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'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAGgtaaattcattcatttatgtctcggcttttggtgctatgacatctgatgagtggtatttgtcatatgtag

Basic information

species Zea mays
transcript GRMZM2G074790_T03
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074790_T03 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os05g46290.1 (Oryza sativa), 5'ss of exon 7
GAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAGgtaaattcattcatttatgtctcggcttttggtgc-tatgacatctgatgagtggtatttgtcatatgtag----------------
|||||||| || ||||||||||| || |||||||||||||||||||  ||| |||| || |||||||  |||||||| ||||||||||| | |   | |  | ||||||| |||| |  ||  |||| ||  || | | | |  || ||  ||   ||                
GAGATGGAAAATCCTCTTATTCTAATTCATGACAAGAAAATCTCAACGATGAATTCACTTCTTCCAGTTTTAGAAATGTCTATCAAGgtgattatgtcccataatgtctcagcttcttttgaatatggcaa-tggtaaattggtttagtactaaccagtgtctcatgtatgcag

upper sequence: GRMZM2G074790_T03 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA07G01190.1 (Glycine max), 5'ss of exon 7
GAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAGgtaaattcattcatttatgtctcg---gcttttggtgctatgacatctgatgagtggtatttgtcatatgtag------------------
||  ||||||||||  ||||||| ||||||||||||||||| ||| ||||  |||| || ||   |  | | ||  |  || | | |||  ||    | ||     |       |||  |  |  | ||  || | |  | | | |||  | |  | ||                   
GAATTGGAGAACCCCTTTATTCTCATCCATGACAAGAAAATTTCAGACATAAATTCACTGCTGAAAATACTGGAGCTGGCTGTAACGgtggataagctaatcctgattcaatgtgctcattttcatttgcaatttcaacattcgcattatttac-tttactattttaatgtttatcag

upper sequence: GRMZM2G074790_T03 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA08G20560.2 (Glycine max), 5'ss of exon 6
GAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAGgtaaattcattcatttatgtctcg---gcttttggtgctatgacatctgatgagtggtatttgtcatatgtag------------------
||  ||||||||||  ||||||| ||||||||||||||||| ||  ||||| ||||  | ||   |  | | ||  |  |  | | |||  ||    | ||     |       |||  |  |  | ||  || | | || |   |||  | |  | ||                   
GAATTGGAGAACCCCTTTATTCTCATCCATGACAAGAAAATTTCTGACATGAATTCATTGCTGAAAATACTGGAGCTGGCAGTAACGgtggataagctaatcctgattcaatgtgctcattttcatttgcaatttcaagattctcattatttac-tttactattttaatgttaatcag

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|18450792|gb|BM429070.1|BM429070
EST:     AAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAG                         AATCGCAAGCCTCTTCTCATTGTTGCTGAGGATGTTGAAGGAGATGCTCTG
genomic: AA-TCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAGgtaaattcat ... tcatatgtagAATCGCAAGCCTCTTCTCATTGTTGCTGAGGATGTTGAAGGAGATGCTCTG
EST: gi|149014572|gb|EE044215.2|EE044215
EST:     AATCTCAAACATGGATTCTCTCCTTCCCAGCATAA-AAATT-CTATCAAG                         AATCGCCAGCCTCTTCTCATTGTTGC
genomic: AATCTCAAACATGGATTCTCTCCTTCC-AGCATTAGAAATTTCTATCAAGgtaaattcat ... tcatatgtagAATCGCAAGCCTCTTCTCATTGTTGC
EST: gi|18649481|gb|BM498300.1|BM498300
EST:     AAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAG                         AATCGCAAGCCTCTTCTCAT
genomic: AAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAGgtaaattcat ... tcatatgtagAATCGCAAGCCTCTTCTCAT
EST: gi|87152753|gb|DY397542.1|DY397542
EST:     AAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAG                         AATCGCAAGCCTCTTCTCATTGTTGCTGAGGATGTTGAAGGAGATGCTCTG
genomic: AAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAGgtaaattcat ... tcatatgtagAATCGCAAGCCTCTTCTCATTGTTGCTGAGGATGTTGAAGGAGATGCTCTG
EST: gi|19822484|gb|BQ048508.1|BQ048508
EST:     AAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAG                         AATCGCNAGCCTCTTCTCATTGTTGCTGAGGATGTTGAAGGAGATGCTCTG
genomic: AAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAGgtaaattcat ... tcatatgtagAATCGCAAGCCTCTTCTCATTGTTGCTGAGGATGTTGAAGGAGATGCTCTG
EST: gi|31351656|gb|CD436013.1|CD436013
EST:     AAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAG                         AATCGCAAGCCTCTTCTCATTGTTGCTGAGGATGTTGAAGGAGATGCTCTG
genomic: AAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAGgtaaattcat ... tcatatgtagAATCGCAAGCCTCTTCTCATTGTTGCTGAGGATGTTGAAGGAGATGCTCTG
EST: gi|31350305|gb|CD434662.1|CD434662
EST:     AAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAG                         AATCGCAAGCCTCTTCTCATTGTTGCTGAGGATGTTGAAGGAGATGCTCTG
genomic: AAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAGgtaaattcat ... tcatatgtagAATCGCAAGCCTCTTCTCATTGTTGCTGAGGATGTTGAAGGAGATGCTCTG
EST: gi|6021191|gb|AW066119.1|AW066119
EST:     AAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAG                         AATCGCAAGCCTCTTCTCATTGTTGCTGAGGATGTTGAAGGAGATGCTCTG
genomic: AAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAGgtaaattcat ... tcatatgtagAATCGCAAGCCTCTTCTCATTGTTGCTGAGGATGTTGAAGGAGATGCTCTG
EST: gi|18450399|gb|BM428677.1|BM428677
EST:     AAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAG                         AATCGCAAGCCTCTTCTCATTGTTGCTGAGGATGTTGAAGGAG
genomic: AAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAGgtaaattcat ... tcatatgtagAATCGCAAGCCTCTTCTCATTGTTGCTGAGGATGTTGAAGGAG
EST: gi|22489691|gb|BU049614.1|BU049614
EST:     AAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAG                         AATCGCAAGCCTCTTCTCATTGTTGCTGAGGATGTTGAAGGAGATGCTCTG
genomic: AAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAGgtaaattcat ... tcatatgtagAATCGCAAGCCTCTTCTCATTGTTGCTGAGGATGTTGAAGGAGATGCTCTG
EST: gi|87153562|gb|DY398351.1|DY398351
EST:     AAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAG                         AATCGCAAGCCTCTTCTCATTGTTGCTGAGGATGTTGAAGGAGATGCTCTG
genomic: AAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAGgtaaattcat ... tcatatgtagAATCGCAAGCCTCTTCTCATTGTTGCTGAGGATGTTGAAGGAGATGCTCTG
EST: gi|18648744|gb|BM497563.1|BM497563
EST:     AAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAG                         AATCGGAAGCCTCTTCTCATTGTTGCTGAGGATGTTGAAGGAGATGCTCTG
genomic: AAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAGgtaaattcat ... tcatatgtagAATCGCAAGCCTCTTCTCATTGTTGCTGAGGATGTTGAAGGAGATGCTCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAGgtaaattcattcatttatgtctcggcttttggtgctatgacatctgatgagtggtatttgtcatatgtag

- - - - - - - - - - - - - - - - - - - - - - -  CATGGA