Sequence
atgc intronic sequence ATGC exonic sequencegtgactatcataagtttaatcattgtgagttgctctcttgccgattcaatctgccttatgtggtgtcttgtcctgttgacacttgaccagGTTGTGATGTCATTTCATGAATGTGGAGGCAATTTTGGTGATGATGTTTGTATTCCATTACCCCATTGGGTTGCTGAGATTGGTAGGAGCAATCCTGACA
Basic information
species | Glycine max |
transcript | GLYMA18G46630.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G46630.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os09g39570.1 (Oryza sativa), 3'ss of exon 3
------------------------------------------------------------------------------------gtgactatcata--agtttaatcattgtgagttgctctcttgccgattcaatctgccttatgtggtgtct-------tgtcctgttga--cacttgaccagGTTGTGATGTCATTTCATGAATGTGGAGGCAATTTTGGTGATGATGTTTGTATTCCATTACCCCATTGGGTTGCTGAGATTGGTAGGAGCAATCCTGACA
| | || | | | | | | | || || | | || | || ||| |||||| | | || ||| | |||| |||| || |||||||| ||||| |||||||||||| |||| |||||||| | |||||| | || |||||||| | ||||| || || |||||||| || |
gttattcctccactccacattatattgtcatgcatgtcaccctttgttgttaatcatgttttggtgtttatgcgcatttcagatttcagtaccgtgctaatacaggatctattcatttatcctctccaattttaccctttctttcatggtgtttcttttaatttcttgtcaaaatacttacttagGTGGTCATGTCATTCCATGAGTGTGGAGGCAATGTTGGAGATGATGTGTCTATTCCTCTCCCACATTGGGTAACAGAGATCGGAAGAAGCAATCCAGATA
upper sequence: GLYMA18G46630.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G45880.1 (Arabidopsis thaliana), 3'ss of exon 5
---------------------gtgactatcata-agtttaatcattgtgagttgctctcttgccgattcaatct-gccttatgtggtgtcttgtcctgttgacacttgaccagGTTGTGATGTCATTTCATGAATGTGGAGGCAATTTTGGTGATGATGTTTGTATTCCATTACCCCATTGGGTTGCTGAGATTGGTAGGAGCAATCCTGACA
|| || ||| ||||| | | || |||||| | | || || | || || | ||| | || | | ||||| | ||||| ||||||||||||||||||||| |||||||||||||||| || ||| | || |||||||| || || || || | | |||||| ||||
gtcagtcttttacctgcatgattggttaagatacagttttcttaatg-aagttgcgttagaatgattgttctcaagcttcatatg-tatctcactttctttctttcttgctagGTTCTAATGTCCTTTCATGAATGTGGAGGCAATGTTGGTGATGATGTTTGCATCCCACTTCCTCATTGGGTGGCAGAAATAGGACGAACCAATCCGGACA
upper sequence: GLYMA18G46630.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv15s0046g02640.t01 (Vitis vinifera), 3'ss of exon 4
-----------gtgactatcataagtttaatcattgtgagttgctct---cttgccgattcaatctgccttatgtggtgtcttgtcctgttgacacttgaccagGTTGTGATGTCATTTCATGAATGTGGAGGCAATTTTGGTGATGATGTTTGTATTCCATTACCCCATTGGGTTGCTGAGATTGGTAGGAGCAATCCTGACA
||| ||| | ||| | |||| || | || | | | |||| || |||| || ||| | | ||||||||| ||||||||||||||||||| |||||| |||||||||||||||| |||||| | ||||||||||| || || || ||| | |||||||||||||
aaagcaggaatgtgtttatttt--gttggaatgttgttgcttttgttaattttcaaggctgattctgtttttgatggtagacaatctc--tgatcttggcccagGTTGTATTGTCATTTCATGAATGTGGTGGCAATGTTGGTGATGATGTTTGCATTCCACTGCCCCATTGGGTGGCAGAAATCGGTCGAAGCAATCCTGACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttgccgattcaatctgccttatgtggtgtcttgtcctgttgacacttgaccagGTTGTGATGTCATTTCATGAATGTGGAGGCAATTTTGGTGATGATGTTTGTATTCCATTACCCCATTGGGTTGCTGAGATTGGTAGGAGCAATCCTGACA
tgttgac putative branch site (score: 3)
attcaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgactatcataagtttaatcattgtgagttgctctcttgccgattcaatctgccttatgtggtgtcttgtcctgttgacacttgaccagGTTGTGATGTCATTTCATGAATGTGGAGGCAATTTTGGTGATGATGTTTGTATTCCATTACCCCATTGGGTTGCTGAGATTGGTAGGAGCAATCCTGACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA