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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatccatctaaccggtttcaacattatttggctattttccaaggtcattcattaccttctcttgattgctgattggccatatcaacttatttcagATGGGGAGCTACTCTAATGAACTCTTTCCTCTTCAATGTCGGCCTCATTCTTCTTTGTTCAATCAG

Basic information

species Arabidopsis thaliana
transcript AT3G08930.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G012284_T01 (Zea mays), 3'ss of exon 8
gtaatccatctaaccggtttcaacattatttggctattttccaaggtcattcattaccttctcttgattgctgattggccatatcaacttatttcagATGGGGAGCTACTCTAATGAACTCTTTCCTCTTCAATGTCGGCCTCATTCTTCTTTGTTCAATCAG
          ||||| | |   || |      ||||||||    |  || |  |||  || ||   ||  || |    | | ||||| || ||||||||||||||  ||| |||||||||| ||||| || ||||| || ||||| || ||||| || |||||
---------gtaaccagctgatacctgggcatgctattttttctg--cagtt-ttattttttcaatatcactaacaaacaa-atcaatttgtttcagATGGGGAGGCACTTTAATGAACTCCTTCCTGTTTAATGTTGGGCTCATACTACTTTGCTCCATCAG

upper sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA18G43020.1 (Glycine max), 3'ss of exon 10
-----gtaatccatctaaccggtttcaacattatttgg-ctattttccaaggtcattcattaccttctcttgattgctgattggccatatcaacttatttcagATGGGGAGCTACTCTAATGAACTCTTTCCTCTTCAATGTCGGCCTCATTCTTCTTTGTTCAATCAG
       |||    || || | ||| | ||| || ||  | |||||      |     || ||||| | |   ||      ||  | ||||    | |  ||| |||||||| ||||| ||||||||||| || || ||||| ||||| |||||||||||||| || ||
gtaataaaattgtgctgacagattt-atcatcatgtgctccattttttgtaatttggtat-accttttgtatcttatgatgtgatcttatc----tctggcagGTGGGGAGCAACTCTCATGAACTCTTTTCTGTTTAATGTGGGCCTTATTCTTCTTTGTTCCATTAG

upper sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 10
-------------gtaatccat--ctaaccggtttcaacattatttggctattttccaaggtcattcattaccttctcttgattgctgattggccatatcaacttatttcagATGGGGAGCTACTCTAATGAACTCTTTCCTCTTCAATGTCGGCCTCATTCTTCTTTGTTCAATCAG
             | |||| ||  ||| |     |  | |||  ||    |||| | | |||||   | | | |||| |||||| || | |      |   |  |||  ||| |||||||| || || ||||||||||| || |||||||| || || |||||||||||||| || ||
gtaattaaactttgcaatctatgactatctatcattcatattgctttttaatttgcaatggtcacatactgc-ttctattgattactcactatgtgaacttatctatggcagGTGGGGAGCGACACTCATGAACTCTTTTCTGTTCAATGTGGGGCTTATTCTTCTTTGTTCCATTAG

upper sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA07G18160.1 (Glycine max), 3'ss of exon 10
-----gtaatccatctaaccggtttcaacattatttggctattttccaaggtcattcattaccttctcttgattgctgattggccatatcaacttatttcagATGGGGAGCTACTCTAATGAACTCTTTCCTCTTCAATGTCGGCCTCATTCTTCTTTGTTCAATCAG
       |||    || || | |||     || | |  | |||||     ||   | ||  |||| | |   ||      ||  ||||||    | |  ||| |||||||  ||||| ||||||||||| || || ||||| ||||| |||||||||||||| || ||
gtaataaaattgtgctgacagatttatcatttttctctccatttttggtagtttgttatc-ccttttgtatcttataatgtgatcatatc----tctggcagGTGGGGAGGAACTCTCATGAACTCTTTTCTGTTTAATGTGGGCCTTATTCTTCTTTGTTCCATTAG

upper sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA01G30400.1 (Glycine max), 3'ss of exon 10
-------------gtaatccat--ctaaccggtttcaacattatttggctattttccaaggtcattcattaccttctcttgattgctgattggccatatcaacttattt----cagATGGGGAGCTACTCTAATGAACTCTTTCCTCTTCAATGTCGGCCTCATTCTTCTTTGTTCAATCAG
             | |||| ||  ||| |     |  | |||  ||    || | |   |||||   | | | |||| |||||| || | |  | || | ||||||| |    ||| |||||||| || || ||||||||||| || |||||||| || || |||||||||||||| || ||
gtaattaaactttgcaatctatgactatctatcattcatattgctttttaatctgcagtggtcacatactgc-ttctattgattact-actcactatgtgaacttatctatggcagGTGGGGAGCGACGCTCATGAACTCTTTTCTGTTCAATGTGGGGCTTATTCTTCTTTGTTCCATTAG

upper sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA16G19230.1 (Glycine max), 3'ss of exon 9
gtaatccatcta-accggtttcaacattatttggctattt-tccaaggtcattcattaccttctcttgattgctgattggccatatcaacttatttcagATGGGGAGCTACTCTAATGAACTCTTTCCTCTTCAATGTCGGCCTCATTCTTCTTTGTTCAATCAG
|||||  |  |   | |        || |||| |||||   |    |||  ||  ||| |   | |  ||     | ||   || | | ||  |  ||| |||||||  ||||| ||||||||||| || || ||||| ||||| |||||||||||||| || ||
gtaataaaattgtgctgacagatttatcattttgctatccatttttggtagtttgttatcccttttgtatcttataatg-tgatcttatctc-tggcagGTGGGGAGGAACTCTCATGAACTCTTTTCTGTTTAATGTGGGCCTTATTCTTCTTTGTTCCATTAG

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|125285159|gb|EL299244.1|EL299244
EST:     TTACCATTCATCCAATGAA                         ATGGGGAGCTACTCTAATGAACTCTTTCCTCTTCAATGTCGGCCTCATTCT
genomic: TTACCATTCATCCAATGAAgtaatccatc ... cttatttcagATGGGGAGCTACTCTAATGAACTCTTTCCTCTTCAATGTCGGCCTCATTCT
EST: gi|163998289|gb|ES019319.1|ES019319
EST:     GAAGCTGGTCTTCATTACCATTCATCCAATGAA                         ATGGGGAGCTACTCTAATGAACTCTTTCCTCTTCAATGTCGGGCTCATTCT
genomic: GAAGCTGGTCTTCATTACCATTCATCCAATGAAgtaatccatc ... cttatttcagATGGGGAGCTACTCTAATGAACTCTTTCCTCTTCAATGTCGGCCTCATTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggtcattcattaccttctcttgattgctgattggccatatcaacttatttcagATGGGGAGCTACTCTAATGAACTCTTTCCTCTTCAATGTCGGCCTCATTCTTCTTTGTTCAATCAG
                          tgctgat  putative branch site (score: 3)
                                             cttatttc  putative PPT
                                      atatcaacttattt  TA-rich tract