Sequence
atgc intronic sequence ATGC exonic sequencegtatttgttgtgacgggtggtatttaatttttatgattctcaatataggagtgtattttaaatctttccaggctgatatcaaacatgaatttcttatgttatccttcttgctttagGTGAATCCAGGAAATGCTCCTCTAGTTGTAGGACAGTTGTTAGATGATGAATGCCCTGAGGATTTCATTAAAGGTCTTATTCTTTCAGTTCGTTCTCTTC
Basic information
species | Glycine max |
transcript | GLYMA02G39360.1 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 21
gtatttgttgtgacgggtggtatttaatttttatgattct-caatataggagtgtattttaaatctttccaggctgatatcaaacatgaatttcttatgttatccttcttgctttagGTGAATCCAGGAAATGCTCCTCTAGTTGTAGGACAGTTGTTAGATGATGAATGCCCTGAGGATTTCATTAAAGGTCTTATTCTTTCAGTTCGTTCTCTTC
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-------------------gtatgcaactcttccaattcagtgttattggagtatc------atcattctcatgtgctatgtat--ttaaatgcttatttt--cctttatattgtagGTGAACCCTGGAAATGCTCCATTAGTTGTTGGACAGCTACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCC
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 21
gtatttgttgtgacgggtggtatttaatttttatgattct-caatataggagtgtattttaaatctttccaggctgatatcaaacatgaatttcttatgttatccttcttgctttagGTGAATCCAGGAAATGCTCCTCTAGTTGTAGGACAGTTGTTAGATGATGAATGCCCTGAGGATTTCATTAAAGGTCTTATTCTTTCAGTTCGTTCTCTTC
|||| || | || |||| ||| ||||| | ||| ||| || ||| | | || ||||||| || |||| | | |||||||| || ||||||||||| ||||||| |||||| | | |||||||| |||||||| ||||||||||| ||| | ||||| || || |||||||| |
-------------------gtatgcaactcttccaattcagtgttattggagtatc------atcattctcatgtgctatgtat--ttaaattcttatttt--cctttatattgtagGTGAACCCTGGAAATGCTCCATTAGTTGTTGGACAGCTACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCC
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 21
--gtatttgttgtgacgggtggtat-ttaatttttatgattctcaatataggagtgtat-----tttaaatctttccaggctgatatc----aaacatgaatttcttatgttatcct--tcttgctt--tagGTGAATCCAGGAAATGCTCCTCTAGTTGTAGGACAGTTGTTAGATGATGAATGCCCTGAGGATTTCATTAAAGGTCTTATTCTTTCAGTTCGTTCTCTTC
| || ||| | | || | | || |||| | | || || | || ||| | ||| ||| | | || || || ||||| ||| || | | || || ||||| ||||| |||||||||||||||||||| || || | ||||||||||||||||||| ||||||||||||||||| |||||||||||||| |||||||
gtacaattactgtaaggagttatttatttatttatttatttttccaaatgaagatgtttcattattttaattgcactgagtccatgtctgcagaagatgaaccatgtattttcttttgtctttaattgatagGTAAATCCGGGAAATGCTCCTCTAGTTGTTGGGCAACTTCTAGATGATGAATGCCCTGAAGATTTCATTAAAGGTCTCATTCTTTCAGTTCGGTCTCTTC
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 21
lower sequence: EFJ13237 (Selaginella moellendorffii), 3'ss of exon 21
gtatttgttgtgacgggtggtatttaatttttatgattctcaatataggagtgtattttaaatctttccaggctgatatcaaacatgaatttcttatgttatccttcttg---ctttagGTGAATCCAGGAAATGCTCCTCTAGTTGTAGGACAGTTGTTAGATGATGAATGCCCTGAGGATTTCATTAAAGGTCTTATTCTTTCAGTTCGTTCTCTTC
| ||| | ||| || || | | ||| || | || |||| ||||| | ||| || | ||| || || || || | |||||||||||||| ||||||||||| |||||| ||| || || || ||||| || | |
---------------------------------------------------------------------gtacggattcaatgcatttgttgctc-tataatcgttttgaaattttcagGTCAATCCTGCAAACGCACATCTGGTCGTGGGCCAACTTTTAGATGATGAATGTCCTGAGGATTTTATTAAAAATCTCATCCTCTCTGTTCGATCGTTAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atctttccaggctgatatcaaacatgaatttcttatgttatccttcttgctttagGTGAATCCAGGAAATGCTCCTCTAGTTGTAGGACAGTTGTTAGATGATGAATGCCCTGAGGATTTCATTAAAGGTCTTATTCTTTCAGTTCGTTCTCTTC
ggctgat putative branch site (score: 4)
ttatccttcttgcttt putative PPT
aatttcttatgttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttgttgtgacgggtggtatttaatttttatgattctcaatataggagtgtattttaaatctttccaggctgatatcaaacatgaatttcttatgttatccttcttgctttagGTGAATCCAGGAAATGCTCCTCTAGTTGTAGGACAGTTGTTAGATGATGAATGCCCTGAGGATTTCATTAAAGGTCTTATTCTTTCAGTTCGTTCTCTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT