgcttccttttacactgcatggaaaactctcagatactaacttg-gttttatgcagGTGGTCTCTGCTTGAAAAATTTAGCTGCAGTGCATCAAAACTGCATCTGAAGCCTCGGAGATTCAAAACTTTCGTAGAAGCATTG
upper sequence: AT2G36960.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g56234.1 (Oryza sativa), 3'ss of exon 4
-tcttccattctcctagatgacatgatttcacatatcatgatcttaattatcactcagctcgtctgactaaagtaaacatgctttttcatgtgtcttgcagGTGGTCTTTGCTTGAAAAGTATAGCTGCAAAGCTTCAAAACTTCATCTCAAGCCCCGGAGATTCAAACTATTTATAGAGGCCTTG
| | | | | || ||| || || | || | | || | | | | || || || || | ||| |||||||||||| |||||||||| | |||||||| || |||||||| ||||| ||||| |||||||||||| ||| |||| || |||
atactgtctgttgtttattgtcattgcttttgatttgatctgatgttgtttcttttacattgcatggaaaactctccgatactgaatt-tgttctatgcagGTGGTCTCTGCTTGAAAAATTTAGCTGCAGTGCATCAAAACTGCATCTGAAGCCTCGGAGATTCAAAACATTCGTAGAAGCATTG
upper sequence: AT2G36960.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G23840.1 (Glycine max), 3'ss of exon 5
------tcttccattctcctagatgacatgatttcacatatcatgatcttaattatcactcagctcgtctgactaaagtaaacatgctttttcatgtgtcttgcagGTGGTCTTTGCTTGAAAAGTATAGCTGCAAAGCTTCAAAACTTCATCTCAAGCCCCGGAGATTCAAACTATTTATAGAGGCCTTG
| | | | || | || | | | |||| ||| | || || | | ||| |||| | | ||||| | || | | |||||||||||| | |||||||||||||||||||| ||||| ||||| || |||||||||||||| ||| | ||| |||| ||||||
tcatattatagtaatttcttgaataagaataggg-gtatattatgggagttttttgcattgaaagtttctcactagttt---ctcacttttacctgagac--acagGTGGTCTTTATTAGAAAAGTATAGCTGCAAAGCCTCAAAGCTTCACCTGAAGCCCCGGAGATTTAAAATTTTTTTAGAAGCCTTG
upper sequence: AT2G36960.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G05420.1 (Glycine max), 3'ss of exon 5
tcttccattctcctagatgacatgatttcacatatcatgatctta--attatcactcagctcgtctg-actaaagtaaacatgctttttcatgtgtcttgcagGTGGTCTTTGCTTGAAAAGTATAGCTGCAAAGCTTCAAAACTTCATCTCAAGCCCCGGAGATTCAAACTATTTATAGAGGCCTTG
| | ||| | || || | ||| | ||| || | | ||| | | | | || | || | ||||| |||||| | |||||||||||| | |||||||||||||||||||| ||||| ||||| || |||||||||||||| ||| | ||| |||| ||||||
tatcatattatggta-atttcttgaataagaataggggtatatcactattgttatgggagttttttgcgttgaaagtttctcacttttacatgtgac--acagGTGGTCTTTATTAGAAAAGTATAGCTGCAAAGCCTCAAAGCTTCACCTGAAGCCCCGGAGATTTAAAATTTTTTTAGAAGCCTTG
upper sequence: AT2G36960.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv08s0040g01460.t01 (Vitis vinifera), 3'ss of exon 4
tcttccattctcctagatgacatgatttcacatatcatgatcttaattatcactcagctcgtctgactaaagtaaacatgctttttc----atgtgtcttgcagGTGGTCTTTGCTTGAAAAGTATAGCTGCAAAGCTTCAAAACTTCATCTCAAGCCCCGGAGATTCAAACTATTTATAGAGGCCTTG
| | | | | ||| || | | | | | | | | || || ||| | | | | | || | | | | ||| || |||||||||||| || ||||| ||||||||||||||||||||||||||||| || |||||||| || || | || ||||| ||| ||
---tattgtatattggttgatgaacttgtaagtttaaacctttggagaaaattacaactgccatgattcagg-attcctgttctgtgtgtgacttgtgttacagGTGGTCTTTACTGGAAAAATATAGCTGCAAAGCTTCAAAACTTCATCTGAAACCCCGGAGGTTTAAGATTTTCATAGAAGCCCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attatcactcagctcgtctgactaaagtaaacatgctttttcatgtgtcttgcagGTGGTCTTTGCTTGAAAAGTATAGCTGCAAAGCTTCAAAACTTCATCTCAAGCCCCGGAGATTCAAACTATTTATAGAGGCCTTG
gactaaa putative branch site (score: 2)
taaagtaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttccattctcctagatgacatgatttcacatatcatgatcttaattatcactcagctcgtctgactaaagtaaacatgctttttcatgtgtcttgcagGTGGTCTTTGCTTGAAAAGTATAGCTGCAAAGCTTCAAAACTTCATCTCAAGCCCCGGAGATTCAAACTATTTATAGAGGCCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT