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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttttctctttatctatctctttgtgttttgttttagttcatatgttctaaattggatgtttttaagGCTTATATTGAATCCATGAGAAGCATATTAAGAAGCAGTTCGTGGAAAACAAAGACAACAGTATGCTGGGGCATGAGAGATCGTTGGCTAAGCTATGATG

Basic information

species Zea mays
transcript GRMZM2G025659_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G025659_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g69060.1 (Oryza sativa), 3'ss of exon 11
gtttttctctttatctatctctttgtgttttgt----tttagttcatatgttctaaattggatgtttt--ta-agGCTTATATTGAATCCATGAGAAGCATATTAAGAAGCAGTTCGTGGAAAACAAAGACAACAGTATGCTGGGGCATGAGAGATCGTTGGCTAAGCTATGATG
  |    |  || |||||| | | |  ||||      |||| ||  |||| ||| ||| |  ||||||  || ||| ||| |||||||||||||| |  ||||||   ||   ||| ||||||||||| || |||||||| |||||| |||||||||||||||| | ||||||||
-gtagcttacttgtctatcacctggccttttcaattatttaatttgtatgatctgaatggcgtgttttattacagGTTTACATTGAATCCATGAGGAATATATTATCGAGTGATTCATGGAAAACAAAAACGACAGTATGTTGGGGCTTGAGAGATCGTTGGCTGAACTATGATG
















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|148950896|gb|EC896526.2|EC896526
EST:     CGGGGTTTGCACTTAATGCAATAAGCAAAGCTATGAAAAAGGACCTTAAG                         GCTTATATTGAATCCATGAGAAGCATATTAAGAAGCAGTTCGTGGAAAACA
genomic: CGGGGTTTGCACTTAATGCAATAAGCAAAGCTATGAAAAAGGACCTTAAGgtttttctct ... tgtttttaagGCTTATATTGAATCCATGAGAAGCATATTAAGAAGCAGTTCGTGGAAAACA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctatctctttgtgttttgttttagttcatatgttctaaattggatgtttttaagGCTTATATTGAATCCATGAGAAGCATATTAAGAAGCAGTTCGTGGAAAACAAAGACAACAGTATGCTGGGGCATGAGAGATCGTTGGCTAAGCTATGATG
                                 ttctaaa  putative branch site (score: 2)
                                             tgttttt  putative PPT
                            atatgttctaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttttctctttatctatctctttgtgttttgttttagttcatatgttctaaattggatgtttttaagGCTTATATTGAATCCATGAGAAGCATATTAAGAAGCAGTTCGTGGAAAACAAAGACAACAGTATGCTGGGGCATGAGAGATCGTTGGCTAAGCTATGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC