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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcagctttttcattgtttgtctgttaacgctctgctacttttctctaaaattgccagacttcatccttttgcttaaaaaaacatattatatttgtcttccttttgctcagTGACGTCTCAAGCAATGATTTGTGTGGAACAATCCCAACAAACGGACCCTTTGCTCACATTCCTTTACAGAA

Basic information

species Arabidopsis thaliana
transcript AT5G21090.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G21090.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g59440.3 (Oryza sativa), 3'ss of exon 3
gtaagttcagctttttcattgtttgtctgttaacgctctgctacttttctctaaaattgccagacttcatccttttgcttaaaaaaacatattatatttgtcttccttttgctcagTGACGTCTCAAGCAATGATTTGTGTGGAACAATCCCAACAAACGGACCCTTTGCTCACATTCCTTTACAGAA
                        ||  ||  |    ||| | ||          | |||  | || ||  |  |   | ||    | | ||| ||     |||  | ||  ||||||| || |||||||||||| ||||||||||||| || |||   ||||| ||||  ||||||||  ||   ||
------------------------gtaagtacaattcctggtgct---------gagtgcttggctgcaaacaatc-ttgaatgtgataaattttaccc-ccttgttctt--tcagTGATGTTTCAAGCAATGATCTGTGTGGAACAATTCCTACATCAGGACCATTTGAGCACATTCCCCTAAGCAA

upper sequence: AT5G21090.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g59440.2 (Oryza sativa), 3'ss of exon 4
gtaagttcagctttttcattgtttgtctgttaacgctctgctacttttctctaaaattgccagacttcatccttttgcttaaaaaaacatattatatttgtcttccttttgctcagTGACGTCTCAAGCAATGATTTGTGTGGAACAATCCCAACAAACGGACCCTTTGCTCACATTCCTTTACAGAA----------------------------
                        ||  ||  |    ||| | ||          | |||  | || ||  |  |   | ||    | | ||| ||     |||  | ||  ||||||| || |||||||||||| ||||||||||||| || |||   ||||| ||||  ||||||||  ||   ||                            
------------------------gtaagtacaattcctggtgct---------gagtgcttggctgcaaacaatc-ttgaatgtgataaattttaccc-ccttgttctt--tcagTGATGTTTCAAGCAATGATCTGTGTGGAACAATTCCTACATCAGGACCATTTGAGCACATTCCCCTAAGCAAGTAAGTTTGACTGCCTTTGTGATACTAT
















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|124887996|gb|EH966898.1|EH966898
EST:     ACCGGTCCAATCCCTAGAGCACTCACGGCAATCCCAAGCCTTAAAGTTGT                         TGACGTCTCAAG
genomic: ACCGGTCCAATCCCTAGAGCACTCACGGCAATCCCAAGCCTTAAAGTTGTgtaagttcag ... ttttgctcagTGACGTCTCAAG
EST: gi|124878319|gb|EH957756.1|EH957756
EST:     CCGGTCCAATCCCTAGAGCACTCACGGCAATCCCAAGCCTTTAAAGTTGT                         TGACGTCTCAAGCAATGATTTGTGTGGAACAATCCCAACAAACGGACCCTT
genomic: CCGGTCCAATCCCTAGAGCACTCACGGCAATCCCAAGCC-TTAAAGTTGTgtaagttcag ... ttttgctcagTGACGTCTCAAGCAATGATTTGTGTGGAACAATCCCAACAAACGGACCCTT
EST: gi|116443563|gb|EG486155.1|EG486155
EST:     ACCGGTCCAATCCCTAGAGCACTCACGGCAATCCCAAGCCTTAAAGTTGT                         TGACGTCTCAAGCAATGATTTGTGTGGAACAATCCCAACAAACGGACCCTT
genomic: ACCGGTCCAATCCCTAGAGCACTCACGGCAATCCCAAGCCTTAAAGTTGTgtaagttcag ... ttttgctcagTGACGTCTCAAGCAATGATTTGTGTGGAACAATCCCAACAAACGGACCCTT
EST: gi|124995931|gb|EL068200.1|EL068200
EST:     CCGGTCCAATCCCTAGAGCACTCACGGCAATCCCAAGCCTTAAAGTTGT                         TGACGTCTCAAGCAATGATTTGTGTGGAACAATCACAACAAACGGACCCTT
genomic: CCGGTCCAATCCCTAGAGCACTCACGGCAATCCCAAGCCTTAAAGTTGTgtaagttcag ... ttttgctcagTGACGTCTCAAGCAATGATTTGTGTGGAACAATCCCAACAAACGGACCCTT
EST: gi|164050418|gb|ES187449.1|ES187449
EST:     GCAATCCCAAGCCTTAAAGTTGT                         TGATGTCTCAAGCAATGATTTGTGTGGAACAATCCCAACAAACGGACCTTT
genomic: GCAATCCCAAGCCTTAAAGTTGTgtaagttcag ... ttttgctcagTGACGTCTCAAGCAATGATTTGTGTGGAACAATCCCAACAAACGGACCCTT
EST: gi|124960013|gb|EL034710.1|EL034710
EST:     ACCGGTCCAATCCCTAGAGCACTCACGGCAATCCCAAGCCTTAAAGTTGT                         TGACGTCTCAAGCAATGATTTGTGTGGAACAATCCCAACAAACGG
genomic: ACCGGTCCAATCCCTAGAGCACTCACGGCAATCCCAAGCCTTAAAGTTGTgtaagttcag ... ttttgctcagTGACGTCTCAAGCAATGATTTGTGTGGAACAATCCCAACAAACGG
EST: gi|301501628|gb|HO207168.1|HO207168
EST:     ACCGGTCCAATCCCTAGAGCACTCACGGCAATCCCAAGCCTTAAAGTTGT                         TGACGTCTCAAGCAATGATTTGTGTGGAACAATCCCA
genomic: ACCGGTCCAATCCCTAGAGCACTCACGGCAATCCCAAGCCTTAAAGTTGTgtaagttcag ... ttttgctcagTGACGTCTCAAGCAATGATTTGTGTGGAACAATCCCA
EST: gi|124975110|gb|EL048628.1|EL048628
EST:     ACCGGTCCAATCCCTAGAGCACTCACGGCAATCCCAAGCCTTAAAGTTGT                         TGACGTCTCAAGCAA
genomic: ACCGGTCCAATCCCTAGAGCACTCACGGCAATCCCAAGCCTTAAAGTTGTgtaagttcag ... ttttgctcagTGACGTCTCAAGCAA
EST: gi|124753442|gb|EH843572.1|EH843572
EST:     CCTAGAGCACTCACGGCAATCCCAAGTTCCTTAAAGTTGT                         TGACGTCTCAAGCAATGATTTGTGTGGAACAATCCCAACAAACGGACCCTT
genomic: CCTAGAGCACTCACGGCAATCCCAAG--CCTTAAAGTTGTgtaagttcag ... ttttgctcagTGACGTCTCAAGCAATGATTTGTGTGGAACAATCCCAACAAACGGACCCTT
EST: gi|125277865|gb|EL291950.1|EL291950
EST:     CACTCACGGCAATCCCAAGCCTTAAAGTTGT                         TGACGTCTCAAGCAATGATTTGTGTGGAACAATCCCAACAAACGGACCCTT
genomic: CACTCACGGCAATCCCAAGCCTTAAAGTTGTgtaagttcag ... ttttgctcagTGACGTCTCAAGCAATGATTTGTGTGGAACAATCCCAACAAACGGACCCTT
EST: gi|152038285|gb|BP812943.2|BP812943
EST:     ACCGGTCCAATCCCTAGAGCACTCACGGCAATCCCAAGCCTTAAAGTTGT                         TGACGTCTCAAGCAATGATTTGTGTGGAACAATCCCAACAAACGGACCCTT
genomic: ACCGGTCCAATCCCTAGAGCACTCACGGCAATCCCAAGCCTTAAAGTTGTgtaagttcag ... ttttgctcagTGACGTCTCAAGCAATGATTTGTGTGGAACAATCCCAACAAACGGACCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agacttcatccttttgcttaaaaaaacatattatatttgtcttccttttgctcagTGACGTCTCAAGCAATGATTTGTGTGGAACAATCCCAACAAACGGACCCTTTGCTCACATTCCTTTACAGAA
                                   tttgtcttccttttgc  CT-rich tract
           ttttgcttaaaaaaac  TA-rich tract