Sequence
atgc intronic sequence ATGC exonic sequencegtaggcaatgcttgtgagatcttgtatgaatgtcatgccttgtctagtctagtttagaaatgaatccaatttttgctttccttccttgcagAATGATTGGAGTGTTGTTAAACGAGGTTGGGATGCACAAGTCCTTGGGGAAGCTCCCCACAAATTTAAAAGCGCTCTTGAAGCAGTTAAGACACTGAGGG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G08590.2 |
intron # | 3 |
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 3
lower sequence: LOC_Os05g40420.1 (Oryza sativa), 3'ss of exon 5
-----------------------------------------------------------gtaggcaatgcttgtgagatcttgtatgaatgtcatgccttgtctagtctagtttagaaatgaatccaatttttgctttcctt--ccttgcagAATGATTGGAGTGTTGTTAAACGAGGTTGGGATGCACAAGTCCTTGGGGAAGCTCCCCACAAATTTAAAAGCGCTCTTGAAGCAGTTAAGACACTGAGGG
| | | | || | | || | | | | | || ||| | | || | | | || || | || ||||||||||| ||| |||||||||||| || |||||||| || || ||||| ||||| || ||||| || ||| |||| ||||||| || || ||||| ||
gtatgaataccctccttcctctctgtcagtttggattgctcatatcttatctctcagctgcattctgtttttattgcaactctttctgacttgggataatatgta--ctaatggaagtattgaactatttgtttaatatctcaattttgcagAATGACTGGGATGTTGTTAAACGTGGATGGGATGCTCAGGTGCTTGGAGAAGCACCTCACAAGTTCCAAAACGCTGTTGAAGCTGTGAAAACACTCCGGT
upper sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM5G833389_T02 (Zea mays), 3'ss of exon 5
gtaggcaatgcttgtgagatcttgtatgaatgtcatgccttgtctagtctagtttagaaatgaatccaatttttgctttccttccttgcagAATGATTGGAGTGTTGTTAAACGAGGTTGGGATGCACAAGTCCTTGGGGAAGCTCCCCACAAATTTAAAAGCGCTCTTGAAGCAGTTAAGACACTGAGGG
|| || | || | || | || | ||| | ||||| | | || | | | ||||| ||| | ||| |||||||| ||| ||| |||||||| ||||||||||| ||||| ||||| ||||| ||| ||||||| ||||| || ||||| || || || |||||||| |
gtgaacactttttccc-gttcaagcatcagtgtt---cactgtctggc--accttggcttacagttttattttg--tttaatatcttccagAATGACTGGGATGTGGTTAAACGTGGTTGGGATGCCCAAGTGCTTGGAGAAGCACCCTACAAATTCAAAAGTGCACTTGAGGCTGTGAAAACACTGAGAG
upper sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 4
-----gtaggcaatgcttgtgagatcttgtatgaatgtcatgccttgtctagtctagtttagaaatgaatccaatttttgctttccttc------cttgcagAATGATTGGAGTGTTGTTAAACGAGGTTGGGATGCACAAGTCCTTGGGGAAGCTCCCCACAAATTTAAAAGCGCTCTTGAAGCAGTTAAGACACTGAGGG
| | ||||| | | | || ||| | | || | | |||| | | | || || || || | | | |||||||| |||| |||||| |||||||| |||||||| ||||| ||||| ||||| || | || |||| || ||||||||||| || |||| |||||||
tttgacaaagaaatgcaaaaaaattgctttaaaaatttgaaatgttttt--atttagtgcatatttctatttaagattcactgttttcaaaacaatctacagAATGACTGGAATGTTGTGAAACGAGGGTGGGATGCTCAAGTTCTTGGTGAAGCCCCTTATAAGTTTACAAATGCTCTTGAAGCTGTCAAGAAGCTGAGGG
upper sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0056g00200.t01 (Vitis vinifera), 3'ss of exon 4
--------gtaggcaatgcttgtgagatcttgtatgaatgtcatgccttgtctagtctagtttagaa-atgaatccaattt-ttgctttccttccttgcagAATGATTGGAGTGTTGTTAAACGAGGTTGGGATGCACAAGTCCTTGGGGAAGCTCCCCACAAATTTAAAAGCGCTCTTGAAGCAGTTAAGACACTGAGGG
|| | ||| ||| || || | ||| | || | | | | |||| ||||| || ||| || | |||||||||||||||| ||||| ||||| || |||||||| ||||| ||||| ||||| || ||||| |||| ||| | ||||| || |||| ||||||||
ttgtgatggttgccaacttgtgtttt-tcctgcaaagctgtggttccatcaatgcaattatctagactgtgaattaaaaaaattgtttggttctcttgcagAATGATTGGGAAGTTGTAAAACGTGGATGGGATGCCCAAGTTCTTGGTGAAGCCCCTCACAAGTTTAGGTCTGCTGTGGAAGCTGTCAAGAAACTGAGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gccttgtctagtctagtttagaaatgaatccaatttttgctttccttccttgcagAATGATTGGAGTGTTGTTAAACGAGGTTGGGATGCACAAGTCCTTGGGGAAGCTCCCCACAAATTTAAAAGCGCTCTTGAAGCAGTTAAGACACTGAGGG
tccaatttttgctttc CT-rich tract
tttagaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggcaatgcttgtgagatcttgtatgaatgtcatgccttgtctagtctagtttagaaatgaatccaatttttgctttccttccttgcagAATGATTGGAGTGTTGTTAAACGAGGTTGGGATGCACAAGTCCTTGGGGAAGCTCCCCACAAATTTAAAAGCGCTCTTGAAGCAGTTAAGACACTGAGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC