Sequence
atgc intronic sequence ATGC exonic sequencegtagtaataccagcagattctttttctgctttcaaggacaattactttcttgggatctctgcatttacatccaaaaaaataaaatgctcatcaaatttctttatcataacttttgacagTTGTGGCCTGAGAAATTCCAGAATAAAACAAATGGGGTGACTCCTAGAAGATGGATCCGTTTCTGCAATCCTGATCTTAGTAAAATCATAACCAAGTGGA
Basic information
species | Glycine max |
transcript | GLYMA20G03250.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G03250.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os03g55090.1 (Oryza sativa), 3'ss of exon 8
gtagtaataccagcagattctttttctgctttcaaggacaattactttcttgggatctctgcatttacatccaa--aaaaataaaatgctcatcaaatttctttatcataacttttgacagTTGTGGCCTGAGAAATTCCAGAATAAAACAAATGGGGTGACTCCTAGAAGATGGATCCGTTTCTGCAATCCTGATCTTAGTAAAATCATAACCAAGTGGA
|| || || || | || || || || || || |||| | || | || || ||| | ||| || || | | | |||||| ||||||| | ||||| || |||||||||||||| |||||||||||| | ||||| || || || |||||||| | ||| |||||| | || ||||
------gtatttacatggcgttatttggaattgggatacttttttttcatttatttccctgcttctataatcatccaattatatgacattcaccatcttcccattttgc------tgacagATGTGGCCCGCTAAATTTCAAAATAAAACAAATGGAGTGACTCCTAGACGTTGGATTCGGTTTTGTAATCCTGAATTAAGTGCAATCATTTCAAAATGGA
upper sequence: GLYMA20G03250.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G074158_T02 (Zea mays), 3'ss of exon 8
gtagtaataccagcagattctttttctgctttcaaggacaattactttcttgggatctctgcatttacatccaaaaaaataaaatgctcatcaaatttctttatcataacttttgacagTTGTGGCCTGAGAAATTCCAGAATAAAACAAATGGGGTGACTCCTAGAAGATGGATCCGTTTCTGCAATCCTGATCTTAGTAAAATCATAACCAAGTGGA
||| ||||| || | | | || || | || |||||| || || ||||| || || ||| | | | | |||| ||| ||||||| ||||| ||||||||||||||||| |||||||| || | |||||||| || || ||||||| | ||| | | || | |||||||
gtattaatatgagaatctgaatcttatgtctccat---------ttttcttataatg-----------atttgggaaaatgc--tgttcgtcatctgttctgttt-----ctttggcagATGTGGCCAACTAAATTTCAGAATAAAACAAATGGAGTGACTCCCAGGCGTTGGATCCGGTTTTGTAATCCTGCATTAAGTGCATTAATTTCAAAGTGGA
upper sequence: GLYMA20G03250.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv01s0011g00730.t01 (Vitis vinifera), 3'ss of exon 8
gtagtaataccagcagattctttttctgctttcaaggacaattactttcttgggatctctgcatttaca---tccaaaaaaataaaatgctcatcaaatt--tcttta------tcataacttttgacagTTGTGGCCTGAGAAATTCCAGAATAAAACAAATGGGGTGACTCCTAGAAGATGGATCCGTTTCTGCAATCCTGATCTTAGTAAAATCATAACCAAGTGGA
||| | |||| || | ||| | | |||| | | | | | | ||| || || | | || ||||| | || | |||| | | | ||| || ||||||||||| |||||||| || || ||||||||||||||||| || ||||||||||| || || |||||||| ||||||||||| ||||||||||||||||
gtaactagaccaacatttaactttctccccctt-----tcattatcctaatagaagatgatgttccacaagttctcaagatagaagttgctctttcaactgatcttcactcacattttgccttctggcagTTGTGGCCAGAGAAATTTCAAAACAAAACAAATGGGGTGACACCAAGAAGATGGATTCGCTTTTGCAATCCCGATCTTAGTAACATCATAACCAAGTGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttacatccaaaaaaataaaatgctcatcaaatttctttatcataacttttgacagTTGTGGCCTGAGAAATTCCAGAATAAAACAAATGGGGTGACTCCTAGAAGATGGATCCGTTTCTGCAATCCTGATCTTAGTAAAATCATAACCAAGTGGA
tcataac putative branch site (score: 2)
ctttt CT-rich tract
aaatttctttatcata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagtaataccagcagattctttttctgctttcaaggacaattactttcttgggatctctgcatttacatccaaaaaaataaaatgctcatcaaatttctttatcataacttttgacagTTGTGGCCTGAGAAATTCCAGAATAAAACAAATGGGGTGACTCCTAGAAGATGGATCCGTTTCTGCAATCCTGATCTTAGTAAAATCATAACCAAGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA