Sequence
atgc intronic sequence ATGC exonic sequencegtcagacatgattccttactagtctttctacctatattgcattttgctttgacattcatattcatcatttctcaaattaccacagAAACTGTATGAGCTTGTTGTTCGCCACTTTTTGGCATGTGTCTCAAAGCCTGCTTTAGGAGCTGAAACCACTGTTGAAATTAATATTGCTGGTGAATTAT
Basic information
species | Glycine max |
transcript | GLYMA06G16200.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G16200.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g06900.1 (Oryza sativa), 3'ss of exon 9
-------------------gtcagacatgat----tccttactagtcttt-----ctacctatattgcattttgct--ttgacattcatattcatcat--ttctcaaattac-cacagAAACTGTATGAGCTTGTTGTTCGCCACTTTTTGGCATGTGTCTCAAAGCCTGCTTTAGGAGCTGAAACCACTGTTGAAATTAATATTGCTGGTGAATTAT
|||| | || | ||| || | ||| | | | || || | | | | | | | || |||| || || || |||||| |||||||||||||||||||||| || | || ||| ||| | ||||| | ||||||||||| ||||| |||||| | |||||||||||| |
gtatgtgtctttcctatatagcagatactatagcatttttaatattttttaaaggcagtatttcttatgttctacaagtgtgtaataaaactcttcatatttgtcttcttgtgtccagAAATTGTATGAGCTTGTTGTTCGCCATTTCCTTGCTTGTTGCTCCCAACCTGCAGTTGGAGCTGAAACAACTGTGGAAATTGACATTGCTGGTGAACAGT
upper sequence: GLYMA06G16200.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv04s0044g01570.t01 (Vitis vinifera), 3'ss of exon 2
--------------------------------------------------gtcagacatgattccttactagtctttctacctatattgcattttgctttgacattcatattcat-catttctcaaatt--accacagAAACTGTATGAGCTTGTTGTTCGCCACTTTTTGGCATGTGTCTCAAAGCCTGCTTTAGGAGCTGAAACCACTGTTGAAATTAATATTGCTGGTGAATTAT
|| ||| || | | | | ||| ||| || || | ||| | | || |||| ||| | |||||||| | ||||||||||| || |||||||| || ||| |||| ||| |||| ||||| || | |||||||||| ||||||| ||||||| ||
gtaagtccaattatttttactattattgaatggcatctggtggtagcggcatctattatgtttttcttttgtgtaacttgaggagcttggttttcactatgttctcttgatttctatgtcactttaattttgttgtagAGATTGTATGAGTTGGTTGTTCGCCATTTCTTGGCATGCGTTTCACAGCCAGCTGTAGGTGCTGAGACAATTGTTGAAATTGATATTGCCGGTGAATCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctatattgcattttgctttgacattcatattcatcatttctcaaattaccacagAAACTGTATGAGCTTGTTGTTCGCCACTTTTTGGCATGTGTCTCAAAGCCTGCTTTAGGAGCTGAAACCACTGTTGAAATTAATATTGCTGGTGAATTAT
ctttgac putative branch site (score: 4)
attcatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagacatgattccttactagtctttctacctatattgcattttgctttgacattcatattcatcatttctcaaattaccacagAAACTGTATGAGCTTGTTGTTCGCCACTTTTTGGCATGTGTCTCAAAGCCTGCTTTAGGAGCTGAAACCACTGTTGAAATTAATATTGCTGGTGAATTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA