Sequence
atgc intronic sequence ATGC exonic sequencegtgggtgatgctttgattatttctgttacataatttgaatattcacttgtgctgatctggaaataaaaaacaatggcgcagATTAAAATAGGCATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCAAGAAACAACCAAATGATGGAGCTCATGTTC
Basic information
species | Glycine max |
transcript | GLYMA06G23080.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G23080.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g20820.1 (Oryza sativa), 3'ss of exon 3
gtgggtgatgctttgattatttctgttacataatttgaatat---tcacttgtgctgatctggaaa--taaaaaacaatgg-----------cgcagATTAAAATAGGCATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCAAGAAACAACCAAATGATGGAGCTCATGTTC
|| | | | | || | | | || | ||| ||| | ||| | | | | | | || || || || || |||||||||||| || |||||||||||||| ||||||||| || |||||||| | ||||| || ||||| ||||| || || |||||||||||||||||||
gtctgcagtcatcttgttttatttcccacct--tttcaatgtggaccaccttttttttttttgtaacttataatactgtgaacccatcctactgcagATTAAAATTGGAATGGATGTTGCAGCATCAGAGTTTCTTACAAAGGATGGAAGCTATGACTTAAACTTTAAGAATCAGCCTAATGATGGAGCTCATGTTC
upper sequence: GLYMA06G23080.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G034848_T01 (Zea mays), 3'ss of exon 3
gtgggtgatgctttgattatttctgttacata---atttgaatattcacttgtgctgatctggaaataaaaaacaa----tggcgcagATTAAAATAGGCATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCAAGAAACAACCAAATGATGGAGCTCATGTTC
||| | || | | | || || || | ||||| | ||| |||| | || | ||| | ||||||| | |||||| ||||| || ||||||||||| || |||||||| || ||||||||||| |||||| | ||||| ||||| || || |||||||||| |||||||
gtgtgatatcatctaactagtttcattggccacttgtttgattgttctcttgattttattttgaattttaaaacaaatcctaatgcagATCAAAATTGGAATGGATGTTGCGGCATCAGAGTTCCTTACAAAGGATGGGAACTATGATCTAAACTTTAAGAATCAGCCTAATGATGGAGTCCATGTTC
upper sequence: GLYMA06G23080.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G74030.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------------------------------gtgggtgatgctttgattatttctgttacataatttgaatattca-cttgtgctgatctggaaataaaaaacaatggcgcagATTAAAATAGGCATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCAAGAAACAACCAAATGATGGAGCTCATGTTC
|| || || | | | | || | | | ||| | || |||| | || | |||||| |||||||| ||||||||||| || ||||| |||| || || ||||| | || |||||||||||||||||||| ||||| ||||||||||| || |
gtaatcaagttctctttctttttaatgctaatacttgctaaagttgcatgtcatctgtgtttccctaaacaacttctggcagcttcggtgtcaatcttacaccactcacataatatataatttt--tgcagATCAAAATAGGAATGGATGTTGCTGCATCAGAATTTTTCATGAAAGATGGTAGATACGATTTGAACTTCAAGAAACAGCCAAACGATGGAGCTCACGTAC
upper sequence: GLYMA06G23080.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 3
gtgggtgatgctttgattat-ttctgttacataatttgaatattcacttgtgctgatctggaaataaaaaacaatggcgcagATTAAAATAGGCATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCAAGAAACAACCAAATGATGGAGCTCATGTTC
|| || | ||| || | || | || | ||||| | | |||| | | | | ||| |||| |||||| |||||||| ||||||||||||||||||||||| | |||||| |||||||| ||||||||||| || |||||||||||||||||||||||||| ||||
gtaggcgggttgttgcttttcttttcttttgcagtttgatt--ttccttgcagcctttaaggactccaaataaatgatgcagATCAAAATAGGAATGGATGTTGCAGCTTCAGAGTTCTTCACTAAAGATGGGAAATATGATTTGAATTTTAAGAAACAACCAAATGATGGAGCTCACGTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacataatttgaatattcacttgtgctgatctggaaataaaaaacaatggcgcagATTAAAATAGGCATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCAAGAAACAACCAAATGATGGAGCTCATGTTC
tgctgat putative branch site (score: 3)
aaataaaaaacaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgggtgatgctttgattatttctgttacataatttgaatattcacttgtgctgatctggaaataaaaaacaatggcgcagATTAAAATAGGCATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCAAGAAACAACCAAATGATGGAGCTCATGTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA