Sequence
atgc intronic sequence ATGC exonic sequence...ggggttatgctgtgaagtctgttgtgcacaatgcacaatgcataaaagttaattgttttgatttctttaaatttgcacctaatatttgtctatttgacagATTGGGACTCCAATTTGCATTCCTTCTAGAGAGTTCATTGATATTGGTCGCATTGCCTCCATTGAGAATAACCACAAACCTGTTGATTATGCAAAGAAGG
Basic information
species | Glycine max |
transcript | GLYMA20G30590.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G30590.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G76820.1 (Arabidopsis thaliana), 3'ss of exon 10
ggggttatgctgtgaagtctgttgtgcacaatgcacaatgcataaaagtta-attgttttgatttctttaaatttgcacctaatatttgtctatttgacagATTGGGACTCCAATTTGCATTCCTTCTAGAGAGTTCATTGATATTGGTCGCATTGCCTCCATTGAGAATAACCACAAACCTGTTGATTATGCAAAGAAGG
| | | | | | |||| | | | | | ||| | | || | | || | | | |||| || | | || ||| | ||| |||| || || || |||||| | || |||||||||| |||||||| ||||||||||| |||||||| |||||||| |||||||| |||||| ||||||
-gtatcctattcttac-tctgctatattctcggtaacttgctcacatgtcataggattctcactccttttaacattcgtct------tgtttgttt--tagATCGGAACCCCCATTTGCGTCCCGGGCAGAGAGTTCACAGATATTGGCCGCATTGCCTCTATTGAGAACAACCACAAGCCTGTTGACTATGCAGAGAAGG
upper sequence: GLYMA20G30590.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G76720.1 (Arabidopsis thaliana), 3'ss of exon 14
ggggttatgctgtgaagtctgttgtgcacaatgcacaatgcataaaagtt-aattgttttgatttctttaaatttgcacctaatatttgtctatttgacagATTGGGACTCCAATTTGCATTCCTTCTAGAGAGTTCATTGATATTGGTCGCATTGCCTCCATTGAGAATAACCACAAACCTGTTGATTATGCAAAGAAGG
| | | | | | |||| | | | | | ||| | | || || || | | | |||| || | | || ||| | ||| |||| || || || |||||| | || |||||||||| |||||||| ||||||||||| |||||||| |||||||| |||||||| |||||| ||||||
-gtatcctattcttac-tctgctatattctcggtaacttgctcacatgtccaaggattctcaatccttttaacattcgtct------tgtttgttt--tagATCGGAACCCCCATTTGCGTCCCGGGCAGAGAGTTCACAGATATTGGCCGCATTGCCTCTATTGAGAACAACCACAAGCCTGTTGACTATGCAGAGAAGG
upper sequence: GLYMA20G30590.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G76810.1 (Arabidopsis thaliana), 3'ss of exon 10
ggggttatgctgtgaagtctgttgtgcacaatgcacaatgcataaaagttaattgttttgatttc-tttaaatttgcacctaatatttgtctatttgacagATTGGGACTCCAATTTGCATTCCTTCTAGAGAGTTCATTGATATTGGTCGCATTGCCTCCATTGAGAATAACCACAAACCTGTTGATTATGCAAAGAAGG
| |||||| | || | | | | || | || | | | | || | || | | || | | |||| | ||| |||||||| || || |||||| | ||| ||||||||||| |||||||| || |||||||| ||||||||||||||||| |||||||| |||||||||||||
gtatctatgcttttaa-tttcctacattctctgtaactctcacccatgatgacacaagtgctagggttcacactttcttatctgtcttgtttgtttt-cagATTGGAACCCCCATTTGCGTCCCTGGCAGAGAGTTCATCGATATTGGCCGAATTGCCTCGATTGAGAATAACCACAAGCCTGTTGACTATGCAAAGAAGG
upper sequence: GLYMA20G30590.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv18s0076g00310.t01 (Vitis vinifera), 3'ss of exon 10
ggggttatgctgtgaagtctgttgtgcacaatgcacaatgc-ataaaagttaattgtt--ttgatttctttaaatttgcacctaatatttgtctatttgacagATTGGGACTCCAATTTGCATTCCTTCTAGAGAGTTCATTGATATTGGTCGCATTGCCTCCATTGAGAATAACCACAAACCTGTTGATTATGCAAAGAAGG
| | | | | | ||||| || | | || | || | | |||| | | | | | || || | || | || |||| |||||||||||||||| |||||| || || || ||||||||||| || ||||| |||||||||||||||||||| || |||||| ||| ||||| |
-gtgatctatgattcatgttgttgcacaaccttaataacactatcagtgctaatgcataacaaacaggtctctgataccatctga--actggattttacacagGTTGGGACTCCAATTTGTATTCCTCAAAGGGATTTTATTGATATTGGCCGGATTGCATCCATTGAGAATAACCACAAGCCAGTTGATATTGCCAAGAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagttaattgttttgatttctttaaatttgcacctaatatttgtctatttgacagATTGGGACTCCAATTTGCATTCCTTCTAGAGAGTTCATTGATATTGGTCGCATTGCCTCCATTGAGAATAACCACAAACCTGTTGATTATGCAAAGAAGG
acctaat putative branch site (score: 3)
tttgtct CT-rich tract
aattgttttgatttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggggttatgctgtgaagtctgttgtgcacaatgcacaatgcataaaagttaattgttttgatttctttaaatttgcacctaatatttgtctatttgacagATTGGGACTCCAATTTGCATTCCTTCTAGAGAGTTCATTGATATTGGTCGCATTGCCTCCATTGAGAATAACCACAAACCTGTTGATTATGCAAAGAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - gctgtga
- - - - - - - - -tctgttg
- - - - - - - - - - - - - - -aatgcac
- - - - - - - - - - - - - - - - - - - tgcataa
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcacct