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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttcaatctctttgttgattattttttatgtaaacagctttcagacgctgttagctacgaacttttcgtgccaaattattcgctttaacatttcaattttctttgttgattttagttgataaatcatcagttctctaatagtggtttcgtttcgagtttagGAAGCTTTGGAAAACAAGCCGAAGCAAAAGGTGATTTCACTATCAGTTGTTTCTTCAATATTTGAGATACCACAAGCTGAATGGGATGCATGTGCGTTGG

Basic information

species Arabidopsis thaliana
transcript AT2G23390.1
intron # 2
splice site 3'
intron type U2

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|47828309|gb|CK117993.1|CK117993
EST:     AATTCGATATATCACTTAGAGATTACACTCTAACTGAATCAAACATTGAG                         GAAGCTTTGGAAAACAAGCCGAAGCAAAAGGTGATTTCACTATCAGTTGTT
genomic: AATTCGATATATCACTTAGAGATTACACTCTAACTGAATCAAACATTGAGgtatttcaat ... tcgagtttagGAAGCTTTGGAAAACAAGCCGAAGCAAAAGGTGATTTCACTATCAGTTGTT
EST: gi|163969838|gb|ES058322.1|ES058322
EST:     AATTCGATATATCACTTAGAGATTACACTCTAACTGAATCAAACATTGAG                         GAAGCTTTGGAAA
genomic: AATTCGATATATCACTTAGAGATTACACTCTAACTGAATCAAACATTGAGgtatttcaat ... tcgagtttagGAAGCTTTGGAAA
EST: gi|124833268|gb|EH917707.1|EH917707
EST:     ATTACACTCTAACTGAATCAAACATTGAG                         GAAGCTTTGGAAAACAAGCCGAAGCAAAAGGTGATTTCACTATCAGTTGTT
genomic: ATTACACTCTAACTGAATCAAACATTGAGgtatttcaat ... tcgagtttagGAAGCTTTGGAAAACAAGCCGAAGCAAAAGGTGATTTCACTATCAGTTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattttagttgataaatcatcagttctctaatagtggtttcgtttcgagtttagGAAGCTTTGGAAAACAAGCCGAAGCAAAAGGTGATTTCACTATCAGTTGTTTCTTCAATATTTGAGATACCACAAGCTGAATGGGATGCATGTGCGTTGG
                          ctctaat  putative branch site (score: 3)
                                      tttcgtttc  putative PPT
         ttgataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttcaatctctttgttgattattttttatgtaaacagctttcagacgctgttagctacgaacttttcgtgccaaattattcgctttaacatttcaattttctttgttgattttagttgataaatcatcagttctctaatagtggtttcgtttcgagtttagGAAGCTTTGGAAAACAAGCCGAAGCAAAAGGTGATTTCACTATCAGTTGTTTCTTCAATATTTGAGATACCACAAGCTGAATGGGATGCATGTGCGTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA