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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgttagctatcactattcctttgcttgttttacttacaatcattgaatgcttgtgtatgtatattctgtttggttgttgactctgttgtattgactttgctaagAACGTAGAGTTGACCCTAAAGATCTTCGCTTGAAGCTCCAAAAGAAACGTCATGGCTCGCAAATTGGTGGACGAGTATTTAGTGTAAGCGTGGCGGATCT

Basic information

species Arabidopsis thaliana
transcript AT5G48680.1
intron # 2
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|164020595|gb|ES196453.1|ES196453
EST:     ATCTTTTCGAAGACGATGACGAGCCTCGGCTTTCAA                         AACGTAGAGTTGACCCTAAAGATCTTCGCTTGAAGCTCCAAAAGAAACGTC
genomic: ATCTTTTCGAAGACGATGACGAGCCTCGGCTTTCAAgtatgttgtt ... ctttgctaagAACGTAGAGTTGACCCTAAAGATCTTCGCTTGAAGCTCCAAAAGAAACGTC
EST: gi|164224800|gb|ES022949.1|ES022949
EST:     CTTTTCGAAGACGATGACGAGCCTCGGCTTTCAA                         AACGTAGAGTTGACCCTAAAGATCTTCGCTTGAAGCTCCAAAAGAAACGTC
genomic: CTTTTCGAAGACGATGACGAGCCTCGGCTTTCAAgtatgttgtt ... ctttgctaagAACGTAGAGTTGACCCTAAAGATCTTCGCTTGAAGCTCCAAAAGAAACGTC
EST: gi|19876604|gb|AU237435.1|AU237435
EST:     TAAGTGGGAGCATGATCTTTTCGAAGACGATGACGAGCCTCGGCTTTCAA                         AACGTAGAGTTGACCCTAAAGATCTTCGCTTGAAGCTCCAAAAGAAACGTC
genomic: TAAGTGGGAGCATGATCTTTTCGAAGACGATGACGAGCCTCGGCTTTCAAgtatgttgtt ... ctttgctaagAACGTAGAGTTGACCCTAAAGATCTTCGCTTGAAGCTCCAAAAGAAACGTC
EST: gi|125066753|gb|EL133510.1|EL133510
EST:     TAAGTGGGAGCATGATCTTTTCGAAGACGATGACGAGCCTCGGCTTTCAA                         AACGTAGAGTTGACCCTAAAGATCTTCGCTTGAAGCTCCAAAAGAAACGTC
genomic: TAAGTGGGAGCATGATCTTTTCGAAGACGATGACGAGCCTCGGCTTTCAAgtatgttgtt ... ctttgctaagAACGTAGAGTTGACCCTAAAGATCTTCGCTTGAAGCTCCAAAAGAAACGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtgtatgtatattctgtttggttgttgactctgttgtattgactttgctaagAACGTAGAGTTGACCCTAAAGATCTTCGCTTGAAGCTCCAAAAGAAACGTCATGGCTCGCAAATTGGTGGACGAGTATTTAGTGTAAGCGTGGCGGATCT
                                       tattgac  putative branch site (score: 2)
                                             ctttgct  CT-rich tract
      tatgtatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttgttagctatcactattcctttgcttgttttacttacaatcattgaatgcttgtgtatgtatattctgtttggttgttgactctgttgtattgactttgctaagAACGTAGAGTTGACCCTAAAGATCTTCGCTTGAAGCTCCAAAAGAAACGTCATGGCTCGCAAATTGGTGGACGAGTATTTAGTGTAAGCGTGGCGGATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA