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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacatatgtataaagcttaacttagtttcagtatctaaactttcactcgaatttttcaattggacgcagGCACAGAGTGAGGATGATGCTGTGAAATTAGGCCTTGTGGTTGCTACGACAGTGAAGGAGTTCAATGCTTTGGACACCTGTGCCTTGTCCAACCTCACTC

Basic information

species Arabidopsis thaliana
transcript AT5G17530.1
intron # 18
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|86075023|gb|DR370780.1|DR370780
EST:     TTCTTCTCAGACTTTCTCTCCATGATCCTGTTCTTCCCCTTAACATCGAG                         GCACAGAGTGAGGATGATGCTGTGAAATTAGGCCTTGTGGTTGCTACGGCA
genomic: TTCTTCTCAGACTTTCTCTCCATGATCCTGTTCTTCCCCTTAACATCGAGgtaaacatat ... ttggacgcagGCACAGAGTGAGGATGATGCTGTGAAATTAGGCCTTGTGGTTGCTACGACA
EST: gi|116416532|gb|EG459124.1|EG459124
EST:     TTCTTCTCAGACTTTCTCTCCATGATCCTGTTCTTCCCCTTAACATCGAG                         GCACAGAGTGAGGATGATGCTGTGAAATTAGGCCTTGTGGTTGCTACGACA
genomic: TTCTTCTCAGACTTTCTCTCCATGATCCTGTTCTTCCCCTTAACATCGAGgtaaacatat ... ttggacgcagGCACAGAGTGAGGATGATGCTGTGAAATTAGGCCTTGTGGTTGCTACGACA
EST: gi|116416533|gb|EG459125.1|EG459125
EST:     NNNNNNNCAGACTTTCTCTCCATGATCCTGTTCTTCCCCTTAACATCGAG                         GCACAGAGTGAGGATGATGCTGTGAAATTAGGCCTTGTGGTTGCTACGACA
genomic: TTCTTCTCAGACTTTCTCTCCATGATCCTGTTCTTCCCCTTAACATCGAGgtaaacatat ... ttggacgcagGCACAGAGTGAGGATGATGCTGTGAAATTAGGCCTTGTGGTTGCTACGACA
EST: gi|116424751|gb|EG467343.1|EG467343
EST:     TTCTTCTCAGACTTTCTCTCCATGATCCTGTTCTTCCCCTTAACATCGAG                         GCACAGAGTGAGGATGATGCTGTGAAATTAGGCCTTGTGGTTGCTACGACA
genomic: TTCTTCTCAGACTTTCTCTCCATGATCCTGTTCTTCCCCTTAACATCGAGgtaaacatat ... ttggacgcagGCACAGAGTGAGGATGATGCTGTGAAATTAGGCCTTGTGGTTGCTACGACA
EST: gi|125083280|gb|EL143903.1|EL143903
EST:     TCTCCATGATCCTGTTCTTACCCCTTAACATCGAG                         GCACAGAGTGAGGATGATGCTGTGAAATTAGGCCTTGTGGTTGCTACGACA
genomic: TCTCCATGATCCTGTTCTT-CCCCTTAACATCGAGgtaaacatat ... ttggacgcagGCACAGAGTGAGGATGATGCTGTGAAATTAGGCCTTGTGGTTGCTACGACA
EST: gi|86023634|gb|DR319387.1|DR319387
EST:     TTCTTCTCAGACTTTCTCTCCATGATCCTGTTCTTCCCCTTAACATCGAG                         GCACAGAGTGAGGATGATGCTGTGAAATTAGGCCTTGTGGTTGCTACG
genomic: TTCTTCTCAGACTTTCTCTCCATGATCCTGTTCTTCCCCTTAACATCGAGgtaaacatat ... ttggacgcagGCACAGAGTGAGGATGATGCTGTGAAATTAGGCCTTGTGGTTGCTACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttaacttagtttcagtatctaaactttcactcgaatttttcaattggacgcagGCACAGAGTGAGGATGATGCTGTGAAATTAGGCCTTGTGGTTGCTACGACAGTGAAGGAGTTCAATGCTTTGGACACCTGTGCCTTGTCCAACCTCACTC
                  atctaaa  putative branch site (score: 3)
                                   aatttttcaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaacatatgtataaagcttaacttagtttcagtatctaaactttcactcgaatttttcaattggacgcagGCACAGAGTGAGGATGATGCTGTGAAATTAGGCCTTGTGGTTGCTACGACAGTGAAGGAGTTCAATGCTTTGGACACCTGTGCCTTGTCCAACCTCACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG