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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacaagatctcttatcatgacattataatcataaactatgaaagctcaatcttaatgactgagagaagatgcatttttttttgtcagAGAAAGGGAAGATGGGTTTCTTCTTCACAGAGTTAGCTTCTCAGAGTTT

Basic information

species Arabidopsis thaliana
transcript AT4G30993.1
intron # 6
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|125220857|gb|EL234942.1|EL234942
EST:     CGAATAATAGTAAGAG                         AGAAAGGGAAGATGGGTTTCTTCTTCACAAAGTTAGCTTCTCAGAGTTT
genomic: CGAATAATAGTAAGAGgtaacaagat ... tttttgtcagAGAAAGGGAAGATGGGTTTCTTCTTCACAGAGTTAGCTTCTCAGAGTTT
EST: gi|124794203|gb|EH883882.1|EH883882
EST:     ACGGTTCCTAATCAACAAGAGAACCAAGGTCCAACGAATAATAGTAAGAG                         AGAAAGGGAAGATGGGTTTCTTCTTCACAGAGTTAGCTTCTCAGAGTTT
genomic: ACGGTTCCTAATCAACAAGAGAACCAAGGTCCAACGAATAATAGTAAGAGgtaacaagat ... tttttgtcagAGAAAGGGAAGATGGGTTTCTTCTTCACAGAGTTAGCTTCTCAGAGTTT
EST: gi|125152003|gb|EL183856.1|EL183856
EST:     ACGGTTCCTAATCAACAAGAGAACCAAGGTCCAACGAATAACAGTAAGAG                         AGAAAGGGAAGATGGGTTTCTTCTTCACAGAGTTAGCTTCTCAGAGTTT
genomic: ACGGTTCCTAATCAACAAGAGAACCAAGGTCCAACGAATAATAGTAAGAGgtaacaagat ... tttttgtcagAGAAAGGGAAGATGGGTTTCTTCTTCACAGAGTTAGCTTCTCAGAGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaactatgaaagctcaatcttaatgactgagagaagatgcatttttttttgtcagAGAAAGGGAAGATGGGTTTCTTCTTCACAGAGTTAGCTTCTCAGAGTTT
                 tcttaat  putative branch site (score: 3)
                                       catttttttttgtc  putative PPT
                                    atgcattttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacaagatctcttatcatgacattataatcataaactatgaaagctcaatcttaatgactgagagaagatgcatttttttttgtcagAGAAAGGGAAGATGGGTTTCTTCTTCACAGAGTTAGCTTCTCAGAGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG