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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgtgttttcctgctcagtttctgcatatgtttaaagaatttgtaaaggatatttcatatttgaggtttgcattgcagGTCCAGGTTGTTCTTCAATTGGTGGAGGAGCTTTCACTGAGTTGGGTCCATTTTACCCCACTGGCGATGGCCGTGGCCTTCGTGTTAACTCCATGTCTTG

Basic information

species Arabidopsis thaliana
transcript AT5G42240.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G42240.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G132154_T01 (Zea mays), 3'ss of exon 1
-------------gtccgtgttttcctgctcagtttctgcat----atgtttaaagaatttgtaaaggatatttcatatttgaggtttgcatt---gcagGTCCAGGTTGTTCTTCAATTGGTGGAGGAGCTTTCACTGAGTTGGGTCCATTTTACCCCACTGGCGATGGCCGTGGCCTTCGTGTTAACTCCATGTCTTG
              | | || |   |  || |  | ||  ||     | | |      ||||      | || | | |  |      |  |||    |||||||||| |||||||| ||||| || || |||||||| ||| | || |||||||||||||  || ||||| || |||||  |  | |||   | ||| ||
gaaggaattgctgttacctgctagacaccttaagtactatattagggtatctttctcttttgatgtcaacatgtgaaaccttgcccgtatattctatcagGTCCAGGCTGTTCTTCTATTGGAGGCGGTGCTTTCACAGAGCTAGGGCCATTTTACCCCAGAGGTGATGGTCGAGGCCTCAGGTTGAACAAGAAGTCATG

upper sequence: AT5G42240.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G41970.1 (Glycine max), 3'ss of exon 1
-----------gtccgtgttttcctgct-cagtttctgcatatg-tttaaagaatttgtaaaggatatttcatatttgag--------gtttgcattgcagGTCCAGGTTGTTCTTCAATTGGTGGAGGAGCTTTCACTGAGTTGGGTCCATTTTACCCCACTGGCGATGGCCGTGGCCTTCGTGTTAACTCCATGTCTTG
               || |   | || | || ||  | |   ||  | | | || ||||  |     ||| |  |  |||         ||    || |||| || || ||||| || ||||| ||||| |||||||||||||||||||| ||||| ||||  || ||||| ||||| || ||    || || ||||||||
aaatatattataaatgtctacacttgttgcaattattactagtgactcataaaacttgtcgaactcctttaac-tcagagcaagcaccattgttttttcagGCCCGGGATGTTCCTCCATTGGAGGAGGTGCTTTCACTGAGTTGGGTCCCTTTTATCCCAAAGGTGATGGACGTGGTCTCCGAAGAAATTCAATGTCTTG
















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|124946296|gb|EL022230.1|EL022230
EST:     GGCTGTGAAACAACCTGACTCAAAGCCATTGACCCTTTGGCTCAATGGAG                         GTCCAGGTTGT
genomic: GGCTGTGAAACAACCTGACTCAAAGCCATTGACCCTTTGGCTCAATGGAGgtccgtgttt ... tgcattgcagGTCCAGGTTGT
EST: gi|164211496|gb|ES164144.1|ES164144
EST:     GGCTGTGAAACAACCTGACTCAAAACCATTGACCCTTTGGCTCAATGGAG                         GTCCAGGTTGTTCTTCAATTAGGTGGAGGAGCTTTCACTGAGTTGGGTCCA
genomic: GGCTGTGAAACAACCTGACTCAAAGCCATTGACCCTTTGGCTCAATGGAGgtccgtgttt ... tgcattgcagGTCCAGGTTGTTCTTCAATT-GGTGGAGGAGCTTTCACTGAGTTGGGTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatatgtttaaagaatttgtaaaggatatttcatatttgaggtttgcattgcagGTCCAGGTTGTTCTTCAATTGGTGGAGGAGCTTTCACTGAGTTGGGTCCATTTTACCCCACTGGCGATGGCCGTGGCCTTCGTGTTAACTCCATGTCTTG
       tttaaagaatttgtaa  TA-rich tract