Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtaggagaaacaactttattaatcgtcgtctgtttggttatgatttactttgttggtgcttattatgtgtaatggaaatttttaatcttgtaagGTATTGAGAAAGTGGAGGTGGATTTGTCCAATCAAGTTGTGAGGATACTTGGATCTTCCCCTGTTAAGGCTATGACTCAAGCTTTGGAGCAAACTGGTCG

Basic information

species Arabidopsis thaliana
transcript AT1G12520.1
intron # 3
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|124962851|gb|EL037228.1|EL037228
EST:     TGCTGTGAAGAACAAATTAGAAACCATTGAAG                         GTATTGAGAAAGTGGAGGTGGATTTGTCCAATCAAGTTGTGAGGATA
genomic: TGCTGTGAAGAACAAATTAGAAACCATTGAAGgtagtaggag ... atcttgtaagGTATTGAGAAAGTGGAGGTGGATTTGTCCAATCAAGTTGTGAGGATA
EST: gi|125192755|gb|EL207709.1|EL207709
EST:     AACAAATTAGAAACCATTGAAG                         GTATTGAGAAAGTGGAGGTGGATTTGTCCAATCAAGTTGTGAGGATACTTG
genomic: AACAAATTAGAAACCATTGAAGgtagtaggag ... atcttgtaagGTATTGAGAAAGTGGAGGTGGATTTGTCCAATCAAGTTGTGAGGATACTTG
EST: gi|124791779|gb|EH881458.1|EH881458
EST:     ATGTGAGGGTTGTGTTAATGCTGTGAAGAACAAATTAGAAACCATTGAAG                         GTATTGAGAAAGTGGAGGTGGATTTGTCCAATCAAGTTGTG
genomic: ATGTGAGGGTTGTGTTAATGCTGTGAAGAACAAATTAGAAACCATTGAAGgtagtaggag ... atcttgtaagGTATTGAGAAAGTGGAGGTGGATTTGTCCAATCAAGTTGTG
EST: gi|164102028|gb|EL986592.1|EL986592
EST:     TTAATGCTGTGAAGAACAAATTAGAAACCATTGAAG                         GTATTGAGAAAGTGGAGGTGGATTTGTCCAATCAAGTTG
genomic: TTAATGCTGTGAAGAACAAATTAGAAACCATTGAAGgtagtaggag ... atcttgtaagGTATTGAGAAAGTGGAGGTGGATTTGTCCAATCAAGTTG
EST: gi|124977924|gb|EL051193.1|EL051193
EST:     ATGTGAGGGTTGTGTTAATGCTGTGAAGAACAAATTAGAAACCATTGAAG                         GTATTGAGAAAGTGGAGGTGGATTTGTCCAATCAAGT
genomic: ATGTGAGGGTTGTGTTAATGCTGTGAAGAACAAATTAGAAACCATTGAAGgtagtaggag ... atcttgtaagGTATTGAGAAAGTGGAGGTGGATTTGTCCAATCAAGT
EST: gi|124792753|gb|EH882432.1|EH882432
EST:     ATGTGAGGGTTGTGTTAATGCTGTGAAGAACAAATTAGAAACCATTGAAG                         GTATTGAGAAA
genomic: ATGTGAGGGTTGTGTTAATGCTGTGAAGAACAAATTAGAAACCATTGAAGgtagtaggag ... atcttgtaagGTATTGAGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgatttactttgttggtgcttattatgtgtaatggaaatttttaatcttgtaagGTATTGAGAAAGTGGAGGTGGATTTGTCCAATCAAGTTGTGAGGATACTTGGATCTTCCCCTGTTAAGGCTATGACTCAAGCTTTGGAGCAAACTGGTCG
                                        ttttaat  putative branch site (score: 3)
                    ttattatgtgtaatgg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtaggagaaacaactttattaatcgtcgtctgtttggttatgatttactttgttggtgcttattatgtgtaatggaaatttttaatcttgtaagGTATTGAGAAAGTGGAGGTGGATTTGTCCAATCAAGTTGTGAGGATACTTGGATCTTCCCCTGTTAAGGCTATGACTCAAGCTTTGGAGCAAACTGGTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA