Sequence
atgc intronic sequence ATGC exonic sequencegttttttgttgtttcaaacataatctttccaagcttttgctttcagcatatccttacttatctttgttctacacaacaacagGCTATAAACAAAAGTTTATCAGCTTTGAGTGATGTAATATTTGCATTGGCTAAGAAAGAAGATCATGTTCCTTTCAGAAACTCAAAGCTAACATATCTGC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G21270.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G21270.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA08G06690.1 (Glycine max), 3'ss of exon 16
----------------gttttttgttgtttcaaacataatctttccaagcttttgctttcagcatatccttacttatctttgttctacacaacaacagGCTATAAACAAAAGTTTATCAGCTTTGAGTGATGTAATATTTGCATTGGCTAAGAAAGAAGATCATGTTCCTTTCAGAAACTCAAAGCTAACATATCTGC
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gtatctatttgatttgcatttctgtgaatttgagctctctgtcaacaattctacttttttttaataacagtaattttctttgctgt-cacatt--cagGCTATCAACAAAAGTCTCTCGTCTTTGAGCGATGTCATATTTGCTTTGGCAAAGAAAGAGGAGCATGTTCCTTTTAGGAATTCAAAGCTGACACACTTTC
upper sequence: AT4G21270.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA07G30580.1 (Glycine max), 3'ss of exon 14
----------gttttttgttgtttcaaacataatctttcca-----agcttttgctttcagc--atatccttacttatctttgttctacacaacaacagGCTATAAACAAAAGTTTATCAGCTTTGAGTGATGTAATATTTGCATTGGCTAAGAAAGAAGATCATGTTCCTTTCAGAAACTCAAAGCTAACATATCTGC
||| |||| | || | | || || | | | |||| ||| | || || ||||| | | |||| |||||||| ||||||||| | ||| | ||||| ||||| |||||||| ||||| |||||||| || ||||||||||| || || |||||||| ||| | | |
gtatctatttaatttgcgttgctatgaatttgagctctctgtcaacaattctaattttcttttaataacagtaatttgctttgctgt-cacatt--cagGCTATCAACAAAAGTCTCTCATCCTTGAGCGATGTCATATTTGCTTTGGCAAAGAAAGAGGAGCATGTTCCTTTTAGGAATTCAAAGCTGACACACTTTC
upper sequence: AT4G21270.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA15G06880.1 (Glycine max), 3'ss of exon 15
gttttttgttgtttcaaacataatctttccaagcttttgctt-tcagcatatccttacttatctttgttctacacaac---aacagGCTATAAACAAAAGTTTATCAGCTTTGAGTGATGTAATATTTGCATTGGCTAAGAAAGAAGATCATGTTCCTTTCAGAAACTCAAAGCTAACATATCTGC
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gtgtctgtttggttcat---ttttttttattaactttaactaataaacaggtaataa---atttttgctatgtacatctttgtcagGCTATCAACAAAAGTCTCTCCTCTTTGAGTGATGTCATATTTGCTTTGGCAAAGAAACAAGAGCATGTACCCTTTAGGAATTCAAAATTGACATACCTTC
upper sequence: AT4G21270.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA13G32450.1 (Glycine max), 3'ss of exon 14
------------------gttttttgttgtttcaaacataatctttccaagcttttgctttc----agcatatccttacttatctttgttctacaca---acaacagGCTATAAACAAAAGTTTATCAGCTTTGAGTGATGTAATATTTGCATTGGCTAAGAAAGAAGATCATGTTCCTTTCAGAAACTCAAAGCTAACATATCTGC
| |||| || | | | || | || || | || | | | || | | |||| | | | | |||||||| ||||||||| | || ||||||||||||| |||||||| ||||| |||||| | || ||||| || || || || ||||| | ||||| || |
gtgtctctttgattcattttattttattaacttgagctctatgtcggaaactttaagtcttttactaataaacaggtaatgaattttgctatgtttatctatgtcagGCTATCAACAAAAGTCTCTCCTCTTTGAGTGATGTCATATTTGCTTTGGCAAAGAAACAGGAGCATGTACCCTTTAGGAATTCAAAATTGACATACCTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccaagcttttgctttcagcatatccttacttatctttgttctacacaacaacagGCTATAAACAAAAGTTTATCAGCTTTGAGTGATGTAATATTTGCATTGGCTAAGAAAGAAGATCATGTTCCTTTCAGAAACTCAAAGCTAACATATCTGC
tccttac putative branch site (score: 2)
ttacttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttttgttgtttcaaacataatctttccaagcttttgctttcagcatatccttacttatctttgttctacacaacaacagGCTATAAACAAAAGTTTATCAGCTTTGAGTGATGTAATATTTGCATTGGCTAAGAAAGAAGATCATGTTCCTTTCAGAAACTCAAAGCTAACATATCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA