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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctacctaattggtgttaagggttgtcgtaatcttcaatcttttctcgcctagctctcgttttaggcttttgtaaagtttacttcagttttaggaaagagtatcgtcttctatgagtttgatatagcttgtacttggctcggctgaattatggctctttaacccttccttgggacttttgtcttattggtgtcagAATTCGTAGAAATTTAGGTTTGCTAAAGCTTGAAGATGAGTTCTACTGTTTGGTGGGAAGGAGCTGAGAAGACACGAGTTCTCATAGCCCCAG

Basic information

species Arabidopsis thaliana
transcript AT4G20325.2
intron # 1
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|116459190|gb|EG501782.1|EG501782
EST:     GTCCTGATTCATTTACCTCACTAATTGCGAGCCTTCTTGCCGTCGTCACG                         AATTCGTAGAAATTTAGGTTTGCTAAAGCTTGAAGATGAGTTCTACTGTTT
genomic: GTCCTGATTCATTTACCTCACTAATTGCGAGCCTTCTTGCCGTCGTCACGgtatgctacc ... ttggtgtcagAATTCGTAGAAATTTAGGTTTGCTAAAGCTTGAAGATGAGTTCTACTGTTT
EST: gi|116411164|gb|EG453756.1|EG453756
EST:     GTCCTGATTCATTTACCTCACTAATTGCGAGCCTTCTTGCCGTCGTCACG                         AATTCGTAGAAATTTAGGTTTGCTAAAGCTTGAAGATGAGTTCTACTGTTT
genomic: GTCCTGATTCATTTACCTCACTAATTGCGAGCCTTCTTGCCGTCGTCACGgtatgctacc ... ttggtgtcagAATTCGTAGAAATTTAGGTTTGCTAAAGCTTGAAGATGAGTTCTACTGTTT
EST: gi|116411167|gb|EG453759.1|EG453759
EST:     GTCCTGATTCATTTACCTCACTAATTGCGAGCCTTCTTGCCGTCGTCACG                         AATTCTTAGAAATTTAGGTTTGCTAAAGCTTGAAGATGAGTTCTACTGTTC
genomic: GTCCTGATTCATTTACCTCACTAATTGCGAGCCTTCTTGCCGTCGTCACGgtatgctacc ... ttggtgtcagAATTCGTAGAAATTTAGGTTTGCTAAAGCTTGAAGATGAGTTCTACTGTTT
EST: gi|116459202|gb|EG501794.1|EG501794
EST:     GTCCTGATTCATTTACCTCACTAATTGCGAGCCTTCTTGCCGTCGTCACG                         AATTCGTAGAAATTTAGGTTTGCTAAAGCTTGAAGATGAGTTCTACTGTTT
genomic: GTCCTGATTCATTTACCTCACTAATTGCGAGCCTTCTTGCCGTCGTCACGgtatgctacc ... ttggtgtcagAATTCGTAGAAATTTAGGTTTGCTAAAGCTTGAAGATGAGTTCTACTGTTT
EST: gi|116411166|gb|EG453758.1|EG453758
EST:     GTCCTGATTCATTTACCTCACTAATTGCGAGCCTTCTTGCCGTCGTCACG                         AATTCGTAGAAATTTAGGTTTGCTAAAGCTTGAAGATGAGTTCTACTGTTT
genomic: GTCCTGATTCATTTACCTCACTAATTGCGAGCCTTCTTGCCGTCGTCACGgtatgctacc ... ttggtgtcagAATTCGTAGAAATTTAGGTTTGCTAAAGCTTGAAGATGAGTTCTACTGTTT
EST: gi|116459198|gb|EG501790.1|EG501790
EST:     GTCCTGATTCATTTACCTCACTAATTGCGAGCCTTCTTGCCGTCGTCACG                         AATTCGTAGAAATTTAGGTTTGCTGAAGCTTGAAGATGAGTTCTACTGTTT
genomic: GTCCTGATTCATTTACCTCACTAATTGCGAGCCTTCTTGCCGTCGTCACGgtatgctacc ... ttggtgtcagAATTCGTAGAAATTTAGGTTTGCTAAAGCTTGAAGATGAGTTCTACTGTTT
EST: gi|116411176|gb|EG453768.1|EG453768
EST:     GTCCTGATTCATTTACCTCACTAATTGCGAGCCTTCTTGCCGTCGTCACG                         AATTCGTAGAAATTTAGGTTTGCTAAAGCTTGAAGATGAGTTCTGCTGTTT
genomic: GTCCTGATTCATTTACCTCACTAATTGCGAGCCTTCTTGCCGTCGTCACGgtatgctacc ... ttggtgtcagAATTCGTAGAAATTTAGGTTTGCTAAAGCTTGAAGATGAGTTCTACTGTTT
EST: gi|116411168|gb|EG453760.1|EG453760
EST:     GTCGTGATTCATTTACCTCACTAATTGCGAGCCTTCTTGCCGTCGTCACG                         AATTCGTAGAAATTTAGGTCTGCTAAAGCTTGAAGATGAGTTCTACTGTTC
genomic: GTCCTGATTCATTTACCTCACTAATTGCGAGCCTTCTTGCCGTCGTCACGgtatgctacc ... ttggtgtcagAATTCGTAGAAATTTAGGTTTGCTAAAGCTTGAAGATGAGTTCTACTGTTT
EST: gi|116459191|gb|EG501783.1|EG501783
EST:     GTCCTGATTCATTTACCTCACTAATTGCGAGCCTTCTTGCCGTCGTCACG                         AATTCGTAGAAATTTAGGTTTGCTAAAGCTTGAAGATGAGTTCTACTGTTT
genomic: GTCCTGATTCATTTACCTCACTAATTGCGAGCCTTCTTGCCGTCGTCACGgtatgctacc ... ttggtgtcagAATTCGTAGAAATTTAGGTTTGCTAAAGCTTGAAGATGAGTTCTACTGTTT
EST: gi|116411162|gb|EG453754.1|EG453754
EST:     GTCCTGATTCATTTACCTCACTAATTGCGAGCCTTCTTGCCGTCGTCACG                         AATTCGTAGAAATTTAGGTTTGCTAAAGCTTGAAGATGAGTTCTACTGTTT
genomic: GTCCTGATTCATTTACCTCACTAATTGCGAGCCTTCTTGCCGTCGTCACGgtatgctacc ... ttggtgtcagAATTCGTAGAAATTTAGGTTTGCTAAAGCTTGAAGATGAGTTCTACTGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggctgaattatggctctttaacccttccttgggacttttgtcttattggtgtcagAATTCGTAGAAATTTAGGTTTGCTAAAGCTTGAAGATGAGTTCTACTGTTTGGTGGGAAGGAGCTGAGAAGACACGAGTTCTCATAGCCCCAG
               ctttaac  putative branch site (score: 3)
                                        tcttatt  putative PPT
     aattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctacctaattggtgttaagggttgtcgtaatcttcaatcttttctcgcctagctctcgttttaggcttttgtaaagtttacttcagttttaggaaagagtatcgtcttctatgagtttgatatagcttgtacttggctcggctgaattatggctctttaacccttccttgggacttttgtcttattggtgtcagAATTCGTAGAAATTTAGGTTTGCTAAAGCTTGAAGATGAGTTCTACTGTTTGGTGGGAAGGAGCTGAGAAGACACGAGTTCTCATAGCCCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA