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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtataaactcaccaccgcccttcctttctctgttttgtttctttggatgctctgtaatttttttatgcgtatgtgtatagGTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACAATGGAGGATATACTGGTACAGTTGAAGAAGGAAATGTCTACGTCGCATA

Basic information

species Arabidopsis thaliana
transcript AT3G52560.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G52560.4 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G21780.1 (Glycine max), 3'ss of exon 2
--------gtacgtataaactcaccaccgcccttcctttctctgttttgtttctt---tggatg-ctctgtaatt---tttttatgcgtatgtgta-tagGTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACAATGGAGGATATACTGGTACAGTTGAAGAAGGAAATGTCTACGTCGCATA
          | || ||   | |  |      ||  | | | |  || | ||  |   |   |  || ||| |     ||| ||  | |   || | ||||| || || ||||||||||| || |||||||| ||||||||||||||||| |||||||| ||||||  ||||||||||||||||||| |  |  | ||||
gacacttctcatgtttatgattatgagaaaatttagtctattttattggcttaataactaattatctttgtgacaagatttatagacttgaatgaaatagGTTGAACCAAAGAAATTTGGTCTTCTTGCAAATTGGCAAAGAGAGTACACCATGGAGGACATACTGACACAGTTGAAGAAGGAAATGGCCGCTCCTCATA
















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|86018900|gb|DR314646.1|DR314646
EST:     GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTG                         GTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA
genomic: GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTGgtacgtataa ... atgtgtatagGTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA
EST: gi|86018875|gb|DR314621.1|DR314621
EST:     GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTG                         GTGGATCCTAAGAAATTTGGGCTACTTGCAA-CTGGCAAAGAGAGTACACA
genomic: GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTGgtacgtataa ... atgtgtatagGTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA
EST: gi|125280115|gb|EL294200.1|EL294200
EST:     ATTCACGTGGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTG                         GTGGATCCTAAGAAATTTGGGCTA
genomic: ATTCACGT-GTCAACATGGCTTGTGTCAACCACGAAACAGGAGTGgtacgtataa ... atgtgtatagGTGGATCCTAAGAAATTTGGGCTA
EST: gi|86018902|gb|DR314648.1|DR314648
EST:     GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTG                         GTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA
genomic: GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTGgtacgtataa ... atgtgtatagGTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA
EST: gi|86018872|gb|DR314618.1|DR314618
EST:     GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTG                         GTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA
genomic: GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTGgtacgtataa ... atgtgtatagGTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA
EST: gi|124715266|gb|EH806668.1|EH806668
EST:     GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTG                         GTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAG
genomic: GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTGgtacgtataa ... atgtgtatagGTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAG
EST: gi|86018874|gb|DR314620.1|DR314620
EST:     GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTG                         GTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA
genomic: GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTGgtacgtataa ... atgtgtatagGTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA
EST: gi|86018885|gb|DR314631.1|DR314631
EST:     GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTG                         GTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA
genomic: GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTGgtacgtataa ... atgtgtatagGTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA
EST: gi|86018891|gb|DR314637.1|DR314637
EST:     GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTG                         GTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA
genomic: GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTGgtacgtataa ... atgtgtatagGTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA
EST: gi|86018898|gb|DR314644.1|DR314644
EST:     GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTG                         GTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA
genomic: GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTGgtacgtataa ... atgtgtatagGTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA
EST: gi|86018881|gb|DR314627.1|DR314627
EST:     GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTG                         GTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA
genomic: GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTGgtacgtataa ... atgtgtatagGTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA
EST: gi|86018878|gb|DR314624.1|DR314624
EST:     GGTTCCATTCACGTGTCAACATGGCTTGTGTCAATCACGAAACAGGAGTG                         GTGGATCCTAAGAAATTTGGGCTACTTGCAA-CTGGCAAAGAGAGTACACA
genomic: GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTGgtacgtataa ... atgtgtatagGTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA
EST: gi|86018884|gb|DR314630.1|DR314630
EST:     GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTG                         GTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA
genomic: GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTGgtacgtataa ... atgtgtatagGTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA
EST: gi|86018901|gb|DR314647.1|DR314647
EST:     GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTG                         GTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA
genomic: GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTGgtacgtataa ... atgtgtatagGTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA
EST: gi|86018887|gb|DR314633.1|DR314633
EST:     GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTG                         GTGGATCCTAAGAAATTTGGGCTACTTGCCAACTGGCAAAGAGAGTACACA
genomic: GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTGgtacgtataa ... atgtgtatagGTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA
EST: gi|86018871|gb|DR314617.1|DR314617
EST:     GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTG                         GTGGATCCTAAGAAATTTGGGCTACTTGCAA-CTGGCAAAGAGAGTACACA
genomic: GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTGgtacgtataa ... atgtgtatagGTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA
EST: gi|86018883|gb|DR314629.1|DR314629
EST:     GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTG                         GTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA
genomic: GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTGgtacgtataa ... atgtgtatagGTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA
EST: gi|86018899|gb|DR314645.1|DR314645
EST:     GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTG                         GTGGATCCTAAGAAATTTGGGCTACTTGCAA-CTGGCAAAGAGAGTATACA
genomic: GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTGgtacgtataa ... atgtgtatagGTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA
EST: gi|86018895|gb|DR314641.1|DR314641
EST:     ATTCCATTCACGTGTCAACATGGCTTTGTGTCAACCACGAAACAGGAGTG                         GTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA
genomic: ATTCCATTCACGTGTCAACATGGCTT-GTGTCAACCACGAAACAGGAGTGgtacgtataa ... atgtgtatagGTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA
EST: gi|86018882|gb|DR314628.1|DR314628
EST:     GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGAAGTG                         GTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA
genomic: GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTGgtacgtataa ... atgtgtatagGTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA
EST: gi|86018873|gb|DR314619.1|DR314619
EST:     GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTG                         GTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA
genomic: GATTCCATTCACGTGTCAACATGGCTTGTGTCAACCACGAAACAGGAGTGgtacgtataa ... atgtgtatagGTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctctgttttgtttctttggatgctctgtaatttttttatgcgtatgtgtatagGTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACAATGGAGGATATACTGGTACAGTTGAAGAAGGAAATGTCTACGTCGCATA
                         tctgtaatttttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtataaactcaccaccgcccttcctttctctgttttgtttctttggatgctctgtaatttttttatgcgtatgtgtatagGTGGATCCTAAGAAATTTGGGCTACTTGCAAACTGGCAAAGAGAGTACACAATGGAGGATATACTGGTACAGTTGAAGAAGGAAATGTCTACGTCGCATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA