Sequence
atgc intronic sequence ATGC exonic sequencegtaattatccacttatctaatgttaacataatagacacctaaagtcctttagcctgagaaccaactaattgctgtattccagGAGCAAGATCGTAAATTATCTGAAGTGGAATCTGAAAATCGAAAGATGAAAGTTGAACTTGAGGAGTTTAGGACAGAAGCGACTCATCTTAAAAATCAGC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G18480.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G18480.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g50300.1 (Oryza sativa), 3'ss of exon 2
----------------------gtaatt-atccacttatctaatgttaacataatagacacctaaagtcc-tttagcctgagaaccaactaattgctgtattccagGAGCAAGATCGTAAATTATCTGAAGTGGAATCTGAAAATCGAAAGATGAAAGTTGAACTTGAGGAGTTTAGGACAGAAGCGACTCATCTTAAAAATCAGC
|||| || ||| | || ||| | | |||| | | | |||| | || | ||| |||| |||||||||||| ||| |||||||| |||| |||||||||| ||||||||| |||| ||||| |||| || ||||||| | || || || || || |
tctaactttaggtgctttcagtataatagataggcttcaattattttatggcact-gacatttctccccaacctgtcctgtttatcatccaatc----cattc-agGAGCAAGATCAGAAACTATCTGAACTGGAGACTGAAAATCGGAAGATGAAACTTGAGCTTGAAGAGTACCGGGCAGAAGCCGCCCACCTAAAGAACCAAC
upper sequence: AT3G18480.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G09890.2 (Glycine max), 3'ss of exon 3
-----------gtaattatccacttatctaatgttaacataatagacacctaaagtccttta---gcctga----gaaccaactaattgctgtattccagGAGCAAGATCGTAAATTATCTGAAGTGGAATCTGAAAATCGAAAGATGAAAGTTGAACTTGAGGAGTTTAGGACAGAAGCGACTCATCTTAAAAATCAGC
| | | | | ||| | ||| | | || | | |||| || || | | | || | | ||||||||||||| || ||||||| | ||||||||||| || || ||||||||||| ||||||||||| |||||||| || ||||| | || |||||||
gatacttgtgtgcattggtgcttatattttatgcatgtagggaaaccatgtgcatatttttatttgcttgttcctgttctgatatgttttcattgtgcagGAGCAAGATCTCAAGATATCTGAGCTTGAATCTGAAAACCGGAAAATGAAAGTTGAGCTTGAGGAGTTCAGGACAGAGGCAACTCACTTGAAGAATCAGC
upper sequence: AT3G18480.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G31920.1 (Glycine max), 3'ss of exon 4
--------------------gtaattatccacttatctaatgttaacataatagacacctaaagtcctttagcctgagaaccaactaattgctgtattccagGAGCAAGATCGTAAATTATCTGAAGTGGAATCTGAAAATCGAAAGATGAAAGTTGAACTTGAGGAGTTTAGGACAGAAGCGACTCATCTTAAAAATCAGC
| || | | || || | | ||| | | | || | | || | | | | || | | ||||||||||||| || ||||||| | ||||||||||| || || ||||||||||| ||||||||||| |||||||| || ||||| | || |||||||
gatacttgtgtggattagtgcttatattttatgcatgtagggaaaccatg-tgcatagttacatttgctt-gttcatgttctgatgtgttttcattgtgcagGAGCAAGATCTCAAGATATCTGAGCTTGAATCTGAAAACCGGAAAATGAAAGTTGAGCTTGAGGAGTTCAGGACAGAGGCAACTCACTTGAAGAATCAGC
upper sequence: AT3G18480.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv17s0000g03970.t01 (Vitis vinifera), 3'ss of exon 3
---gtaattatccacttatctaatgttaac-ataatagacacctaaagtc---ctttagcctgaga-----------accaactaattgctgtattccagGAGCAAGATCGTAAATTATCTGAAGTGGAATCTGAAAATCGAAAGATGAAAGTTGAACTTGAGGAGTTTAGGACAGAAGCGACTCATCTTAAAAATCAGC
| | || || | | | || | | | ||| | ||| | || || || | | || ||| | |||||||||||| ||||| ||||| | || ||||| || || ||||||||||| |||||||||||||| |||||||| || |||||||| || ||||| |
tagtttgctttctgtttgctttgtttaggggattgtgaatgcataagtgcttgcttgtgtatgggagaatctagggcactcatttgatgttgttatgcagGAGCAAGATATGAAATTGTCTGAGCTAGAGTCTGAGAACCGGAAGATGAAAGTGGAACTTGAGGAGTTCAGGACAGAGGCAACTCATCTAAAGAATCAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataatagacacctaaagtcctttagcctgagaaccaactaattgctgtattccagGAGCAAGATCGTAAATTATCTGAAGTGGAATCTGAAAATCGAAAGATGAAAGTTGAACTTGAGGAGTTTAGGACAGAAGCGACTCATCTTAAAAATCAGC
aactaat putative branch site (score: 2)
aactaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattatccacttatctaatgttaacataatagacacctaaagtcctttagcctgagaaccaactaattgctgtattccagGAGCAAGATCGTAAATTATCTGAAGTGGAATCTGAAAATCGAAAGATGAAAGTTGAACTTGAGGAGTTTAGGACAGAAGCGACTCATCTTAAAAATCAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC