Sequence
atgc intronic sequence ATGC exonic sequencegtgtggtttagagtgctccgatcatcttctctgattgttttctaatccagatctggtattatagctctatggagttttgctgacttgatcggattttggtttgactgtgttttgaaatctcagATTAGGACTCATGCTATAAGGAAAGCTCATGAGAATATTGATAGGACTCTTAAGGCTGCTGAAGTTATTTTGTCTCAATTCGATCTCCTCCGTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G03540.3 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G03540.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G34000.1 (Glycine max), 3'ss of exon 1
gtgtggtttagagtgctccgatcatcttctctgattgttttctaatccagatctggtattatagctctatggagttttgctgacttgatcggattttggtttgactgtgttttgaaatctcagATTAGGACTCATGCTATAAGGAAAGCTCATGAGAATATTGATAGGACTCTTAAGGCTGCTGAAGTTATTTTGTCTCAATTCGATCTCCTCCGTCAG
| | |||| | || | | || | | | || | | | | ||| | ||| | ||| | | | | |||| || | ||||| | |||||||| ||||| |||| ||||| |||||||||||||||||||||||| | |||||||| || ||||| ||| |||| ||||||| ||||||
--------ttgggtgcaatggggatttgttttggagggggt-tgttc--gtttttgaattggggatctgaagggtt--gttaaa--agttggatcttt-tccatttgtgtatg-------cagATTAGAACTCACTCTATTAGGAAGGCTCATGAGAATATTGATAGGACTTTGAAGGCTGCGGAGGTTATATTGGCTCACTTCGATCAATATCGTCAG
upper sequence: AT5G03540.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA20G33590.1 (Glycine max), 3'ss of exon 1
gtgtggtttagagtgctccgatcatcttctctgattgttttctaatccagatctggtattatagctctatggagttttgctgacttgatcggattttggtttgactgtgttttgaaatctcagATTAGGACTCATGCTATAAGGAAAGCTCATGAGAATATTGATAGGACTCTTAAGGCTGCTGAAGTTATTTTGTCTCAATTCGATCTCCTCCGTCAG
| | ||||| | | | | ||| | || | | || || | ||| | | || | ||| | | || | | | | | |||| | |||||||| ||||| |||| ||||| |||||||||||||||||||||||| |||| ||| || ||||| ||| |||| ||||||| ||||||
-------cttgggtgctatggggttttgttttgaggggattgt----------tcgtttttcaa----gtggggatctgaagggttgttaaaagttggatct--ttttcatttgggtttgcagATTAGAACTCACTCTATTAGGAAGGCTCATGAGAATATTGATAGGACTTCGAAGGTTGCGGAGGTTATATTGGCTCACTTCGATCAATATCGTCAG
upper sequence: AT5G03540.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv13s0073g00170.t01 (Vitis vinifera), 3'ss of exon 1
gtgtggtttagagtgctccgatcatcttctctgattgttttctaatccagatctggtattatagctctatggagttttgctgacttgatcggattttggtttgactgtgttttgaaatctcagATTAGGACTCATGCTATAAGGAAAGCTCATGAGAATATTGATAGGACTCTTAAGGCTGCTGAAGTTATTTTGTCTCAATTCGATCTCCTCCGTCAG
|| ||| || | || |||| || || || || | | || ||| | | || | || | | || | |||||||| || ||| |||| | | |||||||||||||||||| | |||| | |||||||| || ||||| ||| |||||||||| || ||||||
-----------------------cggaacttgatttggcttttcccccttatctcgtgggatctctgagtgccaatgggttggcttttccttttcttacggttgctaaatctggattttacagATTAGAACGCATTCTATTCGAAGAGCTCATGAGAATATTGACAAGACTTTGAAGGCTGCCGAGGTTATATTGGCTCAATTCGACCTTTATCGTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atggagttttgctgacttgatcggattttggtttgactgtgttttgaaatctcagATTAGGACTCATGCTATAAGGAAAGCTCATGAGAATATTGATAGGACTCTTAAGGCTGCTGAAGTTATTTTGTCTCAATTCGATCTCCTCCGTCAG
ttttgaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtggtttagagtgctccgatcatcttctctgattgttttctaatccagatctggtattatagctctatggagttttgctgacttgatcggattttggtttgactgtgttttgaaatctcagATTAGGACTCATGCTATAAGGAAAGCTCATGAGAATATTGATAGGACTCTTAAGGCTGCTGAAGTTATTTTGTCTCAATTCGATCTCCTCCGTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC