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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgcattccatcttatttcattccaataaatataatcaaataccacaagaagctaatcaacatcttcatgaaagAAGGACTCGCTTGACGAGAAAGAAACGCTCCTTCGTCACACTTACGGTTTAGGATATTCAGAGCCCAATGTGACATTTGCACTTTGCCGTGGAAGTTGGT

Basic information

species Arabidopsis thaliana
transcript AT2G39690.2
intron # 7
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|116384467|gb|EG427059.1|EG427059
EST:     CTTTGGCGATTGAACATTTCGTCTTGCGGCATCCTTGTGAACCAGAAGAT                         AAGGACTCGCTTGACGAGAAAGAAACGCTCCTTCGTCACACTTACGGTTTA
genomic: CTTTGGCGATTGAACATTTCGTCTTGCGGCATCCTTGTGAACCAGAAGATgtaagtgcat ... ttcatgaaagAAGGACTCGCTTGACGAGAAAGAAACGCTCCTTCGTCACACTTACGGTTTA
EST: gi|116384469|gb|EG427061.1|EG427061
EST:     CTTTGGCGATTGAACATTTCGTCTTGCGGCATCCTTGTGAACCAGAAGAT                         AAGGACTCGCTTGACGAGAAAGAAACGCTCCTTCGTCACACTTACGGTTTA
genomic: CTTTGGCGATTGAACATTTCGTCTTGCGGCATCCTTGTGAACCAGAAGATgtaagtgcat ... ttcatgaaagAAGGACTCGCTTGACGAGAAAGAAACGCTCCTTCGTCACACTTACGGTTTA
EST: gi|116384466|gb|EG427058.1|EG427058
EST:     CTTTGGCGATTGAACATTTCGTCTTGCGGCATCCTTGTGAACCAGAAGAT                         AAGGACTCGCTTGACGAGAAAGAAACGCTCCTTCGTCACACTTACGGTTTA
genomic: CTTTGGCGATTGAACATTTCGTCTTGCGGCATCCTTGTGAACCAGAAGATgtaagtgcat ... ttcatgaaagAAGGACTCGCTTGACGAGAAAGAAACGCTCCTTCGTCACACTTACGGTTTA
EST: gi|116383991|gb|EG426583.1|EG426583
EST:     CTTTGGCGATTGAACATTTCGTCTTGCGGCATCCTTGTGAACCAGAAGAT                         --G-ACTCGCTTGACGAGAAAGAAACGCTCCTTCGTCACACTTACGGTTTA
genomic: CTTTGGCGATTGAACATTTCGTCTTGCGGCATCCTTGTGAACCAGAAGATgtaagtgcat ... ttcatgaaagAAGGACTCGCTTGACGAGAAAGAAACGCTCCTTCGTCACACTTACGGTTTA
EST: gi|116383986|gb|EG426578.1|EG426578
EST:     CTTTGGCGATTGAACATTTCGTCTTGCGGCATCCTTGTGAACCAGAAGAT                         ---GACTCGCTTGACGAGAAAGAAACGCTCCTTCGTCACACTTACGGTTTA
genomic: CTTTGGCGATTGAACATTTCGTCTTGCGGCATCCTTGTGAACCAGAAGATgtaagtgcat ... ttcatgaaagAAGGACTCGCTTGACGAGAAAGAAACGCTCCTTCGTCACACTTACGGTTTA
EST: gi|116383984|gb|EG426576.1|EG426576
EST:     CTTTGGCGATTGAACATTTCGTCTTGCGGCATCCTTGTGAACCAGAAGAT                         ---GACTCGCTTGACGAGAAAGAAACGCTCCTTCGTCACACTTACGGTTTA
genomic: CTTTGGCGATTGAACATTTCGTCTTGCGGCATCCTTGTGAACCAGAAGATgtaagtgcat ... ttcatgaaagAAGGACTCGCTTGACGAGAAAGAAACGCTCCTTCGTCACACTTACGGTTTA
EST: gi|116384465|gb|EG427057.1|EG427057
EST:     CTTTGGCGATTGAACATTTCGTCTTGCGGCATCCTTGTGAACCAGAAGAT                         AAGGACTCGCTTGACGAGAAAGAAACGCTCCTTCGTCACACTTACGGTTTA
genomic: CTTTGGCGATTGAACATTTCGTCTTGCGGCATCCTTGTGAACCAGAAGATgtaagtgcat ... ttcatgaaagAAGGACTCGCTTGACGAGAAAGAAACGCTCCTTCGTCACACTTACGGTTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attccaataaatataatcaaataccacaagaagctaatcaacatcttcatgaaagAAGGACTCGCTTGACGAGAAAGAAACGCTCCTTCGTCACACTTACGGTTTAGGATATTCAGAGCCCAATGTGACATTTGCACTTTGCCGTGGAAGTTGGT
                               agctaat  putative branch site (score: 3)
                                         catcttc  putative PPT
     aataaatataatcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgcattccatcttatttcattccaataaatataatcaaataccacaagaagctaatcaacatcttcatgaaagAAGGACTCGCTTGACGAGAAAGAAACGCTCCTTCGTCACACTTACGGTTTAGGATATTCAGAGCCCAATGTGACATTTGCACTTTGCCGTGGAAGTTGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG