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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatgggatctcatccacaccctttctattttggttttgctatctcttctttaatgttttcgtgaagcaaaatcacctcatttcttattattatccagATCGAGGGAAACCGCTCAAAAGAGGAAGTGTTTGCCCAGATCGATTCTTCTCTGTCCGAATTGCTTCAAGAGAGGAACACTGCTCCAAGTTCACTTTTAA

Basic information

species Arabidopsis thaliana
transcript AT5G47840.1
intron # 5
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|125237233|gb|EL251318.1|EL251318
EST:     ACCAAAATGTGAGTGATGTGCTTTCTATGTACGACGATATAACAATTAAG                         ATCGAGGGAAACCGCTCAAAAGAGGAAGTGTTTG
genomic: ACCAAAATGTGAGTGATGTGCTTTCTATGTACGACGATATAACAATTAAGgcatgggatc ... tattatccagATCGAGGGAAACCGCTCAAAAGAGGAAGTGTTTG
EST: gi|124735677|gb|EH827079.1|EH827079
EST:     ACCAAAATGTGAGTGATGTGCTTTCTATGTACGACGATATAACAATTAAG                         ATCGAGGGAAACCGCTCAAAAGA
genomic: ACCAAAATGTGAGTGATGTGCTTTCTATGTACGACGATATAACAATTAAGgcatgggatc ... tattatccagATCGAGGGAAACCGCTCAAAAGA
EST: gi|124825906|gb|EH910772.1|EH910772
EST:     ACCAAAATGTGAGTGATGTGCTTTCTATGTACGACGATATAACAATTAAG                         ATCGAGGGAAACC
genomic: ACCAAAATGTGAGTGATGTGCTTTCTATGTACGACGATATAACAATTAAGgcatgggatc ... tattatccagATCGAGGGAAACC
EST: gi|125093883|gb|EL151422.1|EL151422
EST:     TCTATGTACGACGATATAACAATTAAG                         ATCGAGGGAAACCGCTCAAAAGAGGAAGTGTTTGCCCAGATCGATTCTTCT
genomic: TCTATGTACGACGATATAACAATTAAGgcatgggatc ... tattatccagATCGAGGGAAACCGCTCAAAAGAGGAAGTGTTTGCCCAGATCGATTCTTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttctttaatgttttcgtgaagcaaaatcacctcatttcttattattatccagATCGAGGGAAACCGCTCAAAAGAGGAAGTGTTTGCCCAGATCGATTCTTCTCTGTCCGAATTGCTTCAAGAGAGGAACACTGCTCCAAGTTCACTTTTAA
     ctttaat  putative branch site (score: 4)
                                cctcatttcttatt  putative PPT
                                  tcatttcttattatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgggatctcatccacaccctttctattttggttttgctatctcttctttaatgttttcgtgaagcaaaatcacctcatttcttattattatccagATCGAGGGAAACCGCTCAAAAGAGGAAGTGTTTGCCCAGATCGATTCTTCTCTGTCCGAATTGCTTCAAGAGAGGAACACTGCTCCAAGTTCACTTTTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA