Sequence
atgc intronic sequence ATGC exonic sequencegtgtccaatttatgtgattgacccatgttttactttgtatgtgaacagTCTAGAGTAGTCCAATGCAACGAAGGGGAAAGGTCATATCATATATTTTATCAGCTATGTGCTGGAGCACCATCATCACTTAGGG
Basic information
species | Glycine max |
transcript | GLYMA20G23660.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G23660.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G50360.1 (Arabidopsis thaliana), 3'ss of exon 9
---------------------------------------------------gtgtccaatttatgtgattgacccatgttttact-ttgtatgtgaacagTCTAGAGTAGTCCAATGCAACGAAGGGGAAAGGTCATATCATATATTTTATCAGCTATGTGCTGGAGCACCATCATCACTTAGGG
| | ||| | || || |||||| | | | | | | |||| ||||| || ||||| | ||||| |||||||||||||||||||| ||||| || |||||||| || || | ||||||| |
gtaaattcctcaatatttttgctgcttcagtttctttcatgttgaaaaatgatttttaatat-tgacatcctttcatgttctgttgtcacactttcatagTCAAGAGTGGTTCAATGTACGGAAGGAGAAAGGTCATATCATATATTCTATCAACTTTGTGCTGGGGCTTCACCTACACTTAGAG
upper sequence: GLYMA20G23660.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 10
-------------------------------------------------gtgtccaatttatgtgattgacccatgttt-tactttg---tatgtgaacagTCTAGAGTAGTCCAATGCAACGAAGGGGAAAGGTCATATCATATATTTTATCAGCTATGTGCTGGAGCACCATCATCACTTAGGG
|| ||| | | | ||| || ||| || | ||||||||||||| |||||||| ||||||||||||||||||||||| |||||||| || |||||||| || || | ||||||| |
gtagcttctttggatgattttatttgcttgatttctttcctttttaaacatgattcattaacattgacattttttctttgtatgttgactcattttaacagTCTAGAGTGGTCCAATGTGCTGAAGGGGAAAGGTCATATCATATTTTTTATCAACTTTGTGCTGGGGCTTCACCTGCACTTAGAG
upper sequence: GLYMA20G23660.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 8
-------------------------gtgtccaatttatgtgattgacccatg------------ttttactttgtatgtgaacagTCTAGAGTAGTCCAATGCAACGAAGGGGAAAGGTCATATCATATATTTTATCAGCTATGTGCTGGAGCACCATCATCACTTAGGG
||| | | | ||||| | ||| || | | | | ||||||||||||||| |||||||| ||||| || ||||||||||||||||||||||| || ||||||||||| ||| || | ||||| |
gtaattctttctttatctgtatctattgtttggtctgtttgattttctcataatgggttgttaattgtgtctcttttatgaacagTCTAGAGTGGTCCAATGTGCAGAAGGAGAGAGGTCATATCATATATTTTATCAACTCTGTGCTGGAGCTCCACCAGCTCTTAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgtccaatttatgtgattgacccatgttttactttgtatgtgaacagTCTAGAGTAGTCCAATGCAACGAAGGGGAAAGGTCATATCATATATTTTATCAGCTATGTGCTGGAGCACCATCATCACTTAGGG
gattgac putative branch site (score: 3)
aatttatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtccaatttatgtgattgacccatgttttactttgtatgtgaacagTCTAGAGTAGTCCAATGCAACGAAGGGGAAAGGTCATATCATATATTTTATCAGCTATGTGCTGGAGCACCATCATCACTTAGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA