Sequence
atgc intronic sequence ATGC exonic sequencegtaacccatttaaccaaagactagattcagtttcatgttagctaggaaagtgattcatcttaaaacttaaaaaaactgctctgtgtttttgtttgttgtagATGAAGGGAGAGTATTCTGCTGGGGATGGAACAAATACGGACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G55580.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G55580.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os01g62810.1 (Oryza sativa), 3'ss of exon 9
gtaacccatttaaccaaagactagattcagtttcatgttagctaggaaagtg--attcatcttaaaacttaaaaaaactgctctgtgtttttgtttgttgtagATGAAGGGAGAGTATTCTGCTGGGGATGGAACAAATACGGACAG
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gttaatc-tttggcctccctgacaatttgtttaaacatgcccgtagaaagtgctgttcctggtctaacatctactgacaaaa-tgtggtgacatttat-gcagATGAAGGCGAGGTCTTCTGCTGGGGATGGAACAAGTACGGACAG
upper sequence: AT3G55580.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G302245_T01 (Zea mays), 3'ss of exon 7
--gtaacccatttaaccaaagactagattcagtttcatgttagctaggaaagtgattcatcttaaaacttaaaaaaactgctctgtgtttttgtttgttgtagATGAAGGGAGAGTATTCTGCTGGGGATGGAACAAATACGGACAG
||| | | ||| ||| | || || || | || || | || || || | | | | | | ||| ||||||||| ||||||||||||||||||||||| ||||| |||
aactaaggcggtgaacaaaaa--tgtatctagagaaat-cgaaaggggtaactatatcctcaggaagtcttctcatctgacaaaggttacacaactattgcagATGAAGGCGAGGTATTCTGCTGGGGATGGAACAAGTACGGCCAG
upper sequence: AT3G55580.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA02G41810.1 (Glycine max), 3'ss of exon 9
gtaacccatttaaccaaagactagattcagtttcatgttagctaggaaagtgattcatcttaaaacttaaaaaaactgctctgtgtttt-tgtttgttgt---agATGAAGGGAGAGTATTCTGCTGGGGATGGAACAAATACGGACAG
| | |||| | | || | || || || | ||| | || | ||| || | | ||| | |||| | | |||| | ||| | || | ||| ||||||||||||||||||||||| ||||||
-tgaattttttattttattggcaatttaaaacacaaattggc----acgtctattttttttgtatattataattagttttctttcttttgtttctgttcttcaagAGGGCGGAAAAGTTTTCTGCTGGGGATGGAACAAATATGGACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaagtgattcatcttaaaacttaaaaaaactgctctgtgtttttgtttgttgtagATGAAGGGAGAGTATTCTGCTGGGGATGGAACAAATACGGACAG
tttttgttt CT-rich tract
attcatcttaaaactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacccatttaaccaaagactagattcagtttcatgttagctaggaaagtgattcatcttaaaacttaaaaaaactgctctgtgtttttgtttgttgtagATGAAGGGAGAGTATTCTGCTGGGGATGGAACAAATACGGACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA