Sequence
atgc intronic sequence ATGC exonic sequencegttgtgttctatgccctcttgtttttcttaaaatgtcctattattcatttaaagtgtctatatgctcagtcttctactgtaaatatcatctggaatacttgcagGAAACTCAAGAAGCTGAGCTTAAGATGCTAAGGAAGAGTCTGAACTTCAAAGCCACACCTATGCCTACCTTCTATCAAGAACCTCAGCTACCTAAAACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G25480.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G25480.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA17G31990.1 (Glycine max), 3'ss of exon 7
gttgtgttctatgccctcttgtttttcttaaaatgtcctattattcatttaaagtgtctat---atgctcagtcttctactgtaaatatcatctggaatacttgcagGAAACTCAAGAAGCTGAGCTTAAGATGCTAAGGAAGAGTCTGAACTTCAAAGCCACACCTATGCCTACCTTCTATCAAGAACCTCAGCTACCTAAAACAG
| | ||| || | |||| ||| || | | || | | ||||| || ||||||| |||||||| ||| |||||||||| |||||||||||||| || ||||| || || ||||| | || || || || ||| | |||| | |
--------------------------gtgagaatacttcatatctaggctaaattgtgaattgagaatttatcttttaatcatgtcaatcattcaccccttttatagGAAACCCAAGAAGCCGAGATTAAGATGCTTAGGAAGAGTCTGAATTTTAAAGCAACTCCAATGCCAAGTTTTTACCAGGAGCCTGCTCCTGCTAAGGCGG
upper sequence: AT2G25480.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA14G14400.2 (Glycine max), 3'ss of exon 6
gttgtgttctatgccctcttgtttttcttaaaatgtcctattattcatttaaa--gtgtctatatgctcagtcttcta-ctgtaaatatcatctggaatacttgcagGAAACTCAAGAAGCTGAGCTTAAGATGCTAAGGAAGAGTCTGAACTTCAAAGCCACACCTATGCCTACCTTCTATCAAGAACCTCAGCTACCTAAAACAG
| | | | || | |||| ||| | | | ||||||| | ||||| || |||| || |||||||| ||| |||||||||| |||||||||||||| || ||||| || || ||||| | || || || || ||| | |||| | |
--------------------------gtgagagtacttgatatctgggctaaaacgtgatttgagaatttatcttctaatcatgtcaatcattcaccccttttatagGAGACCCAAGAAGCCGAGATTAAGATGCTTAGGAAGAGTCTGAATTTTAAAGCAACTCCAATGCCAAGTTTTTACCAGGAGCCTGCTCCTGCTAAGGCGG
upper sequence: AT2G25480.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv04s0008g05480.t01 (Vitis vinifera), 3'ss of exon 7
gttgtgttctatgccctcttgtttttcttaaaatgtcctattattcatttaaagtgtctatat-gctcagtcttctactgtaaatatcatctggaatacttgcagGAAACTCAAGAAGCTGAGCTTAAGATGCTAAGGAAGAGTCTGAACTTCAAAGCCACACCTATGCCTACCTTCTATCAAGAACCTCAGCTACCTAAAACAG
||||| | | | || ||| | ||| | | | ||| ||| || | | |||| | ||| || || ||| | || ||||||||||||||||||||| |||||||||| ||||||||| ||| ||| ||||| || || ||||| | ||||||||| ||||| | | |||||| |
gttgtactattttatgcctagtt--ccataatgcaat-tgtggagactctaatttgttagtaaagtttgttctttttctgacaagttcttctattgt-tttacagGAAACTCAAGAAGCTGAGATTAAGATGCTTAGGAAGAGTTTGACCTTTAAAGCAACGCCCATGCCAAGCTTCTATCAGGAACCCCCACCTCCTAAAGTGG
upper sequence: AT2G25480.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv11s0016g05460.t01 (Vitis vinifera), 3'ss of exon 7
gttgtgttctatgccctcttgtttttcttaaaatgtcctattattcatttaaagt-gtctatatgctcagtcttctactgtaaatatcatctggaatact-tgcagGAAACTCAAGAAGCTGAGCTTAAGATGCTAAGGAAGAGTCTGAACTTCAAAGCCACACCTATGCCTACCTTCTATCAAGAACCTCAGCTACCTAAAACAG---
||| | || | || | || |||| | | || | || | | | || | | ||| | | || | | | | || ||| | | |||| ||||||||||| ||| ||||||||||| ||||||| | || || ||||| || |||||||| | |||||| || |||||| ||| || |
---gtgaga-acattctgtgtttactgtttgaatggttt--tgttgactttgattcattgatttcagctgtcctttttggtgactttgagctcaaatgttctatagGAGACTCAAGAAGCAGAGATTAAGATGCTACGGAAGAGCTTAAATTTTAAAGCAACCCCTATGCCAAGCTTCTACCATGAACCT---ACACCCAAGGTGGAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaagtgtctatatgctcagtcttctactgtaaatatcatctggaatacttgcagGAAACTCAAGAAGCTGAGCTTAAGATGCTAAGGAAGAGTCTGAACTTCAAAGCCACACCTATGCCTACCTTCTATCAAGAACCTCAGCTACCTAAAACAG
taaatatcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgtgttctatgccctcttgtttttcttaaaatgtcctattattcatttaaagtgtctatatgctcagtcttctactgtaaatatcatctggaatacttgcagGAAACTCAAGAAGCTGAGCTTAAGATGCTAAGGAAGAGTCTGAACTTCAAAGCCACACCTATGCCTACCTTCTATCAAGAACCTCAGCTACCTAAAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT