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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggctgctctacttttcgagtttgatttctttgagtccttaagatggaagctgtttatttctgagtttgagtttgttcttctgatctctaatggtggagtggtttgttttatttgtgtagCTATTGGGCAAATATCTCACACGAGCAAG

Basic information

species Arabidopsis thaliana
transcript AT3G11620.2
intron # 4
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|86060665|gb|DR356422.1|DR356422
EST:     CTTTTTGGAATCTTTATACGAGTTTCTTGGTGGAAATGCTTCTGTAATTG                         CTATTGGGCAAATATCTCACACGAGCAAG
genomic: CTTTTTGGAATCTTTATACGAGTTTCTTGGTGGAAATGCTTCTGTAATTGgtatggctgc ... atttgtgtagCTATTGGGCAAATATCTCACACGAGCAAG
EST: gi|19876798|gb|AU237629.1|AU237629
EST:     CTTTTTGGAATCTTTATACGAGTTTCTTGGTGGAAATGCTTCTGTAATTG                         CTATTGGGCAAATATCTCACACGAGCAAG
genomic: CTTTTTGGAATCTTTATACGAGTTTCTTGGTGGAAATGCTTCTGTAATTGgtatggctgc ... atttgtgtagCTATTGGGCAAATATCTCACACGAGCAAG
EST: gi|86060664|gb|DR356421.1|DR356421
EST:     CTTTTTGGAATCTTTATACGAGTTTCTTGGTGGAAATGCTTCTGTAATTG                         CTATTGGGCAAATATCTCACACGAGCAAG
genomic: CTTTTTGGAATCTTTATACGAGTTTCTTGGTGGAAATGCTTCTGTAATTGgtatggctgc ... atttgtgtagCTATTGGGCAAATATCTCACACGAGCAAG
EST: gi|86060666|gb|DR356423.1|DR356423
EST:     CTTTTTGGAATCTTTATACGAGTTTCTTGGTGGAAATGCTTCTGTAATTG                         CTATTGGGCAAATATCTCACACGAGCAAG
genomic: CTTTTTGGAATCTTTATACGAGTTTCTTGGTGGAAATGCTTCTGTAATTGgtatggctgc ... atttgtgtagCTATTGGGCAAATATCTCACACGAGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgagtttgttcttctgatctctaatggtggagtggtttgttttatttgtgtagCTATTGGGCAAATATCTCACACGAGCAAG
                    ctctaat  putative branch site (score: 3)
                                         ttttattt  putative PPT
                                     tttgttttatttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggctgctctacttttcgagtttgatttctttgagtccttaagatggaagctgtttatttctgagtttgagtttgttcttctgatctctaatggtggagtggtttgttttatttgtgtagCTATTGGGCAAATATCTCACACGAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG