Sequence
atgc intronic sequence ATGC exonic sequencegtaaagtcagccacccttttcctttttcattttcttgttttgatatctctgtctgtgcattgttttatgatcaacatgggatattaattcgtgtggcttttgttaatggtatgtggaacatggaacagCTGCAGTGGCATGGGGAGCTGGGGAAGCATTGGTGATAGAGGAAGTGGAAGTGAGTCCTCCTCAACCAATGGAGATTAGGATTAAGGTTGTCTCCACTTC
Basic information
species | Glycine max |
transcript | GLYMA16G23820.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G23820.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G24760.3 (Arabidopsis thaliana), 3'ss of exon 1
----gtaaagtcagccacccttttcctttttcattttcttgttttgat--atctctgtctgtgcattgttttatgatcaacatgggatattaattcgtgtggcttttgttaat--ggtatgtggaacatggaac-----agCTGCAGTGGCATGGGGAGCTGGGGAAGCATTGGTGATAGAGGAAGTGGAAGTGAGTCCTCCTCAACCAATGGAGATTAGGATTAAGGTTGTCTCCACTTC
| ||| | | | | | ||| | ||| | ||||| | ||| | || || || | || | || | | || | || || | | || | || ||| || ||||||||| | ||||| || ||||||| || |||||||| ||||||||||| ||||||||| |
gtaagaaaatttgggagaacaatgtcggcttcttcttcctcctttgaacaacctcaagtcataacctgcaacggtataaaaaaaggttttttttgtatttgttgatgaaagATTAGGGTTTTTGATTGAGAAATTCTGTAGCGGCGGTGGCATGGCGTGCTGGTGAGCCATTGGTTATGGAGGAAGTTGAAGTGAGTCCACCTCAACCACT------------------------------
upper sequence: GLYMA16G23820.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G24760.1 (Arabidopsis thaliana), 3'ss of exon 1
gtaaagtcagccacccttttcctttttcattttcttgttttgatatctctgtctgtgcattgttttatgatcaacatgggatattaattcgtgtggcttttgttaatggtatgtggaacatggaacagCTGCAGTGGCATGGGGAGCTGGGGAAGCATTGGTGATAGAGGAAGTGGAAGTGAGTCCTCCTCAACCAATGGAGATTAGGATTAAGGTTGTCTCCACTTC
|| | | | ||| | | | || || || | || ||||| | || | || ||| || ||||||||| | ||||| || ||||||| || |||||||| ||||||||||| ||||||||| | ||||| || ||||| ||||| | || ||
--------------------------------------------------gtataaaaaaaggttttttttgtatttgttg-atgaaagattagggtttttgat---------tgagaaattctgtagCGGCGGTGGCATGGCGTGCTGGTGAGCCATTGGTTATGGAGGAAGTTGAAGTGAGTCCACCTCAACCACTTGAGATCAGAATTAAAGTTGTATGTACATC
upper sequence: GLYMA16G23820.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0039g00320.t01 (Vitis vinifera), 3'ss of exon 1
gtaaagtcagccacccttttcctttttcattttcttgttttgatatctctgtctgtgcattgttttatgatcaacatgggatattaattcgtgtggcttttgttaatgg-tatgtggaacatggaacagCTGCAGTGGCATGGGGAGCTGGGGAAGCATTGGTGATAGAGGAAGTGGAAGTGAGTCCTCCTCAACCAATGGAGATTAGGATTAAGGTTGTCTCCACTTC
| || | | ||| || | ||||| | | | ||| ||| || || || | | | || | ||| || | | | | |||||| |||| || |||||||| || |||||||||||||| ||||||||||| || || || || || ||||||||||||||||| ||||||||||||||
---------------gtaagaacttgccgcatcgttgcttcaaaatctccat------aatttttcccgataaattaatgaactttttgtat-tcatgttcataaataaataaataaataaatatatagCTGCTGTGGGATATGGAGCTGGAGAGGCATTGGTGATAGAAGAAGTGGAAGTCAGCCCGCCACAGCCTATGGAGATTAGGATTAAAGTTGTCTCCACTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acatgggatattaattcgtgtggcttttgttaatggtatgtggaacatggaacagCTGCAGTGGCATGGGGAGCTGGGGAAGCATTGGTGATAGAGGAAGTGGAAGTGAGTCCTCCTCAACCAATGGAGATTAGGATTAAGGTTGTCTCCACTTC
atattaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagtcagccacccttttcctttttcattttcttgttttgatatctctgtctgtgcattgttttatgatcaacatgggatattaattcgtgtggcttttgttaatggtatgtggaacatggaacagCTGCAGTGGCATGGGGAGCTGGGGAAGCATTGGTGATAGAGGAAGTGGAAGTGAGTCCTCCTCAACCAATGGAGATTAGGATTAAGGTTGTCTCCACTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT