Sequence
atgc intronic sequence ATGC exonic sequence...ctcactttttcttgatgagattataccgttgatggttagttacatataatgaatgaattctcagctattaacctattaaaattttatttcactgaaacagTGAGACTGTGAAGTTTGGCCATGTAACCTTCTTCTGGAATGGCAACCGCTCTGGATATTTCAATGAAAAGTTAGAAGAGTACGTTGAGATTCCAAGTGAT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G08590.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os05g40420.1 (Oryza sativa), 3'ss of exon 6
ctcactttttcttgatgagattataccgttg-atggttagttacatataa-tgaatgaattctcagctattaacctattaaaattttatttcactgaaacagTGAGACTGTGAAGTTTGGCCATGTAACCTTCTTCTGGAATGGCAACCGCTCTGGATATTTCAATGAAAAGTTAGAAGAGTACGTTGAGATTCCAAGTGAT
| | | || | | || |||| | || | || | ||| | | |||| || || || | || || | | || |||||| ||||||||||| |||||||| || || ||||||||||| |||||||||||||| ||| |||||| |||||||| || || || || |||||
agtaacataattggaaaataacttatagttgcactgtaatttctttctaactctaccaatttgtccaactttacttactgaa--ttgactcatttgttccagTGAAACTGTGAAGTTCGGCCATGTCACATTTTTCTGGAATGGAAACCGCTCTGGATACTTCGATGAAACAAAGGAAGAGTATGTGGAAATCCCTAGTGAC
upper sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g60190.1 (Oryza sativa), 3'ss of exon 6
---------ctcactttttcttgatgagattataccgttgatggttagttacatataatgaatgaattctcagctattaacctattaaaattttatttcactgaaacagTGAGACTGTGAAGTTTGGCCATGTAACCTTCTTCTGGAATGGCAACCGCTCTGGATATTTCAATGAAAAGTTAGAAGAGTACGTTGAGATTCCAAGTGAT
| | || | || | ||||| || | | | || | || | | | |||| ||| | ||| ||| | |||||||||| ||||||||||||||||| || || |||||||| || ||||| |||||||| || |||||| |||||||||||||| ||||| ||||||
attgtggagtttatagttgtctattgtgcttatataa--aataatattctgtct-tagtccatttgtatttatgctgtaactcattga---tttgttttttt---acagTGAGACAGTGAAGTTTGGCCATGTCACATTTTTCTGGAACGGAAACCGATCTGGATACTTTGATGAAACTAAGGAAGAGTACGTTGAAATTCCTAGTGAT
upper sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G003385_T02 (Zea mays), 3'ss of exon 6
ctcactttttc-ttgatgagattataccgttgatggttagttacatataatgaatgaattctcagctattaacctat--taaaatttt-atttcactgaaacagTGAGACTGTGAAGTTTGGCCATGTAACCTTCTTCTGGAATGGCAACCGCTCTGGATATTTCAATGAAAAGTTAGAAGAGTACGTTGAGATTCCAAGTGAT
| | || |||||| || || | || | | | | ||| | | | | | || | || || ||| | || || |||| || |||||||||| ||||| ||||||||||| || || ||||||||||| |||||||| ||||| || |||||| |||||||| || || |||| |||||
--gattgactcattgatgt-atcatccttgtgcttgc-aatggcatttcttcattttttcttcttatttttacttatgctgcaacattgatttgtgtgtgacagTGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTCGGGATACTTTGATGAAACTAAGGAAGAGTATGTAGAAGTTCCTAGTGAC
upper sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 5
ctcactttttcttgatgagatta--taccgttgatggttagttacata--taatgaatgaattctcagctattaacctattaaaattttatttcactgaaacagTGAGACTGTGAAGTTTGGCCATGTAACCTTCTTCTGGAATGGCAACCGCTCTGGATATTTCAATGAAAAGTTAGAAGAGTACGTTGAGATTCCAAGTGAT
| | | ||| | | ||| || || || | ||| || | | ||||| | || | || | | ||||| || |||||||||||||| || ||||| || || || |||||||||||||| ||||||||||| ||||| ||| | | || || ||||| || || ||||| |||||
tttgcaacattttgtttaccttaagaactcttcattatctagtacttatctgttaaatgatggccatcatagtcacttgtatgaatttctttgtc----aacagTGAGACTGTTAAATTTGGTCACGTCACATTCTTCTGGAATGGAAACCGCTCTGGGTATTTTAATTCAGAATTGGAGGAGTATGTGGAAATTCCCAGTGAC
upper sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0056g00200.t01 (Vitis vinifera), 3'ss of exon 5
--ctcactttttcttgatgag-attataccgttgatggttagtt-acatataatgaatga-attctcagctattaacctattaaaattttatttcactgaaacagTGAGACTGTGAAGTTTGGCCATGTAACCTTCTTCTGGAATGGCAACCGCTCTGGATATTTCAATGAAAAGTTAGAAGAGTACGTTGAGATTCCAAGTGAT
| |||| || | || || || | | | || || | | ||| |||||| ||| | | || | ||| | | || |||||||||||||| || ||||| ||||| ||||| ||||||||||| || ||||| || ||||| || || | || || || || || ||||| ||||||
gagggtttatttcatggttagtgataggttctttttcttcaattcaccagtttttaataccattctctgctgtctaactct-----ctttttctttctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTCAGGGTATTTTGATCCAAGTATGGAGGAATATGTAGAAATTCCCAGTGAT
upper sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ26058 (Selaginella moellendorffii), 3'ss of exon 5
ctcactttttcttgatgagattataccgttgatggttagttacatataatgaatgaattctcagctattaacctattaaaattttatttcactgaaacagTGAGACTGTGAAGTTTGGCCATGTAACCTTCTTCTGGAATGGCAACCGCTCTGGATATTTCAATGAAAAGTTAGAAGAGTACGTTGAGATTCCAAGTGAT
|| || | |||| || || | | || | | | || || ||| |||||||||||||| || ||||| || || |||||||| || ||| | ||||| ||||| || | ||| | |||||||||||||||||||| || |||
-------------------------------------------gtaagatttactc-ttctttgcaatgtatccgctactaaactgtctctttg---cagCGAGACTGTGAAGTTCGGGCATGTCACATTTTTCTGGAACGGAAACAGGTCTGGCTATTTTGATAACAAGCTGGAAGAGTACGTTGAGATTCCTAGCGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataatgaatgaattctcagctattaacctattaaaattttatttcactgaaacagTGAGACTGTGAAGTTTGGCCATGTAACCTTCTTCTGGAATGGCAACCGCTCTGGATATTTCAATGAAAAGTTAGAAGAGTACGTTGAGATTCCAAGTGAT
tattaac putative branch site (score: 1)
tttcact putative PPT
tattaacctattaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctcactttttcttgatgagattataccgttgatggttagttacatataatgaatgaattctcagctattaacctattaaaattttatttcactgaaacagTGAGACTGTGAAGTTTGGCCATGTAACCTTCTTCTGGAATGGCAACCGCTCTGGATATTTCAATGAAAAGTTAGAAGAGTACGTTGAGATTCCAAGTGAT
- - - - - - - - - - - - - - - - - - - - -acatata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attaaaa