Sequence
atgc intronic sequence ATGC exonic sequence...gtacgaaataggttatgtattgtgtggtttttcctggaactgtaggtttatttctatttaggtaaatggacttttatgatgttgacatgtgctctttcagGCTTGGGAAGGGAGGGCTTATGACTACTGTATGGAAAACCTTAAGAATATGGGTTTCCCTGTTGATGGACTTGCCTTTGATCCTGACCTG
Basic information
species | Glycine max |
transcript | GLYMA13G17950.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G17950.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g14810.2 (Oryza sativa), 3'ss of exon 3
----gtacgaaataggttatgtattgtgtggtttttcctggaactgtaggtttatttctatttaggtaaatggacttttatgatgttgacatgtgctctttcagGCTTGGGAAGGGAGGGCTTATGACTACTGTATGGAAAACCTTAAGAATATGGGTTTCCCTGTTGATGGACTTGCCTTTGATCCTGACCTG
| || ||| | | || || || || | | | | || | | | | ||||| | | | ||||||||||||||| | |||||||| || |||||| || || ||| |||||||||||||| |||| |||| |||||||||||||||
tcacatcagacataaaaaa-acaacatg-agtgctttgtgtccttccatatggtccttgtggtaaattgcagaaaaaccaaattgttgttacat--ctatgcagGCTTGGGAAGGGCGTGCTTATGATTATGGTATGGCCAATCTGAAGGGCATGGGTTTCCCTGTAGATGACCTTGAATTTGATCCTGACCTG
upper sequence: GLYMA13G17950.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G48960.1 (Arabidopsis thaliana), 3'ss of exon 3
gtacgaaataggttatgtattgtgtggtttttcctggaactgtaggtttatttctatttaggtaaatggacttttatgatgttgacatgtgctctt--tcagGCTTGGGAAGGGAGGGCTTATGACTACTGTATGGAAAACCTTAAGAATATGGGTTTCCCTGTTGATGGACTTGCCTTTGATCCTGACCTG
|| || || | | || || | ||||| | | | || |||| | | | || |||| ||||||||||||||| | |||||||||||| || |||||||| || |||| |||||||||||||||||||||||||| |||||||| || |||
-------------------gtgagttcttcctttctcagacataagtaggaaac-atttatgcacccatattt----gatgctaatttatggtcttgttcagGCTTGGGAAGGAAAGGCTTATGACTATTGCATGGAAAATCTAAAGAGCATGGGTTTCCCTGTTGATGGACTTGCTTTTGATCCGGAACTG
upper sequence: GLYMA13G17950.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0020g00880.t01 (Vitis vinifera), 3'ss of exon 3
-gtacgaaataggttatgtattgtgtggtttttcctggaactgtaggtttatt-tctatttaggtaaatggacttttatgatgttgacatgtgctcttt---cagGCTTGGGAAGGGAGGGCTTATGACTACTGTATGGAAAACCTTAAGAATATGGGTTTCCCTGTTGATGGACTTGCCTTTGATCCTGACCTG
|| | |||| | | || | || || | || | || || |||| || || | ||| | | | ||| | | |||||||||||||| |||| ||||| || |||||||| ||||| | ||| ||||| || ||||| ||||||||||| ||||| || || ||
cctatctgcttggtttagcttcatgga----taattgaaaaaggagttcctttgtccatttgaactggtgagattat-tgacataggtttatgcccctggtgcagGCTTGGGAAGGACGGGCGTATGAATATTGTATGGACAACCTAAGGAACATGGGGTTTCCTGTGGATGGACTTGCATTTGACCCAAACTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttatttctatttaggtaaatggacttttatgatgttgacatgtgctctttcagGCTTGGGAAGGGAGGGCTTATGACTACTGTATGGAAAACCTTAAGAATATGGGTTTCCCTGTTGATGGACTTGCCTTTGATCCTGACCTG
tgttgac putative branch site (score: 3)
tgctctttc putative PPT
tttctattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgaaataggttatgtattgtgtggtttttcctggaactgtaggtttatttctatttaggtaaatggacttttatgatgttgacatgtgctctttcagGCTTGGGAAGGGAGGGCTTATGACTACTGTATGGAAAACCTTAAGAATATGGGTTTCCCTGTTGATGGACTTGCCTTTGATCCTGACCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - ggttatg
- - - - - - - - - - tgtgtgg
- - - - - - - - - - - - - - - -tcctgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgac