Sequence
atgc intronic sequence ATGC exonic sequencegtaaaggcttaagttgcctggctttgtgatgtctctcagtgggatttctgttagattgaggtgttaattttatcctgttgctaaaaaattttgacagGGTGTTTTAGCTGGCAAGAGCAGTGGTAATGAAGAGAAATGCTTAGAGGATCAATTAAGGGATGCAAAGGTAGCAGTTGGGAGTACTGAAACAGAATTGA
Basic information
species | Glycine max |
transcript | GLYMA12G36520.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G36520.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G62410.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaaaggcttaagttgcctggctttgtgatgtctctcagtgggatttctgttagattgaggtgttaattttatcctgttgctaaaaaattttgacagGGTGTTTTAGCTGGCAAGAGCAGTGGTAATGAAGAGAAATGCTTAGAGGATCAATTAAGGGATGCAAAGGTAGCAGTTGGGAGTACTGAAACAGAATTGA
||| | | | || | || | | || || || | || | |||||||| | | || | || |||| || ||||||| ||||| ||||| ||||||||||||||||||| |||||| || ||||||||||| | || ||||| | ||| |||||| ||||
gtagtaccactaaaaaagtatctct---attccatgccaaataatatccattcgtttta--tgttaattggctttatgtcctttga----ttattagGGCGTACTAGCTGGTAAGAGTAGTGGAGATGAAGAGAAATGCTTAGAAGATCAACTACGGGATGCAAAGATTGCTGTTGGAACAGCTGGAACAGAGTTGA
upper sequence: GLYMA12G36520.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv16s0022g00230.t01 (Vitis vinifera), 3'ss of exon 3
----gtaaaggcttaagttgcctggctttgtgatgtctctcagtgggattt-ctgttagattgaggtgt---taattttatcctgttgctaaaaa------------attttgacagGGTGTTTTAGCTGGCAAGAGCAGTGGTAATGAAGAGAAATGCTTAGAGGATCAATTAAGGGATGCAAAGGTAGCAGTTGGGAGTACTGAAACAGAATTGA
|||| ||| | || | || || || |||| ||| | || | | | | || | | | | || | | ||| |||||||| |||| || ||||||||||| | ||| || |||||| | || |||||| || |||||||| |||||||||||||| | |||||||||||||
gtaaaaaaagttctaatatatctcattctgctattgaacttgatgggctttgttattgctctcatttataggcaagctgagctgaatatagaagagatgttgtacataccatgatagGGTGTTCTAGCCGGTAAGAGCAGTGGAAGTGAGGAAAAATGCCTTGAAGATCAACTAGCTGATGCAAAAGTAGCAGTTGGGAGAGCAGAAACAGAATTGA
upper sequence: GLYMA12G36520.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv16s0022g00060.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------gtaaaggcttaagttgcctggctttgtgatgtctctcagtgggatttctgttagattgaggtgttaattttatcctgttgctaaaaa-attttgacagGGTGTTTTAGCTGGCAAGAGCAGTGGTAATGAAGAGAAATGCTTAGAGGATCAATTAAGGGATGCAAAGGTAGCAGTTGGGAGTACTGAAACAGAATTGA
| || ||| ||| |||| || |||||| | | | | |||| ||| | || | | || | | | | ||| |||||||| ||||||| ||||||||||| | ||| || |||||| | || |||||| || ||||| || ||||||||||||||| | |||||||||||||
gtaaaaagagtgctaatgtatcacattctgccattgaacttgatgggcattgttattgctctcatt-----tatgggcaagctgagctgt--acttaaaagcgatgttgtacataccatgatagGGTGTTCTAGCTGGTAAGAGCAGTGGAAGTGAGGAAAAATGCCTTGAAGATCAACTAGCTGATGCTAAAGTAGCAGTTGGGAGTGCAGAAACAGAATTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatttctgttagattgaggtgttaattttatcctgttgctaaaaaattttgacagGGTGTTTTAGCTGGCAAGAGCAGTGGTAATGAAGAGAAATGCTTAGAGGATCAATTAAGGGATGCAAAGGTAGCAGTTGGGAGTACTGAAACAGAATTGA
tgctaaa putative branch site (score: 2)
ttgctaaaaaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaggcttaagttgcctggctttgtgatgtctctcagtgggatttctgttagattgaggtgttaattttatcctgttgctaaaaaattttgacagGGTGTTTTAGCTGGCAAGAGCAGTGGTAATGAAGAGAAATGCTTAGAGGATCAATTAAGGGATGCAAAGGTAGCAGTTGGGAGTACTGAAACAGAATTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG