Sequence
atgc intronic sequence ATGC exonic sequencegtaataactttctaatttttttctctgtcggtttcatttgttacttttgatttgagttttttgtttctatgattgatttgatttgattttatattgcagGATGATGAGCGATTATAAAGTGGAAACGATCAACGATGGCATGCAAGAATTCTATGTTGAATTCAATGGTCCCAAAGACA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G41340.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G41340.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G37650.1 (Glycine max), 3'ss of exon 1
----gtaataactttctaatt--tttttctctgtcggtttcatttgttact-tttgatttgagttttttgt---ttctatgattgatttgatttgattttatattg-------------cagGATGATGAGCGATTATAAAGTGGAAACGATCAACGATGGCATGCAAGAATTCTATGTTGAATTCAATGGTCCCAAAGACA
|| || || |||| |||| | ||| |||||| | | ||| | | | ||| |||| || | ||| || ||| || | || | |||||||||||| ||||| || ||||| ||||||||||||||||||||||| |||| ||| |||||| | || ||||||||||
gtctgtgatcttttcggaattgtttttgtattttcgatttcataaagtgttcttttgtataaatttgttgtcttttttccatttggggtgtgttggattgacatggatcaggtcatcatcagGATGATGAGTGATTACAAGGTGGAGACGATCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA
upper sequence: AT5G41340.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G01940.2 (Glycine max), 3'ss of exon 1
gtaataactttctaatttttttctc----tgtcggtttcatttgtta--cttttgatttgagttttttgtttctatgattgatttgatttgattttatattg----------cagGATGATGAGCGATTATAAAGTGGAAACGATCAACGATGGCATGCAAGAATTCTATGTTGAATTCAATGGTCCCAAAGACA
|| || || | ||||||||| | | ||| ||||| | |||||| | | | || | ||| | ||| || ||| || | || | |||||||||||| ||||| || ||||| ||| ||||||||||||||||||| |||| ||| |||||| | || ||||||||||
gtgatcttttccgaattttttttttgtattttcgatttcagaaagtgttcttttgcataaattgttgtctttttccatttggggtgcgttggattgacatggatcaggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA
upper sequence: AT5G41340.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G01940.3 (Glycine max), 3'ss of exon 1
----gtaataactttctaatttttttctc----tgtcggtttcatttgtta--cttttgatttgagttttttgtttctatgattgatttgatttgattttatattg----------cagGATGATGAGCGATTATAAAGTGGAAACGATCAACGATGGCATGCAAGAATTCTATGTTGAATTCAATGGTCCCAAAGACA
|| || || | ||||||||| | | ||| ||||| | |||||| | | | || | ||| | ||| || ||| || | || | |||||||||||| ||||| || ||||| ||| ||||||||||||||||||| |||| ||| |||||| | || ||||||||||
gtctgtgatcttttccgaattttttttttgtattttcgatttcagaaagtgttcttttgcataaattgttgtctttttccatttggggtgcgttggattgacatggatcagGTCATCAGGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgatttgagttttttgtttctatgattgatttgatttgattttatattgcagGATGATGAGCGATTATAAAGTGGAAACGATCAACGATGGCATGCAAGAATTCTATGTTGAATTCAATGGTCCCAAAGACA
tatgattgatttgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaataactttctaatttttttctctgtcggtttcatttgttacttttgatttgagttttttgtttctatgattgatttgatttgattttatattgcagGATGATGAGCGATTATAAAGTGGAAACGATCAACGATGGCATGCAAGAATTCTATGTTGAATTCAATGGTCCCAAAGACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA