Sequence
atgc intronic sequence ATGC exonic sequence...ttgtgacgtaaacgtccggatccttgtctctatttccactgatattgagaaaacttcttcaagacatatattacctaaaatcacatcatgcattttgtagTGATCGCTGGGGAAATAGCCAATTTTGCAGCTTATGCGTTCGCTCCTGCAATCCTTGTAACTCCTTTGGGAGCTTTGAGCATCATTTTCAG
Basic information
| species | Glycine max |
| transcript | GLYMA11G36550.1 |
| intron # | 3 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G36550.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g30450.1 (Oryza sativa), 3'ss of exon 2
--------------------------------------------------------------------------------ttgtgacgtaaacgtccggatccttgtctctatttccactga--tattgagaaaacttcttca-agacatatattacctaaaatcacatcatgcattttgtagTGATCGCTGGGGAAATAGCCAATTTTGCAGCTTATGCGTTCGCTCCTGCAATCCTTGTAACTCCTTTGGGAGCTTTGAGCATCATTTTCAG
|||| | | | ||| || || || || || || |||| | ||||| | | | | ||| | || ||| | | || |||||| ||| || | ||||| || ||||| ||||| || ||||||||||| ||||| |||||| | ||||| |||||||||| |||||
gtaagtatggattacattgtgctcttttctgttgataatgcgtggcaaagaaggcattctcagtctaatccagtttccttttgttatatgatactccatatttatggaaataatttattggaactactgaggtagcttctacgtaagttcacactac---agattttatctctc-tgttacagTGATTCTTGGTGAGGTGGCCAACTTCGCAGCATATGCATTTGCTCCTGCAATACTTGTCACTCCTCTAGGAGCGCTGAGCATCATATTCAG
upper sequence: GLYMA11G36550.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G13800.1 (Arabidopsis thaliana), 3'ss of exon 2
ttgtgacgtaaacgtccggatccttgtctctatttccactgatattgagaaaacttcttcaagacatatattacctaaaatcacat-catgca---ttttgtagTGATCGCTGGGGAAATAGCCAATTTTGCAGCTTATGCGTTCGCTCCTGCAATCCTTGTAACTCCTTTGGGAGCTTTGAGCATCATTTTCAG
||| ||| | | | |||| || |||||| | || || | | | | ||| || |||| || || ||| | | || ||||||| | |||||| ||||||||||||||||| ||||| || || || || || || ||||| |||||||||||||| || || ||||||||
ttgggacat--gttttggaatccaagtttctattggatttaatcaatggacatcaaactttgg--ttatgataactaatattgtattcatactaattcttatagTGATTGTTGGGGAGATAGCCAATTTTGCAGCATATGCATTTGCACCGGCTATTCTAGTAACACCTTTGGGAGCTTTAAGTATTATTTTCAG
upper sequence: GLYMA11G36550.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0029g00620.t01 (Vitis vinifera), 3'ss of exon 1
ttgtgacgtaaacgtccg--gatccttgtctctatttccactgatattgagaaaacttcttcaagacatatattacctaaaatcacatcatgca-ttttgtagTGATCGCTGGGGAAATAGCCAATTTTGCAGCTTATGCGTTCGCTCCTGCAATCCTTGTAACTCCTTTGGGAGCTTTGAGCATCATTTTCAG
| || | | | | | || || | ||| | || || |||| | | | | | || | | | | |||| ||||||| |||||| ||||| |||||||| |||||||| || ||||||||||| |||||||| |||||||||||| | ||||| ||||||||
---ttactttttctcctattgcttctagtattgtttttctacaattatgtgaaattccttccttcatgctttgtgtttatgctaagtttctatgcttttatagTGATTTTTGGGGAGATAGCTAATTTTGCTGCTTATGCATTTGCTCCTGCAATTCTTGTAACCCCTTTGGGAGCTCTAAGCATTATTTTCAG
upper sequence: GLYMA11G36550.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ16080 (Selaginella moellendorffii), 3'ss of exon 2
ttgtgacgtaaacgtccggatccttgtctctatttccactgatattgagaaaacttcttcaagacatatat------tacctaaaatcacatcatgcattttgtagTGATCGCTGGGGAAATAGCCAATTTTGCAGCTTATGCGTTCGCTCCTGCAATCCTTGTAACTCCTTTGGGAGCTTTGAGCATCATTTTCAG
| || | || | || || | || || | || | | | | || | |||||| ||| || | || || |||||||| |||||||| |||||||| || ||||| || ||||| ||||||||||| || || | ||
--------------------------------------------gtaagctagtttgtccaggatgaaaatgcgaaataacaaagtttgctcacttctttgagcagTGATATTTGGCGAGGTTGCAAACTTTGCAGCGTATGCGTTTGCTCCTGCGATACTTGTCACGCCTTTAGGAGCTTTGAGTATTATAGTAAG
upper sequence: GLYMA11G36550.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ15113 (Selaginella moellendorffii), 3'ss of exon 2
ttgtgacgtaaacgtccggatccttgtctctatttccactgatattgagaaaacttcttcaagacatatattacctaaaatcacatcatgcattttgtagTGATCGCTGGGGAAATAGCCAATTTTGCAGCTTATGCGTTCGCTCCTGCAATCCTTGTAACTCCTTTGGGAGCTTTGAGCATCATTTTCAG
| || | || | | | || | | || | || | | | | || | |||||| ||| || | || || |||||||| |||||||| |||||||| || ||||| || ||||| ||||||||||| || || | ||
---------------------------------gtaagctagtttttccagga-----tgaaaatgcgaaataacaaagtttgctcacttctttgagcagTGATATTTGGCGAGGTTGCAAACTTTGCAGCGTATGCGTTTGCTCCTGCGATACTTGTCACGCCTTTAGGAGCTTTGAGTATTATAGTAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgagaaaacttcttcaagacatatattacctaaaatcacatcatgcattttgtagTGATCGCTGGGGAAATAGCCAATTTTGCAGCTTATGCGTTCGCTCCTGCAATCCTTGTAACTCCTTTGGGAGCTTTGAGCATCATTTTCAG
acctaaa putative branch site (score: 3)
atatattacctaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgtgacgtaaacgtccggatccttgtctctatttccactgatattgagaaaacttcttcaagacatatattacctaaaatcacatcatgcattttgtagTGATCGCTGGGGAAATAGCCAATTTTGCAGCTTATGCGTTCGCTCCTGCAATCCTTGTAACTCCTTTGGGAGCTTTGAGCATCATTTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - -ccttgtc
- - - - - - - - - - - - - - - - - tccactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacatca
