Sequence
atgc intronic sequence ATGC exonic sequencegtaaacatatcttctttctctttgaaatctcagtctattgaaccacctcaagtttctaatggtgatcttctttaacttcagGTTGCTGACTTTGGCCTCTCCAGAGAAGAAATGGTAGACAAACATGCAGCTAACATCAGAGGAACATTTGGCTACCTCGATCCCGAATACATTTCAACAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G54590.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G54590.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA06G41510.1 (Glycine max), 3'ss of exon 6
------------------------------------------------------------------------------gtaaacatatcttctttctctttgaaatctcagtctattgaaccacctcaagtttctaat--ggtgatcttctttaactt---cagGTTGCTGACTTTGGCCTCTCCAGAGAAGAAATGGTAGACAAACATGCAGCTAACATCAGAGGAACATTTGGCTACCTCGATCCCGAATACATTTCAACAA---
| | | | ||| || ||| || | ||||| | | |||| || || | || | | ||||||||||| ||||| || || |||||||| ||||| || ||||||||||||| | | || || |||||||| || || ||||| || || || |
gtatgatgatactcatccctcatatttcatcacaaaaagtagtttgcaccaaatatacacacccctatacaaagctaaattactaactattcattagtgttgtcataatcatttattgcttt-taggatgcttcttattctgtagttaatgttgaatcaagcagGTTGCTGATTTTGGACTTTCAAGAGAAGAGATGGTGGATAAACATGCAGCTA---TTCGGGGTACCTTTGGCTATCTTGACCCCGAGTATATATCTTCCGGAA
upper sequence: AT5G54590.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G36140.2 (Glycine max), 3'ss of exon 6
-------------------gtaaacatatcttctttctctttgaaatctca-gtctattgaaccacctcaagtttctaatggt-gatcttctttaacttcagGTTGCTGACTTTGGCCTCTCCAGAGAAGAAATGGTAGACAAACATGCAGCTAACATCAGAGGAACATTTGGCTACCTCGATCCCGAATACATTTCAACAA---
| | || ||| ||||| || | || | || || | || |||| || ||| | | | ||||||||||| ||||| ||||| |||||||| ||||| || |||||||| || | | | || || |||||||| || || || || || || || ||
tgtctagtgatattgcttaatgattatgtcta-tttcttttagtcatttagtgttggttaggatgcttcttacacataattgttgatgctgaatcaaa-cagGTTGCTGATTTTGGACTCTCAAGAGAAGAGATGGTGGATAAACATGCTGCAA---TTCGGGGTACCTTTGGCTATCTTGACCCTGAGTATATATCCTCAGGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atctcagtctattgaaccacctcaagtttctaatggtgatcttctttaacttcagGTTGCTGACTTTGGCCTCTCCAGAGAAGAAATGGTAGACAAACATGCAGCTAACATCAGAGGAACATTTGGCTACCTCGATCCCGAATACATTTCAACAA
tcttctttaacttc CT-rich tract
tttctaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaacatatcttctttctctttgaaatctcagtctattgaaccacctcaagtttctaatggtgatcttctttaacttcagGTTGCTGACTTTGGCCTCTCCAGAGAAGAAATGGTAGACAAACATGCAGCTAACATCAGAGGAACATTTGGCTACCTCGATCCCGAATACATTTCAACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA