Sequence
atgc intronic sequence ATGC exonic sequencegtatatcacttctaagttctaacccaatggatcttgaaatttttaccatttcaaagttaaaattgaccttaatgatttatggtagATTTGTACCGGGATTGACGAGAATGCCGTTGGAGCTTGTTCTGAACTGATATTTGCTCCGATTAATGAGATGTTCCCGGATGATGCTCCACTTGTTCCCT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G60690.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 13
-----gtatatcacttctaagttctaacccaatggatcttgaaatttttaccatttcaaagttaaaattgaccttaatgatttatg-----------gtagATTTGTACCGGGATTGACGAGAATGCCGTTGGAGCTTGTTCTGAACTGATATTTGCTCCGATTAATGAGATGTTCCCGGATGATGCTCCACTTGTTCCCT
| ||| | | ||| | | | || | || | | ||| | | ||| | | || || ||| || | |||| |||| |||||||| |||||||| || || ||||||||||| || |||||||||| ||| |||| |||||||| |||||||||||| | |||| |
ttcttttctat-gcatttaaatgatgcacgaacgaatataattaatttaggtaggtaggttctaaggtgctcttttgtgttttgtgttatcttttctgcagATATGTAGTGGGATTGATGAGAATGCTGTGGGGGCTTGTTCTGAGCTTGTATTTGCTCCAATTGATGAAATGTTCCCCGATGATGCTCCATTGATTCCTT
upper sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA11G20520.1 (Glycine max), 3'ss of exon 13
-------------gtatat-cacttctaagttcta-acccaatggatcttga--aatttttaccatttcaaagttaaaattgaccttaatgatttatggtagATTTGTACCGGGATTGACGAGAATGCCGTTGGAGCTTGTTCTGAACTGATATTTGCTCCGATTAATGAGATGTTCCCGGATGATGCTCCACTTGTTCCCT
| ||| || || | ||| || || | | | | | ||| | |||| ||| | || | | || | | |||| |||| |||||||| |||||||| || || |||||||| || || |||||||||| ||| |||| |||||||| |||||||||||| | ||||| |
gtttttagttcttttctatgcatttaaatgttttatacacgaacaaatataattaatataggtagtttctaaggtgctttt--ttgtgttatctttttgcagATATGTAGTGGGATTGATGAGAATGCTGTGGGGGCTTGTTCAGAGCTCGTATTTGCTCCAATTGATGAAATGTTCCCTGATGATGCTCCATTGGTTCCTT
upper sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv06s0004g02800.t01 (Vitis vinifera), 3'ss of exon 13
------------------gtatatcacttctaagttctaacccaatggatcttgaaatttttacc-atttcaaagttaaaattgaccttaatgatttatggtagATTTGTACCGGGATTGACGAGAATGCCGTTGGAGCTTGTTCTGAACTGATATTTGCTCCGATTAATGAGATGTTCCCGGATGATGCTCCACTTGTTCCCT
| | | || | | | || || | | ||||||| | | || |||| || || | || | ||| || |||| |||| || ||||||||||||| || ||||||||||||||||| | |||||||| ||| |||| ||||| || |||||||||||||| | ||||
tttcttgttttctgagtggagtttttttttttaccctgtgtaggaggggtcataacctttttacttactgcatagttgaa--tggcatttttatttt--ggcagATATGTAGTGGAGTTGACGAGAATGCAGTGGGAGCTTGTTCTGAACTTGTTTTTGCTCCAATTGATGAAATGTTTCCAGATGATGCTCCACTGTTACCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcttgaaatttttaccatttcaaagttaaaattgaccttaatgatttatggtagATTTGTACCGGGATTGACGAGAATGCCGTTGGAGCTTGTTCTGAACTGATATTTGCTCCGATTAATGAGATGTTCCCGGATGATGCTCCACTTGTTCCCT
aaatttttaccatttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatcacttctaagttctaacccaatggatcttgaaatttttaccatttcaaagttaaaattgaccttaatgatttatggtagATTTGTACCGGGATTGACGAGAATGCCGTTGGAGCTTGTTCTGAACTGATATTTGCTCCGATTAATGAGATGTTCCCGGATGATGCTCCACTTGTTCCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG