Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGCGTGCCACTGCATTTGGCCTGATGAAGATTGATGAAGAGGGGCGTATAATTGAATTCGCCGAAAAGCCAAAAGGAGAACAGTTGAAAGCTATGAAGgtaagcccatataacatgtattatatgttgttatttatctggaaattattacctgagcaattgcttaaaaatgccactag

Basic information

species Glycine max
transcript GLYMA02G47460.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G47460.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os09g12660.2 (Oryza sativa), 5'ss of exon 3
AAAGCGTGCCACTGCATTTGGCCTGATGAAGATTGATGAAGAGGGGCGTATAATTGAATTCGCCGAAAAGCCAAAAGGAGAACAGTTGAAAGCTATGAAGgtaagcccatataacatgtatt------atatgttgttatttatctggaaattattacctgagcaattgcttaaaaatgccactag-----
| | ||||| || ||||||||||| |||||||||||||| || ||| | || |||||||| || |||||||||||||||||  |||||||| | |||| |||||    ||    |||   ||      |||||        | | | |||      |  | ||  ||||  |  |  |     |       
AGAACGTGCTACAGCATTTGGCCTTATGAAGATTGATGATGAAGGGAGGATCATTGAATTTGCAGAAAAGCCAAAAGGAGAGAAGTTGAAATCAATGATGgtaa-ttgatgagtcatccgttgagaccatatgcaacctgatctgttgaagcatacatttcagtgattgtctgcatgttttgatcttgcag

upper sequence: GLYMA02G47460.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os08g25734.2 (Oryza sativa), 5'ss of exon 3
AAAGCGTGCCACTGCATTTGGCCTGATGAAGATTGATGAAGAGGGGCGTATAATTGAATTCGCCGAAAAGCCAAAAGGAGAACAGTTGAAAGCTATGAAGgtaagcccatataacatgtattatatgttgttatttatctggaaattattacctgagcaattgcttaa--aaatgccactag-------------------------------------
 || ||||| |||||||| ||||| ||||| ||||| || || ||| | ||| ||||||| || || || |||||||||||||| |||||||| |||| |||| ||  | || || ||  ||   || |    | |       | || | |  | | || ||  |  |  | || |  | |                                      
GAAACGTGCAACTGCATTCGGCCTCATGAAAATTGACGAGGAAGGGAGAATAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATGgtatgc--aaatgacgtgcctttcttgctaacttgtgatatacagttgtgagat-atcagttattacaccacatacttccatatcaaaactcattttgttgcctattttcgtcttgtag

upper sequence: GLYMA02G47460.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G068506_T03 (Zea mays), 5'ss of exon 3
AAAGCGTGCCACTGCATTTGGCCTGATGAAGATTGATGAAGAGGGGCGTATAATTGAATTCGCCGAAAAGCCAAAAGGAGAACAGTTGAAAGCTATGAAGgtaagcccatataacatgtattatatgttgttatttatctggaaattattacctgagcaattgcttaaaaatgccactag---------------------------
 || ||||| |||||||||||||| ||||| ||||||||||| ||| | || ||||| || || || || || |||||||| ||||||||||| |||| ||||    || |||| |||  ||     ||   |  || || ||  |   |   ||  ||||   ||   ||  | || |                            
GAAACGTGCAACTGCATTTGGCCTCATGAAAATTGATGAAGAAGGGAGGATCATTGAGTTTGCTGAGAAACCGAAAGGAGAGCAGTTGAAAGCAATGATGgta----cacataatatgctttcc---tttcaagctaacttgatttacatttgtggacaatcattttgtaaacctacaatattccattttactcctttggattgtag

upper sequence: GLYMA02G47460.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G106213_T02 (Zea mays), 5'ss of exon 3
AAAGCGTGCCACTGCATTTGGCCTGATGAAGATTGATGAAGAGGGGCGTATAATTGAATTCGCCGAAAAGCCAAAAGGAGAACAGTTGAAAGCTATGAAGgtaagcccatataacatgtattatatgttgttatt-tatctggaaattattacctgagcaattgcttaaaaatgccactag----------------------------
| | ||||| ||||||||||| || ||||| |||||||| || ||| | ||| |||| ||||| ||||| |||||||||||  || ||| | | |||| ||||      |   | |  | ||     | ||| || | |||    ||| |||      |  ||||      ||      ||                            
ACAACGTGCAACTGCATTTGGTCTTATGAAAATTGATGATGAAGGGAGGATAGTTGAGTTCGCAGAAAAACCAAAAGGAGAGAAGCTGAGATCAATGATGgtacaaatgtgataaactttttgaccctagttcttatgtctcctgattgttagagctccttttgcgattgcattttttcagttaagttttgcttgttttaccttttcag

upper sequence: GLYMA02G47460.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G163437_T01 (Zea mays), 5'ss of exon 3
AAAGCGTGCCACTGCATTTGGCCTGATGAAGATTGATGAAGAGGGGCGTATAATTGAATTCGCCGAAAAGCCAAAAGGAGAACAGTTGAAAGCTATGAAGgtaagc-ccatataacatgtattatatg-----ttgttatttatct---ggaaattatt------acctgagcaattgc--ttaaaaatgccactag--------------------------
 || ||||| || ||||||||||| ||||| ||||| ||||| ||| | || ||||| || || || || || |||||||| ||||||||||| |||| ||||  |   || |  | | | ||  | |     |||  ||  || |   |  ||| |||      |||| |   ||| |  || ||||||||   |                           
GAAACGTGCAACCGCATTTGGCCTCATGAAAATTGACGAAGAAGGGAGGATTATTGAGTTTGCTGAGAAACCGAAAGGAGATCAGTTGAAAGCAATGATGgtacacataatttgccttttctttcaagctaacttgacatacatttgttgacaatcatttagtgaacctaaaatattcccctttaaaatgccttcatctcatatttctgtctgattgatgtag

upper sequence: GLYMA02G47460.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv12s0057g01480.t01 (Vitis vinifera), 5'ss of exon 3
AAAGCGTGCCACTGCATTTGGCCTGATGAAGATTGATGAAGAGGGGCGTATAATTGAATTCGCCGAAAAGCCAAAAGGAGAACAGTTGAAAGCTATGAAGgtaagcc-catataacat--------gtatta---tatgttgttattta-------tctggaaattattacctgagcaattgcttaaaaatgccactag-----------------------------
||| || |||||||||||||| || |||||||||||||| || || |||||||||||||| || || || ||||||||||| || ||||||||||||||||||      || | | ||        ||||||   |||| | || | |        |||  || ||  ||  |    | ||| |||| || ||   ||                              
AAAACGAGCCACTGCATTTGGTCTAATGAAGATTGATGAGGAAGGCCGTATAATTGAATTTGCAGAGAAACCAAAAGGAGAGCAATTGAAAGCTATGAAGgtagatgatatttgaaataaacattcgtattaatttatgcttttgtgttcctctattctacaattttgtagttttaaagttggttaagaaggctgatacgttttcctttctgaactgttccttttaag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|208055837|gb|GD854160.1|GD854160
EST:     AAAGCTATGAAG                         GTTGATACTACAATTTTGGGTCTTGATGACGAGAGAGCAAAGGAATTGCCT
genomic: AAAGCTATGAAGgtaagcccat ... atgccactagGTTGATACTACAATTTTGGGTCTTGATGACGAGAGAGCAAAGGAATTGCCT
EST: gi|298174060|gb|HO017396.1|HO017396
EST:     TAATTGAATTTGCTGAAAAGCCAAAAGGAGAACAGTTGAAAGCTATGAAG                         GTTGATACTACAATTTTGGGTCTTGATGACGAGAGAGCAAAAGAAATGCCT
genomic: TAATTGAATTCGCCGAAAAGCCAAAAGGAGAACAGTTGAAAGCTATGAAGgtaagcccat ... atgccactagGTTGATACTACAATTTTGGGTCTTGATGACGAGAGAGCAAAGGAATTGCCT
EST: gi|16277058|gb|BI942182.1|BI942182
EST:     TAATTGAATTCGCCGAAAAGCCAAAAGGAGAACAGTTGAAAGCTATGAAG                         GTTGATACTACAATTTTGGGTCTTGATGACGAGAGAGCAAAGGAATTGCCT
genomic: TAATTGAATTCGCCGAAAAGCCAAAAGGAGAACAGTTGAAAGCTATGAAGgtaagcccat ... atgccactagGTTGATACTACAATTTTGGGTCTTGATGACGAGAGAGCAAAGGAATTGCCT
EST: gi|46492701|gb|CN472257.1|CN472257
EST:     TAATTGAATTTGCTGAAAAGCCAAAAGGAGAACAGTTGAAAGCTATGAAG                         GTTGATACTACAATTTTGGGTCTTGATGACGAGAGAGCAAAAGAAATGCCT
genomic: TAATTGAATTCGCCGAAAAGCCAAAAGGAGAACAGTTGAAAGCTATGAAGgtaagcccat ... atgccactagGTTGATACTACAATTTTGGGTCTTGATGACGAGAGAGCAAAGGAATTGCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGCGTGCCACTGCATTTGGCCTGATGAAGATTGATGAAGAGGGGCGTATAATTGAATTCGCCGAAAAGCCAAAAGGAGAACAGTTGAAAGCTATGAAGgtaagcccatataacatgtattatatgttgttatttatctggaaattattacctgagcaattgcttaaaaatgccactag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA