Sequence
atgc intronic sequence ATGC exonic sequence...tttttcgcattctcaaagaaagttcgaaagttgatagtggcatgttatgtttatttatttcggtcagtagttgaaattactgacgataagtttctttcagGGAATGAGTCAACTTGAGTTGGAAGACCAAGTACAAGATGACCTAAAGCGTGCAACTGGAGAATTCACCAAGGACGAGAACGATGCTAACAAACTTAACC
Basic information
| species | Arabidopsis thaliana |
| transcript | AT4G31480.1 |
| intron # | 2 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G31480.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os11g07280.1 (Oryza sativa), 3'ss of exon 1
---tttttcgcattctcaaagaaagttcgaaagttgatagtggcatgttatgtttatttat--ttcggtcagtagttgaaattactgacgataagtttctttcagGGAATGAGTCAACTTGAGTTGGAAGACCAAGTACAAGATGACCTAAAGCGTGCAACTGGAGAATTCACCAAGGACGAGAACGATGCTAACAAACTTAACC
| || || | | | || || | | | | ||| || | | || | | || |||| ||||||||||| ||||||||||||||||| ||| |||||||| | ||| ||| ||||| ||||| || || || | | || || |||| ||| || |
tggactgacgtgttactatgttactgttttttcctgtctagtatttgaaaagatggcctgcggttctttcttcactaaaacatgccattcat-----tcttgcagGGAATGAGCCAACTTGAGTTGGAAGATGCAGTCCAAGATGATTTGAAGGCTGCTACTGGTGAATTTACAAAAGATGCAGATGACGCAAACAGACTGAATC
upper sequence: AT4G31480.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g17430.1 (Oryza sativa), 3'ss of exon 1
tttttcgcattctcaaagaaagttcgaaagttgatagtggcatgttatgt------ttatttatttcggtcagtagttgaaattactgacgataagtttctttcagGGAATGAGTCAACTTGAGTTGGAAGACCAAGTACAAGATGACCTAAAGCGTGCAACTGGAGAATTCACCAAGGACGAGAACGATGCTAACAAACTTAACC
| || ||| || | || | ||| ||||| | |||||||| || || | |||| |||| | |||| | |||| |||||||| |||||||||||||| |||| ||||||||| | ||| ||||||||| | || || ||||| | | ||||| |||| ||||||||
--ggtgtcaatctggttgataacctttcctttcctgagtgcaagttatatgctgccttatttatgtctccttgttagtaaaatg--tgacatt--gtttttcctagGGCATGAGTCAGCTTGAGTTGGAAGATGAAGTTCAAGATGACTTGAAGGCTGCAACTGGTGGGTTTACTAAGGATGCATATGATGCAAACAGACTTAACC
upper sequence: AT4G31480.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv04s0008g02320.t01 (Vitis vinifera), 3'ss of exon 1
--tttttcgcattctcaaagaaagttcgaaagttgatagtggcatgttatgtttatttatttcggtcagtagttgaaattactgacgataagtttctttcagGGAATGAGTCAACTTGAGTTGGAAGACCAAGTACAAGATGACCTAAAGCGTGCAACTGGAGAATTCACCAAGGACGAGAACGATGCTAACAAACTTAACC
||| | | | || || | || | ||| |||| | | |||| || | || | || || | ||| ||||| |||||||| || ||||||||||| |||| |||||||| |||| |||||||||||||| |||| |||||| | | | ||||| || || || ||||
tatttattttcctttatctttgaggtcaaggttttggtttttcatag-atgtgtgtg-atttaaatctccactttgtttccctaactagcttcaacttccagGGCATGAGTCAGCTGGAGTTGGAAGATGAAGTCCAAGATGATTTAAAACGTGCAACTGGAGAGTTCATCAAGGATGGGGATGATGCAAATAAGCTAAACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgtttatttatttcggtcagtagttgaaattactgacgataagtttctttcagGGAATGAGTCAACTTGAGTTGGAAGACCAAGTACAAGATGACCTAAAGCGTGCAACTGGAGAATTCACCAAGGACGAGAACGATGCTAACAAACTTAACC
tactgac putative branch site (score: 1)
tttctttc putative PPT
ttatttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttttcgcattctcaaagaaagttcgaaagttgatagtggcatgttatgtttatttatttcggtcagtagttgaaattactgacgataagtttctttcagGGAATGAGTCAACTTGAGTTGGAAGACCAAGTACAAGATGACCTAAAGCGTGCAACTGGAGAATTCACCAAGGACGAGAACGATGCTAACAAACTTAACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
