Sequence
atgc intronic sequence ATGC exonic sequence...acattagctttcggttaatgtttttgtcactatgtcaatggctttaaaaggggtttcttaaatttgcgctcttatccgctcctttctttttccattgtagGTTATTGCAGCTGGAATGAATCCTGTTCAAATTGCTCGTGGCATTGAGAAGACAGCAACAGCGCTTGTTTCTGAACTCAGATTGATGTCAAGAGAA
Basic information
species | Glycine max |
transcript | GLYMA01G09520.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G09520.1 (Glycine max), 3'ss of exon 3
lower sequence: 13113.m00214 (Oryza sativa), 3'ss of exon 3
-----------------------acattagctttcggttaatgtttttg-tcactatgtcaatggctttaaaag--gggtttcttaa---atttgcgctcttatccgctcctttctttttccatt------gtagGTTATTGCAGCTGGAATGAATCCTGTTCAAATTGCTCGTGGCATTGAGAAGACAGCAACAGCGCTTGTTTCTGAACTCAGATTGATGTCAAGAGAA
| || | | | ||| || | | | | || || | || | || | | | |||||||| | || | | || |||||| ||||||||||||| |||||||| || ||||| || |||||||||||||| || | || | || |||||||||||||||||||| | ||
gtgtgttgcgtgctcctgtcctctccttgtccgtgccctgtaatttgtgattaacaggaaaactatccggaatgatggatacgttgagacactctgaatcttatcctgtatcttatgatcatgttcatgaagtagGTGCTTGCAGCTGGAATTAATCCTGTCCAGATTGCGCGGGGCATTGAGAAGACTGCTTCTGCTTTGGTGTCTGAACTCAGATTGATGTCCCGGGAG
upper sequence: GLYMA01G09520.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G042253_T01 (Zea mays), 3'ss of exon 2
------------------acattagctttcggt-taatgttttt----------gtcactatgtcaatggctttaaaaggggtttcttaaatttgcgctcttatccgctcctt----tctttttccattgtagGTTATTGCAGCTGGAATGAATCCTGTTCAAATTGCTCGTGGCATTGAGAAGACAGCAACAGCGCTTGTTTCTGAACTCAGATTGATGTCAAGAGAA
||||| |||| | | || | || ||||| | | || | | | | | | || ||| ||| | ||| | ||||||| ||||||||||||| || || ||||| | || ||||||||||||||||| || | || | || ||||| |||||| ||||||| | |
gtgtgcctatctcttctctaattagttttctatacactggtaacagcgaaaaaagttgctatgatgaagttgttgatttatagattctgagtcaggatcctgcattgcttcttataattgtttcataaagtagGTTCTTGCAGCTGGAATCAACCCAGTTCAGGTCGCACGTGGCATTGAGAAGACTGCTGCTGCTTTGGTGTCTGAGCTCAGACTGATGTCGCGGGTG
upper sequence: GLYMA01G09520.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0010g00920.t01 (Vitis vinifera), 3'ss of exon 3
----acattagctttcggttaatgtttttgtcactatgtca-atggctttaaaaggggtttcttaaatttgcgctcttatccgctcctttctttttccattgtagGTTATTGCAGCTGGAATGAATCCTGTTCAAATTGCTCGTGGCATTGAGAAGACAGCAACAGCGCTTGTTTCTGAACTCAGATTGATGTCAAGAGAA
||| || | | || | | | |||| | ||| |||| || ||| || | | | | ||| || | | | ||||| |||||||| |||||||| || |||||||| ||||||| ||||||||||| |||| || |||||||||||||||| ||||||||| |||||
taaactattttctctgattaaagacacatttgattatgatatatgacttt----ggttcttcatatgatgtcaactctttatgctaagggctact-ctttcctagGTAATTGCAGCAGGAATGAACCCCATTCAAATTTCTCGTGGGATTGAGAAGACTGCAATGGCCCTTGTTTCTGAACTCAAATTGATGTCGAGAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaaggggtttcttaaatttgcgctcttatccgctcctttctttttccattgtagGTTATTGCAGCTGGAATGAATCCTGTTCAAATTGCTCGTGGCATTGAGAAGACAGCAACAGCGCTTGTTTCTGAACTCAGATTGATGTCAAGAGAA
tttgcgctcttatccg CT-rich tract
tttcttaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acattagctttcggttaatgtttttgtcactatgtcaatggctttaaaaggggtttcttaaatttgcgctcttatccgctcctttctttttccattgtagGTTATTGCAGCTGGAATGAATCCTGTTCAAATTGCTCGTGGCATTGAGAAGACAGCAACAGCGCTTGTTTCTGAACTCAGATTGATGTCAAGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - -ctatgtc
- - - - - - - - - - - - - - - - - - - - - - - - -ggggttt