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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtatgatctctcacaggacataagattctaagacactgcaaaagctaaaattgtgtctaactattatcaccgtttcctttcaacctcaattctttcttgtcacagGTAGCTACAGATAAATGCATAATGGCGTTCCTGTTTCTGATTGTCTGTGGTGTTATAGCTATAATCATTGTGAAG

Basic information

species Arabidopsis thaliana
transcript AT1G48240.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G48240.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os07g44350.1 (Oryza sativa), 3'ss of exon 8
---------------------------------------------------------gtttgtatgatc-tctcacaggacataagattctaagacactgcaaaagctaaaattg-tgtctaactattatcaccgtttcctttcaacctcaattctttcttgtcacagGTAGCTACAGATAAATGCATAATGGCGTTCCTGTTTCTGATTGTCTGTGGTGTTATAGCTATAATCATTGTGAAG
                                                          |  ||     | |||      |  |   | |  ||| |    |  |   |   |  | ||    |   ||      | |     |  || |  |   ||  |||   ||||| || || || |||||||| ||||| ||||| |||||||| ||||||||||| || || || ||  |||| |||
gttctctctctctctctccccccctgcacacacgtatgttactcgtttcgtcccaaaataagtgcagccctctagttcaaatttgaactagaaggctgcactcattttgggacagatggagtatatttgaagtggctgtgcctagacttacaagattcattgctgcagGTTGCAACTGACAAATGCATCATGGCATTCCTATTTCTGATAGTCTGTGGTGTGATTGCAATCATTGTTGTTAAG

upper sequence: AT1G48240.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G381370_T01 (Zea mays), 3'ss of exon 2
gtttgtatgatctctcacaggacataagattctaagacactgcaaaagctaaaattgtgtctaactattatcaccgtttcctttcaacctcaattctttcttgtcacagGTAGCTACAGATAAATGCATAATGGCGTTCCTGTTTCTGATTGTCTGTGGTGTTATAGCTATAATCATTGTGAAG-------------------------
                            ||||     | ||  |  |   |||    ||| ||  | |||   |    |   |  |    |||   ||| |  |  ||||| ||||| || |||||||| ||||||||||||||||||||||||||||| ||||| || |||||  |||| |||                         
---------------------gtgctccattccc---ctctctagcactcaaatgcatgtttatttgttactcctaagtggctgaagttacaagatttt-tcatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGCGTTATTGCAATAATTGTTGTTAAGGTAGGTTGCCGACTCCGAAGGGTAG

upper sequence: AT1G48240.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G170191_T01 (Zea mays), 3'ss of exon 2
gtttgtatgatctctcacaggacataagattctaagacactgcaaaagctaaaattgtgtctaactattatcaccgtttcctttcaacctcaattctttcttgtcacagGTAGCTACAGATAAATGCATAATGGCGTTCCTGTTTCTGATTGTCTGTGGTGTTATAGCTATAATCATTGTGAAG
                            ||||     | ||  |  |   |||    ||| ||  | |||   |    |   |  |    |||   ||| |  |  ||||| ||||| || |||||||| ||||||||||||||||||||||||||||| ||||| || |||||  |||| |||
---------------------gtgctccattccc---ctctctagcactcaaatgcatgtttatttgttactcctaagtggctgaagttacaagatttt-tcatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGCGTTATTGCAATAATTGTTGTTAAG

upper sequence: AT1G48240.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G000718_T01 (Zea mays), 3'ss of exon 8
gtttgtatgatctctcacaggacataagattctaagacactgcaaaagctaaaattgtgtctaactattatcaccgtttcctttcaacctcaattctttcttgtcacagGTAGCTACAGATAAATGCATAATGGCGTTCCTGTTTCTGATTGTCTGTGGTGTTATAGCTATAATCATTGTGAAG
        | |||| | |           || |    |||| |||| |||    || | | |   || |   ||         |   |   ||          |  ||||| ||||| || |||||||| |||||||||||||||||||||||||||||||| || || |||||  |||| |||
--------gttctccctcg----------ttttctagcact-caaatgcttg--tttttttttgttactcctacgtggctgaatttgcaaaaaaaaaaaaacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAG

upper sequence: AT1G48240.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G102903_T02 (Zea mays), 3'ss of exon 8
gtttgtatgatctctcacaggacataagattctaagacactgcaaaagctaaaat-tgtgtctaactattatcaccgtttcctttcaacctcaattctttcttgtcacagGTAGCTACAGATAAATGCATAATGGCGTTCCTGTTTCTGATTGTCTGTGGTGTTATAGCTATAATCATTGTGAAG
                              || |   |    | |   || ||||   ||| ||  |  |||  |    |   |  |    |||   ||| |  |  ||||| ||||| || |||||||| ||||||||||||||||||||||||||||| ||||| || |||||  |||| |||
--------------------------gtgctccatcccctctctagcactcaaatgcatgtttatttgctattcctaagtggctgaagttacaagatttt-tcatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGCGTTATTGCAATAATTGTTGTTAAG

upper sequence: AT1G48240.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv05s0020g00750.t01 (Vitis vinifera), 3'ss of exon 8
gtttgtatgatctctcacaggacataagattctaagacactgcaaaagctaaaattgtgtctaactattatcaccgtttcctttcaacctcaattctttcttgtcacagGTAGCTACAGATAAATGCATAATGGCGTTCCTGTTTCTGATTGTCTGTGGTGTTATAGCTATAATCATTGTGAAG
                   |    ||   || |  ||  |     | ||| || ||   |   | |  | || |  ||     | |||| |||   |||       ||||| ||||| |||||||||||||||   ||||| ||||| ||||| |||||||| ||||| || ||||||||||||
-------------------gtgtgtatt-ttttctgattcc----atgctcaatttacattccatttatttctcgtttataactaaaccccaaacattttc-----cagGTGGCTACGGATAAATGCATAATGCTTTTCCTATTTCTTATTGTGTGTGGTGTAATAGCCATTATCATTGTGAAG

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|86077216|gb|DR372973.1|DR372973
EST:     AGTTCTCTCTTAAGAAA-SKTCGCAGCTGGTGAAAGAGATAGGAAGACAG                         GTAGCTACAGATAAATGCATAATGGCGTYCCTGTTTCTGATTGTCTGTGGT
genomic: AGTTCTCTCTTAAGAAAGCTTCGCAGCTGGTGAAAGAGATAGGAAGACAGgtttgtatga ... cttgtcacagGTAGCTACAGATAAATGCATAATGGCGTTCCTGTTTCTGATTGTCTGTGGT
EST: gi|19797491|gb|AU229297.1|AU229297
EST:     TCTCTTAAGAAAGCTTCCCAGCTGGTGAAAGAGATAGGAAGACAG                         GTAGCTACAGATAAATGCATAATGGCGTTCCTGTTTCTGATTGTCTGTGGT
genomic: TCTCTTAAGAAAGCTTCGCAGCTGGTGAAAGAGATAGGAAGACAGgtttgtatga ... cttgtcacagGTAGCTACAGATAAATGCATAATGGCGTTCCTGTTTCTGATTGTCTGTGGT
EST: gi|125321153|gb|EL335238.1|EL335238
EST:     AGTTCTCTCTTAAGAAAGCTTCGCAGCTGGTGAA-GAGATAGGAAGACAG                         GTAGCTACAGATAAA
genomic: AGTTCTCTCTTAAGAAAGCTTCGCAGCTGGTGAAAGAGATAGGAAGACAGgtttgtatga ... cttgtcacagGTAGCTACAGATAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgtctaactattatcaccgtttcctttcaacctcaattctttcttgtcacagGTAGCTACAGATAAATGCATAATGGCGTTCCTGTTTCTGATTGTCTGTGGTGTTATAGCTATAATCATTGTGAAG
    gtctaac  putative branch site (score: 2)
                                 cctcaattctttctt  putative PPT
       taactattat  TA-rich tract