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'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaatgaggacagtatacaagataaggtctcactattttataatttctgacatattgccatttgccaatgattgatttctccagAGTGCAGCTCTCACGCTAGATCAATCTACCTTGGATGTTGATCAAGTGGAGAATCTCATAAAGTTCTGTCCTACGAAAGAAGAAATGGAACTTCTCAAG

Basic information

species Zea mays
transcript GRMZM2G414002_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G414002_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g40510.1 (Oryza sativa), 3'ss of exon 3
gtaagaatgaggacagtatacaagataaggtctcactattttataatttctgacatattgccatttgccaatgattgatttctccagAGTGCAGCTCTCACGCTAGATCAATCTACCTTGGATGTTGATCAAGTGGAGAATCTCATAAAGTTCTGTCCTACGAAAGAAGAAATGGAACTTCTCAAG
        |     |   || || | |||     |  ||  ||  ||   |||  | ||     ||            |||||| ||||||| ||| |  | || || ||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||
--------gtaattatcttataaaacaagcaaagataatggtaacatgattgattttttatatcttaatggcttaaattttctctagAGTGCGGCTTTGGCACTGGACCAATCTACCTTGGATGTTGATCAAGTGGAGAATCTCATAAAGTTCTGTCCTACAAAAGAAGAAATGGAACTTCTCAAG

upper sequence: GRMZM2G414002_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA06G21190.1 (Glycine max), 3'ss of exon 9
-gtaagaa----tgaggacagtataca-----agataaggtctcactattttataatttctgacatattgccatttgccaat---gattgatttctccagAGTGCAGCTCTCACGCTAGATCAATCTACCTTGGATGTTGATCAAGTGGAGAATCTCATAAAGTTCTGTCCTACGAAAGAAGAAATGGAACTTCTCAAG
 |||| |     |      |  ||| |     | || |  |||| |   | ||   |||   |  ||||| | ||  |   |    ||| || |   |||  |||||  ||  |  | ||| | ||    || ||||||||||| ||||| |||||||| || || |||||||| ||||| ||||| || ||| | |||
ggtaacagattcttgccttatcatatatgtggaaattaaatctcccccctgtaactttttcaatttattgtctttaacatgttgaaattcatattatcagGCTGCAGTACTGGCTATGGATGATTCAGTGTTAGATGTTGATCAGGTGGAAAATCTCATTAAATTTTGTCCTACCAAAGAGGAAATAGAGCTTTTAAAG

upper sequence: GRMZM2G414002_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA17G11100.1 (Glycine max), 3'ss of exon 9
------------------------------gtaagaatg--aggacagt-atacaagataaggtctcactatttta------taatttctgaca--tattgccatt--tgccaat----gattgatttctccagAGTGCAGCTCTCACGCTAGATCAATCTACCTTGGATGTTGATCAAGTGGAGAATCTCATAAAGTTCTGTCCTACGAAAGAAGAAATGGAACTTCTCAAG
                               |||   ||  ||   ||| ||  ||| ||| | ||    ||  ||       |||   ||  |  ||||  | ||  |  || |     || ||| |   |||  |||||  ||  |  | ||| | ||    |||||||||||||||||||| |||||||| ||||| |||||||| ||||| || ||||| ||| | |||
gtaggctgatactttgatgtgggaatctttataatcttgcaagagtagttatttaagttaaaggctgctgatagtagataaacaatcaatggtaaatattatctttcctaacactttgaaatggatattctcagGCTGCAGTACTAGCTTTGGATGAGTCAGTATTGGATGTTGATCAAGTGGAAAATCTCATTAAGTTTTGTCCTACCAAAGAGGAGATGGATCTTTTGAAG

upper sequence: GRMZM2G414002_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA05G00820.1 (Glycine max), 3'ss of exon 7
----------------------------------------------------------------------------------------------------gtaagaatgaggacagtatacaagataaggtctcactattttataatttctgaca--tattgccatttgccaatg-------attgatttctccagAGTGCAGCTCTCACGCTAGATCAATCTACCTTGGATGTTGATCAAGTGGAGAATCTCATAAAGTTCTGTCCTACGAAAGAAGAAATGGAACTTCTCAAG
                                                                                                          |  |      | ||     | |  |||||  ||   |  ||   ||  |  ||||  | ||| | ||         || ||| |   |||  |||||  ||  |  | ||| | ||    |||||||||||||||||||| |||||||| ||||| |||||||| ||||| || ||||| ||| | |||
gtaggctgacacgttgatgtgggcatttttaaaatcatgcaagagtagttatttaagttaaaggctgctgatagtagataaacaatcttttggcaccatatctgctacaaactttttctaacttctgaaatctcaacatggaactatcaatggtaagtattatc-tttcctaacacgttgaaatggatattctcagGCTGCAGTACTAGCTTTGGATGAGTCGGTATTGGATGTTGATCAAGTGGAAAATCTCATTAAGTTTTGTCCTACCAAAGAGGAGATGGATCTTTTGAAG

upper sequence: GRMZM2G414002_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv17s0000g06640.t01 (Vitis vinifera), 3'ss of exon 8
-------------gtaagaatgaggacagtatacaagataaggtctcactattttataatttctgacat--attgccatttgccaatgattgatttctccagAGTGCAGCTCTCACGCTAGATCAATCTACCTTGGATGTTGATCAAGTGGAGAATCTCATAAAGTTCTGTCCTACGAAAGAAGAAATGGAACTTCTCAAG
              |  |    |  |   | || | | |    | | | | |||| || | |  | ||     ||   ||| |   || |  || |   |||  ||||| |||  |  | ||| | || |  || ||||||||||||||||| ||||||||||||||||| ||||| ||||| || ||||||||||| |||
attgctttcttttttgggtccaactatgatttata-gtttgattattagttttttttattgttaggcagtagctgttgtttactgttg-tacatattctcagGCTGCAGTTCTAGCAATGGATGAGTCAATTTTAGATGTTGATCAAGTGGAAAATCTCATAAAGTTCTGCCCTACTAAAGAGGAGATGGAACTTCTTAAG

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|32938513|gb|CF043332.1|CF043332
EST:     TCGGATTTGGTG                         AGTGCAGCTCTCGCGCTAGATCAATCTACCTTGGATGTTGATCAAGTGGAG
genomic: TCGGATTTGGTGgtaagaatga ... atttctccagAGTGCAGCTCTCACGCTAGATCAATCTACCTTGGATGTTGATCAAGTGGAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcactattttataatttctgacatattgccatttgccaatgattgatttctccagAGTGCAGCTCTCACGCTAGATCAATCTACCTTGGATGTTGATCAAGTGGAGAATCTCATAAAGTTCTGTCCTACGAAAGAAGAAATGGAACTTCTCAAG
                                              tttctcc  CT-rich tract
     attttataatttctga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaatgaggacagtatacaagataaggtctcactattttataatttctgacatattgccatttgccaatgattgatttctccagAGTGCAGCTCTCACGCTAGATCAATCTACCTTGGATGTTGATCAAGTGGAGAATCTCATAAAGTTCTGTCCTACGAAAGAAGAAATGGAACTTCTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA