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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttatctgtacgtgttttctttgtaagatgagtttaatggttacaatacataataagagaattgggctttttagGTAACTGTGTTCAAACAGCAAGCTAGCAAATTGGCTGCGCTTAACAAGAGATTGTTTGGGATCAAAGTTGGTGACTTCTG

Basic information

species Arabidopsis thaliana
transcript AT3G04820.1
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|116462950|gb|EG505542.1|EG505542
EST:     CATTCGGATTCTCTGGAACAAAAGATAAGCGGTCTGTTTCTACTCAGCGT                         GTAACTGTGTTCAAACAGCAAGCTAGCAAATTGGCTGCGCTTAACAA
genomic: CATTCGGATTCTCTGGAACAAAAGATAAGCGGTCTGTTTCTACTCAGCGTgtaagttatc ... ggctttttagGTAACTGTGTTCAAACAGCAAGCTAGCAAATTGGCTGCGCTTAACAA
EST: gi|116421231|gb|EG463823.1|EG463823
EST:     CATTCGGATTCTCTGGAACAAAAGATAAGCGGTCTGTTTCTACTCAGCGT                         GTAACTGTGTTCAAACAGCAAGCTAGCAAATTGGCTGCGCTTAACAAGAGA
genomic: CATTCGGATTCTCTGGAACAAAAGATAAGCGGTCTGTTTCTACTCAGCGTgtaagttatc ... ggctttttagGTAACTGTGTTCAAACAGCAAGCTAGCAAATTGGCTGCGCTTAACAAGAGA
EST: gi|125106890|gb|EL160279.1|EL160279
EST:     CATTCGGATTCTCTGGAACAAAAGATAAGCGGTCTGTTTCTACTCAGCGT                         GTAACTGTGTTCAAACAGCAAG
genomic: CATTCGGATTCTCTGGAACAAAAGATAAGCGGTCTGTTTCTACTCAGCGTgtaagttatc ... ggctttttagGTAACTGTGTTCAAACAGCAAG
EST: gi|116421229|gb|EG463821.1|EG463821
EST:     CATTCGGATTCTTTGGAACAAAAGATAAGCGGTCTGTTTCTACTCAGCGT                         GTAACTGTGTTCAAACAGCAAGCTAGCAAATTGGCTGCGCTTAACAAGAGA
genomic: CATTCGGATTCTCTGGAACAAAAGATAAGCGGTCTGTTTCTACTCAGCGTgtaagttatc ... ggctttttagGTAACTGTGTTCAAACAGCAAGCTAGCAAATTGGCTGCGCTTAACAAGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtaagatgagtttaatggttacaatacataataagagaattgggctttttagGTAACTGTGTTCAAACAGCAAGCTAGCAAATTGGCTGCGCTTAACAAGAGATTGTTTGGGATCAAAGTTGGTGACTTCTG
            gtttaat  putative branch site (score: 4)
                                               cttttt  putative PPT
                     ttacaatacataataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttatctgtacgtgttttctttgtaagatgagtttaatggttacaatacataataagagaattgggctttttagGTAACTGTGTTCAAACAGCAAGCTAGCAAATTGGCTGCGCTTAACAAGAGATTGTTTGGGATCAAAGTTGGTGACTTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA