Sequence
atgc intronic sequence ATGC exonic sequencegtaagctaatactaacctatggacttctagttattttatcacatctattcaagttctcccatcactgataccttttctgtagGAAAATTGCATTACTTATTGGAGGAAATTTGTGGCAGAATACTTCTCACCTCGTGCAAAGCAGAGGTTGTGCTTGTCACAGTACGAAAGTGTTGGGCACC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G25515.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G25515.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G32260.1 (Glycine max), 3'ss of exon 3
------------gtaagctaatactaacctatggacttctagtta-ttttatcacatctattcaagttctcccatcactga-----taccttttctgtagGAAAATTGCATTACTTATTGGAGGAAATTTGTGGCAGAATACTTCTCACCTCGTGCAAAGCAGAGGTTGTGCTTGTCACAGTACGAAAGTGTTGGGCACC
|| || || | | || | | || |||| | | | | | | || | | | | ||| || |||| ||| | ||| | |||||||| ||||||||||| ||||| | ||| |||||||||||| | ||| |||||||||| || | ||||||||| |
gtttattatgttatatctgaacacacttgttttatattttggctacttttgaagttcttgattagttacaactattattcaatttttctttttgcttcagGATAATAGTATTGCCTATTGGAGAAAATTTGTGGCTGAATATTACTCTCCTCGTGCAAAGAAACGGTGGTGCTTGTCATTATATAGTAATGTTGGGCATC
upper sequence: AT4G25515.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv16s0100g00500.t01 (Vitis vinifera), 3'ss of exon 1
-----------------------------------------------------------------------------------------gtaagctaata---ctaacc---tatggacttctagttattttatc----acatctattcaa---gttctcccatcactgataccttttctgt---agGAAAATTGCATTACTTATTGGAGGAAATTTGTGGCAGAATACTTCTCACCTCGTGCAAAGCAGAGGTTGTGCTTGTCACAGTACGAAAGTGTTGGGCACC
|||| | | |||| | | | || | |||| | | | || | || | | | | | | | | || |||| | | |||| || ||| | ||||||||||||||||||||||| || | ||||| ||||||||| | || | ||||||||| || || | |||||| | |
gtgagttgatcctttctattttttatctttatttttatttactgcatctttagtgcattgcctgttacacatgcatgatatctatccagctaagttggtgtttctaattctgttttgcaatccaattatagaagcttgaagatttgtttgatctgctattgctttatttatttattttttattacagGACAAGACTATTGCCTATTGGAGGAAATTTGTGGCAGAGTATTATTCACCCCGTGCAAAGAAAAGATGGTGCTTGTCCTTATATGACAATGTTGGAAATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagttattttatcacatctattcaagttctcccatcactgataccttttctgtagGAAAATTGCATTACTTATTGGAGGAAATTTGTGGCAGAATACTTCTCACCTCGTGCAAAGCAGAGGTTGTGCTTGTCACAGTACGAAAGTGTTGGGCACC
cactgat putative branch site (score: 3)
taccttttct CT-rich tract
attttatca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagctaatactaacctatggacttctagttattttatcacatctattcaagttctcccatcactgataccttttctgtagGAAAATTGCATTACTTATTGGAGGAAATTTGTGGCAGAATACTTCTCACCTCGTGCAAAGCAGAGGTTGTGCTTGTCACAGTACGAAAGTGTTGGGCACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG