Sequence
atgc intronic sequence ATGC exonic sequence...ttaggttatttattgtgtggtttttactttttcttggaactgtaggtttatttctattctggtaaatggacttttatgatgttgacttgtgctctttcagGCTTGGGAAGGGAGGGCTTATGACTACTGTATGGAAAACCTTAAGAATATGGGTTTCCCTGTTGATGGACTTGCCTTTGATCCTGACCTG
Basic information
species | Glycine max |
transcript | GLYMA17G04580.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G04580.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g14810.2 (Oryza sativa), 3'ss of exon 3
ttaggttatttattgtgtggtttttactttttcttggaactgtaggtttatttctattctggtaaat----ggacttttatgatgttgacttgtgctctttcagGCTTGGGAAGGGAGGGCTTATGACTACTGTATGGAAAACCTTAAGAATATGGGTTTCCCTGTTGATGGACTTGCCTTTGATCCTGACCTG
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tcacatcagacataaaaaaacaacatgagtgctttgtgtccttccatatggtcct--tgtggtaaattgcagaaaaaccaaattgttg--ttacatctatgcagGCTTGGGAAGGGCGTGCTTATGATTATGGTATGGCCAATCTGAAGGGCATGGGTTTCCCTGTAGATGACCTTGAATTTGATCCTGACCTG
upper sequence: GLYMA17G04580.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G48960.1 (Arabidopsis thaliana), 3'ss of exon 3
ttaggttatttattgtgtggtttttactttttcttggaactgtaggtt-tatttctattctggtaaatggacttttatgatgttgacttgtgctctt--tcagGCTTGGGAAGGGAGGGCTTATGACTACTGTATGGAAAACCTTAAGAATATGGGTTTCCCTGTTGATGGACTTGCCTTTGATCCTGACCTG
||| ||| || |||| || | ||||| |||| | | || | ||||| | | || || |||| ||||||||||||||| | |||||||||||| || |||||||| || |||| |||||||||||||||||||||||||| |||||||| || |||
--------------gtg-agttcttcctttctcagacataagtaggaaacatttatgcacccata----------tttgatgctaatttatggtcttgttcagGCTTGGGAAGGAAAGGCTTATGACTATTGCATGGAAAATCTAAAGAGCATGGGTTTCCCTGTTGATGGACTTGCTTTTGATCCGGAACTG
upper sequence: GLYMA17G04580.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0020g00880.t01 (Vitis vinifera), 3'ss of exon 3
ttaggttattta-ttgtgtggtttttactttttcttggaactgtaggtttatt-tctattctggtaaatggacttttatgatgttgacttgtgctcttt---cagGCTTGGGAAGGGAGGGCTTATGACTACTGTATGGAAAACCTTAAGAATATGGGTTTCCCTGTTGATGGACTTGCCTTTGATCCTGACCTG
||| | ||| | || | | ||| || | || | || || ||| || || | ||| | | || ||| | | |||||||||||||| |||| ||||| || |||||||| ||||| | ||| ||||| || ||||| ||||||||||| ||||| || || ||
----cctatctgcttggtttagcttcatggataattgaaaaaggagttcctttgtccatttgaactggtgagattat-tgacataggtttatgcccctggtgcagGCTTGGGAAGGACGGGCGTATGAATATTGTATGGACAACCTAAGGAACATGGGGTTTCCTGTGGATGGACTTGCATTTGACCCAAACTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttatttctattctggtaaatggacttttatgatgttgacttgtgctctttcagGCTTGGGAAGGGAGGGCTTATGACTACTGTATGGAAAACCTTAAGAATATGGGTTTCCCTGTTGATGGACTTGCCTTTGATCCTGACCTG
tgttgac putative branch site (score: 3)
tgctctttc putative PPT
ttttatgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaggttatttattgtgtggtttttactttttcttggaactgtaggtttatttctattctggtaaatggacttttatgatgttgacttgtgctctttcagGCTTGGGAAGGGAGGGCTTATGACTACTGTATGGAAAACCTTAAGAATATGGGTTTCCCTGTTGATGGACTTGCCTTTGATCCTGACCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - -tgtgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgac