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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactcttctaactccatgaatccagaacaattggttgccatgtcagctcataagccaaaggaccaaactctcacaaattcttcctgtctgcagGATTCCAAGAGCTCTTGGCTGATTTGGTTGAGGCCGCTATTGCTCATTGCCAATTGATTGTTGTTTCCAA

Basic information

species Arabidopsis thaliana
transcript AT4G16760.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G16760.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA11G03800.1 (Glycine max), 3'ss of exon 11
------gtactcttctaactccatg--aatccagaacaattggttgccatgtcagctcataagccaaaggaccaaactctcacaa-attcttcctgtctgcagGATTCCAAGAGCTCTTGGCTGATTTGGTTGAGGCCGCTATTGCTCATTGCCAATTGATTGTTGTTTCCAA
        | || | |||||  |||   ||  |  |   |   |||   ||| |  |  |  |  |        || | |   ||     || ||| | ||||| || ||||| ||    |||||||| ||||| |||||  ||||||||||||| || ||||||||||||||
tgtaaaaaattcatataactgaatgttgatttattattgtaatttg---tgtaacatggttggatattattttgaaatttgctaatggcttttctggcagcagGTTTTCAAGAACTAGCTGCTGATTTAGTTGATGCCGCGGTTGCTCATTGCCAGTTAATTGTTGTTTCCAA

upper sequence: AT4G16760.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA05G04940.1 (Glycine max), 3'ss of exon 11
---gtactcttctaactccat--gaatccagaacaattggttgccatgtcagc-tcataagccaaaggaccaaactctcacaaattcttcctgtctgcagGATTCCAAGAGCTCTTGGCTGATTTGGTTGAGGCCGCTATTGCTCATTGCCAATTGATTGTTGTTTCCAA
   ||  |   |  |  | ||   | |   |    | ||  |   |||      | || ||  |      || |    |  |   | ||   |    |||| |||||||| ||||  |  ||| | |||||||| ||| ||||||||||||| || ||||||||||||||
gtagtggttaccctaaccgattcaacttttgtttgagtgcatattatgatgttgtaattagatatgatctcataaatgctgatggttttttggatgacagGTTTCCAAGAACTCTCAGTCGATCTAGTTGAGGCAGCTGTTGCTCATTGCCAGTTAATTGTTGTTTCCAA

upper sequence: AT4G16760.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv00s0389g00020.t01 (Vitis vinifera), 3'ss of exon 9
------gtactcttctaactccatgaatccagaacaattggttgccatgtcagctcataagccaaaggac-caaactctcacaaattcttcctgtctg--cagGATTCCAAGAGCTCTTGGCTGATTTGGTTGAGGCCGCTATTGCTCATTGCCAATTGATTGTTGTTTCCAA
      | |   |  |||   | |   |  |       |||||    |||    ||  | || | | |      | ||  |  | |   | || | ||  |||| ||    || || |  |||||||| || ||||| ||  |||| ||||||||||||||||||||||||||
ctatgtggaggttggtaatggcttctctttaactgttctggttcaagtgtt---tctcatgctatatgttatgtattccaatcattgtcttctctttgttcagGCTTTGCTGAACTATCAGCTGATTTAGTGGAGGCGGCAGTTGCACATTGCCAATTGATTGTTGTTTCCAA

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|116448278|gb|EG490870.1|EG490870
EST:     GTTTGAGAATCAGGAACAAG                         GATTCCAAGAGCTCTTGGCTGATTTGGTTGAGGCCGCTATTGCTCATTGCC
genomic: GTTTGAGAATCAGGAACAAGgtactcttct ... ctgtctgcagGATTCCAAGAGCTCTTGGCTGATTTGGTTGAGGCCGCTATTGCTCATTGCC
EST: gi|116448274|gb|EG490866.1|EG490866
EST:     GGCTGTTACGTGTGCCAAAAATCTCAGCAAGTTTGAGAATCAGGAACAAG                         GATTCCAAGAGCTCTTGGCTGATTTGGTTGAGGCCGCTATTGCTCATTGCC
genomic: GGCTGTTACGTGTGCCAAAAATCTCAGCAAGTTTGAGAATCAGGAACAAGgtactcttct ... ctgtctgcagGATTCCAAGAGCTCTTGGCTGATTTGGTTGAGGCCGCTATTGCTCATTGCC
EST: gi|116441440|gb|EG484032.1|EG484032
EST:     GGCTGTTACGTGTGCCAAAAATCTCAGCAAGTTTGAGAATCAGGAACAAG                         GATTCCAAGAGCTCTTGGCTGATTTGGTTGAGGCCGCTATTGCTCATTGCC
genomic: GGCTGTTACGTGTGCCAAAAATCTCAGCAAGTTTGAGAATCAGGAACAAGgtactcttct ... ctgtctgcagGATTCCAAGAGCTCTTGGCTGATTTGGTTGAGGCCGCTATTGCTCATTGCC
EST: gi|116448277|gb|EG490869.1|EG490869
EST:     GGCTGTTACGTGTGCCAAAAATCTCAGCAAGTTTGAGAATCAGGAACAAG                         GATTCCAAGAGCTCTTGGCTGATTTGGTTGAGGCCGCTATTGCTCATTGCC
genomic: GGCTGTTACGTGTGCCAAAAATCTCAGCAAGTTTGAGAATCAGGAACAAGgtactcttct ... ctgtctgcagGATTCCAAGAGCTCTTGGCTGATTTGGTTGAGGCCGCTATTGCTCATTGCC
EST: gi|301501186|gb|HO206726.1|HO206726
EST:     GGCTGTTACGTGTGCCAAAAATCTCAGCAAGTTTGAGAATCAGGAACAAG                         GATTCCAAGAGCTCTTGGCTGATTTGGTTGAGGCCGCTATTGCTCATTGCC
genomic: GGCTGTTACGTGTGCCAAAAATCTCAGCAAGTTTGAGAATCAGGAACAAGgtactcttct ... ctgtctgcagGATTCCAAGAGCTCTTGGCTGATTTGGTTGAGGCCGCTATTGCTCATTGCC
EST: gi|116479261|gb|EG521853.1|EG521853
EST:     GGCTGTTACGTGTGCCAAAAATCTCAGCAAGTTTGAGAATCAGGAACAAG                         GATTCCAAGAGCTCTTGGCTGATTTGGTTGAGGCCGCTATTGCTCATTGCC
genomic: GGCTGTTACGTGTGCCAAAAATCTCAGCAAGTTTGAGAATCAGGAACAAGgtactcttct ... ctgtctgcagGATTCCAAGAGCTCTTGGCTGATTTGGTTGAGGCCGCTATTGCTCATTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgtcagctcataagccaaaggaccaaactctcacaaattcttcctgtctgcagGATTCCAAGAGCTCTTGGCTGATTTGGTTGAGGCCGCTATTGCTCATTGCCAATTGATTGTTGTTTCCAA
                             ctctcac  putative branch site (score: 3)
                                       ttcttcctgtctgc  putative PPT
                                    aaattctt  TA-rich tract