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

gtttgttaagattttagaaagtgatatttgtgtgaagttccttttccagtcttcttcagtatgtgcatgtaaagtgcagATTGGTGGAGCTAGTGAAGCTGAAGTTGGTGAGAAAAAAGATAGGGTGACAGATGCTCTAAATGCTGCAAGGGCTGCTGTGGAGGAGGGCATTGTGCCAG

Basic information

species Zea mays
transcript GRMZM2G074790_T03
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074790_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os05g46290.1 (Oryza sativa), 3'ss of exon 12
gtttgttaagattttag---aaagtgatatttgtgtgaagttccttttccagtctt-----cttcagtatgtgcatgtaaagtgcagATTGGTGGAGCTAGTGAAGCTGAAGTTGGTGAGAAAAAAGATAGGGTGACAGATGCTCTAAATGCTGCAAGGGCTGCTGTGGAGGAGGGCATTGTGCCAG
||||||||   ||   |   | |||||| |||   || | ||| ||| ||    ||       |||| || | ||| |  | |||||||||| ||||||||||||| ||||||||||||||||||||||||||| ||||| ||| || |||| ||||||||||||||||||||||||||||| ||||
gtttgttatttttcaggtgcacagtgatgtttcactgtatttcttttccccactttgctcctctcaggatatccattttgactgcagATTGGGGGAGCTAGTGAAGTTGAAGTTGGTGAGAAAAAAGATAGGGTAACAGACGCTTTACATGCAGCAAGGGCTGCTGTGGAGGAGGGCATTGTACCAG

upper sequence: GRMZM2G074790_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA08G20560.2 (Glycine max), 3'ss of exon 11
gtttgttaag-attttagaaagtgatatttgtgtgaagttccttttccagtcttcttc------agtatgtgcatgtaaa-gtgcagATTGGTGGAGCTAGTGAAGCTGAAGTTGGTGAGAAAAAAGATAGGGTGACAGATGCTCTAAATGCTGCAAGGGCTGCTGTGGAGGAGGGCATTGTGCCAG
|||||| |   ||  | || | |  || |  | | | | |   |||  |||| || ||       | |  ||||   |||  | ||| |||| || |||||||| || |||||||| || |  |||||||| || ||||||||| |||||||  | || ||||||||||| ||||| ||||| ||||
gtttgtcactcatccttgagaatactagt-atataatgattaatttatagtcatcatctcacatggaagatgcaaccaaatattcagGTTGGGGGGGCTAGTGAGGCCGAAGTTGGGGAAAGGAAAGATAGAGTAACAGATGCTTTAAATGCCACTAGAGCTGCTGTGGAAGAGGGAATTGTTCCAG

upper sequence: GRMZM2G074790_T02 (Zea mays), 3'ss of exon 11
lower sequence: EFJ32351 (Selaginella moellendorffii), 3'ss of exon 11
gtttgttaagattttagaaagtgatatttgtgtgaagttccttttccagtcttcttcagtatgtgcatgtaaagtgcagATTGGTGGAGCTAGTGAAGCTGAAGTTGGTGAGAAAAAAGATAGGGTGACAGATGCTCTAAATGCTGCAAGGGCTGCTGTGGAGGAGGGCATTGTGCCAG
          || |     |  ||  ||||||  |     | |||  | | || ||  |   | |       || | ||||||| |||| ||||||||| ||||| ||||| || || ||| ||||||| ||||| || |||||| ||| |||||| ||||||||||| || |||||||
--------gtatgtacaccaaagacttttgtggcag----cgtttttattattgtttcgcgcgcg-------agcgtagATTGGAGGAGGTAGTGAAGCGGAAGTCGGTGAAAAGAAGGATCGGGTGACCGATGCGCTGAATGCTACAAAGGCTGCAGTGGAGGAGGGAATCGTGCCAG

upper sequence: GRMZM2G074790_T02 (Zea mays), 3'ss of exon 11
lower sequence: EFJ20894 (Selaginella moellendorffii), 3'ss of exon 11
gtttgttaagattttagaaagtgatatttgtgtgaagttccttttccagtcttcttcagtatgtgcatgtaaagtgcagATTGGTGGAGCTAGTGAAGCTGAAGTTGGTGAGAAAAAAGATAGGGTGACAGATGCTCTAAATGCTGCAAGGGCTGCTGTGGAGGAGGGCATTGTGCCAG
          |  |  |  |  ||  ||||||  |     | |||  | | || ||  |   | |       |||| ||||||| |||| ||||||||| |||||  |||| || || ||| ||||||| ||||| || |||||| ||| |||||| ||||||||||| || |||||||
--------gtacgtacgccaaagacttttgtggcag----cgtttttattattgtttcgcgcgcg-------agtgtagATTGGAGGAGGTAGTGAAGCGGAAGTCAGTGAAAAGAAGGATCGGGTGACGGATGCGCTGAATGCTACAAAGGCTGCAGTGGAGGAGGGAATCGTGCCAG

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|67028320|gb|CO457069.1|CO457069
EST:     AGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAG                         ATTGGTGGAGCTAGTGAAGCTGAAGTTGGTGAGAAAAAAGATAGGGTGACA
genomic: AGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAGgtttgttaag ... taaagtgcagATTGGTGGAGCTAGTGAAGCTGAAGTTGGTGAGAAAAAAGATAGGGTGACA
EST: gi|166512699|gb|EG211950.1|EG211950
EST:     AGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAG                         ATTGGTGGAGCTAGTGAAGCTGAAGTTGGTG
genomic: AGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAGgtttgttaag ... taaagtgcagATTGGTGGAGCTAGTGAAGCTGAAGTTGGTG
EST: gi|76911014|gb|DV164129.1|DV164129
EST:     AGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAG                         ATTGGTGGAGCTAGTGAAGCTGAAGTTGGTGAGAAAAAAGATAGGGTGACA
genomic: AGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAGgtttgttaag ... taaagtgcagATTGGTGGAGCTAGTGAAGCTGAAGTTGGTGAGAAAAAAGATAGGGTGACA
EST: gi|211181730|gb|FL012621.1|FL012621
EST:     AGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAG                         ATTGGTGGAGCTAGTGAAGCTGAAGTTGGTGAGAAAAAGGATAGGGTGACA
genomic: AGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAGgtttgttaag ... taaagtgcagATTGGTGGAGCTAGTGAAGCTGAAGTTGGTGAGAAAAAAGATAGGGTGACA
EST: gi|211184128|gb|FL012625.1|FL012625
EST:     AGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAG                         ATTGGTGGAGCTAGTGAAGCTGAAGTTGGTGAGNNNNNNNGATAGGGTGAC
genomic: AGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAGgtttgttaag ... taaagtgcagATTGGTGGAGCTAGTGAAGCTGAAGTTGGTGAG-AAAAAAGATAGGGTGAC
EST: gi|31352804|gb|CD437161.1|CD437161
EST:     AGGCTCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAG                         ATTGGTGGAGCTAGTGAAGCTGAAGTTGGTGAGAAAAAAGATAGGGTGACA
genomic: AGGCCCAAGAGCGTTTATCTAAGTTATCTGGAGGTGTTGCTGTACTCAAGgtttgttaag ... taaagtgcagATTGGTGGAGCTAGTGAAGCTGAAGTTGGTGAGAAAAAAGATAGGGTGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttgtgtgaagttccttttccagtcttcttcagtatgtgcatgtaaagtgcagATTGGTGGAGCTAGTGAAGCTGAAGTTGGTGAGAAAAAAGATAGGGTGACAGATGCTCTAAATGCTGCAAGGGCTGCTGTGGAGGAGGGCATTGTGCCAG
                                          atgtaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttaagattttagaaagtgatatttgtgtgaagttccttttccagtcttcttcagtatgtgcatgtaaagtgcagATTGGTGGAGCTAGTGAAGCTGAAGTTGGTGAGAAAAAAGATAGGGTGACAGATGCTCTAAATGCTGCAAGGGCTGCTGTGGAGGAGGGCATTGTGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG