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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataaacaaacatagtaacacctactcgcagctttaagacaattgtttctttaatgtattgggaaaatccgccaacattatgtatttttttggtccagATATGCTGGTTACTCATCCTGCTTTAGAAAAGAAGCCGGTTCACATGGAAGAGACACCCTTGGTATTTTCCGTGTTCACCAGTTTGAGAAAATTGAACAG

Basic information

species Arabidopsis thaliana
transcript AT5G27470.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G27470.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G29600.1 (Glycine max), 3'ss of exon 6
gtataaacaaacatagtaacacctactcgcagctttaagacaattgtttctttaatgtattgggaaaatccgccaacattatgtatttttttggtccagATATGCTGGTTACTCATCCTGCTTTAGAAAAGAAGCCGGTTCACATGGAAGAGACACCCTTGGTATTTTCCGTGTTCACCAGTTTGAGAAAATTGAACAG
            |   |||    |  | |   |||    ||||| |    |  ||     ||       ||   ||| ||    || |  ||  | |||||||||||| || ||||| |||||| | |||||||| || || |||||  ||||||| || || || ||||| |||||||| ||||||||| | || || 
----------gtaatataatttttttttgtcacttgttaacaatggagcttggaagactatgttg----cctttaactttggaaatatgctttctgcagATATGCTGGATATTCATCATGCTTTCGTAAAGAAGCTGGATCTCATGGTCGAGACACTCTAGGAATATTCCGAGTTCACCAATTTGAGAAAGTGGAGCAA

upper sequence: AT5G27470.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G37700.1 (Glycine max), 3'ss of exon 6
gtataaacaaacatagtaacacctactcgcagctttaagacaattgtttctttaatgtattgggaaaatccgccaacattatgtatttttttggtccagATATGCTGGTTACTCATCCTGCTTTAGAAAAGAAGCCGGTTCACATGGAAGAGACACCCTTGGTATTTTCCGTGTTCACCAGTTTGAGAAAATTGAACAG
            |   | |    |  | |   | |    ||| |||   |||  | | | |  |     ||   ||| ||    || | |||  | |||||||||||| || ||||| |||||| | |||||||| || || |||||  ||||||| || || || ||||| || ||||| ||||||||| | || |||
----------gtaatatgatttttttttgtcacctgttaaca-ttggagcttggaag-actatgttg--ccattaactttggaaatatgttttctgcagATATGCTGGATATTCATCATGCTTTCGTAAAGAAGCTGGATCTCATGGTCGAGACACTCTAGGAATATTCCGAGTCCACCAATTTGAGAAAGTGGAGCAG

upper sequence: AT5G27470.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S13_192V6.2 (Physcomitrella patens), 3'ss of exon 4
-gtataaacaaacatagtaacacctactcgcagctttaagacaattgtttctttaatgtattgggaaaatccgccaacattatgtatttttttg-gtccagATATGCTGGTTACTCATCCTGCTTTAGAAAAGAAGCCGGTTCACATGGAAGAGACACCCTTGGTATTTTCCGTGTTCACCAGTTTGAGAAAATTGAACAG
    |      |        ||  ||||    | ||  | |  | | ||||| | || | ||    |   |  |    | |||||  ||| |   ||  || ||||||||||| ||| | ||||||||||| || || ||||| || |||||||| || ||||| || ||| | || || |||||||||||  | || |||
atcgtcggtcgagggctcctcatatacttagtggttgcacatgaatttttctcttat-tcttatagatgccttcttttaatatgttgtttgtcatgtttagGTATGCTGGTTATTCAACTTGCTTTAGAAAGGAGGCTGGTTCTCACGGAAGAGATACGCTTGGAATATTCAGAGTACATCAGTTTGAGAAGGTGGAGCAG

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|125301217|gb|EL315302.1|EL315302
EST:     TCCGACTGAGCTTCCCCTAAG                         ATATGCTGGTTACTCATCCTGCTTTAGAAAAGAAGCCGGTTCACATGGAAG
genomic: TCCGACTGAGCTTCCCCTAAGgtataaacaa ... tttggtccagATATGCTGGTTACTCATCCTGCTTTAGAAAAGAAGCCGGTTCACATGGAAG
EST: gi|125303581|gb|EL317666.1|EL317666
EST:     TCATCCGACTGAGCTTCCCCTAAG                         ATATGCTGGTTACTCATCCTGCTTTAGAAAAGAAGCCGGTTCACATGGAAG
genomic: TCATCCGACTGAGCTTCCCCTAAGgtataaacaa ... tttggtccagATATGCTGGTTACTCATCCTGCTTTAGAAAAGAAGCCGGTTCACATGGAAG
EST: gi|86059858|gb|DR355615.1|DR355615
EST:     TGTGCGTACCATATTGATGAATGGATTCATCCGACTGAGCTTCCCCTAAG                         ATATGCTGGTTACTCATCCTGCTTTAGAAAAGAAGCCGGTTCACATGGAAG
genomic: TGTGCGTACCATATTGATGAATGGATTCATCCGACTGAGCTTCCCCTAAGgtataaacaa ... tttggtccagATATGCTGGTTACTCATCCTGCTTTAGAAAAGAAGCCGGTTCACATGGAAG
EST: gi|125270023|gb|EL284108.1|EL284108
EST:     TGTGCGTACCATATTGATGAATGGATTCATCCGACTGAGCTTCCCCTAAG                         ATATGCTGGTTACTCATCCTGCTTTAGAAAAGAAGCCGGTTCACA
genomic: TGTGCGTACCATATTGATGAATGGATTCATCCGACTGAGCTTCCCCTAAGgtataaacaa ... tttggtccagATATGCTGGTTACTCATCCTGCTTTAGAAAAGAAGCCGGTTCACA
EST: gi|47831831|gb|CK121515.1|CK121515
EST:     TGTGCGTACCATATTGATGAATGGATTCATCCGACTGAGCTTCCCCTAAG                         ATATGCTGGTTACTCATCCTGCTTTAGAAAAGAAGCCGGTTCACATGGAAG
genomic: TGTGCGTACCATATTGATGAATGGATTCATCCGACTGAGCTTCCCCTAAGgtataaacaa ... tttggtccagATATGCTGGTTACTCATCCTGCTTTAGAAAAGAAGCCGGTTCACATGGAAG
EST: gi|124740221|gb|EH831383.1|EH831383
EST:     GACTGAGCTTCCCCTAAG                         ATATGCTGGTTACTCATCCTGCTTTAGAAAAGAAGCCGGTTCACATGGAAG
genomic: GACTGAGCTTCCCCTAAGgtataaacaa ... tttggtccagATATGCTGGTTACTCATCCTGCTTTAGAAAAGAAGCCGGTTCACATGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttctttaatgtattgggaaaatccgccaacattatgtatttttttggtccagATATGCTGGTTACTCATCCTGCTTTAGAAAAGAAGCCGGTTCACATGGAAGAGACACCCTTGGTATTTTCCGTGTTCACCAGTTTGAGAAAATTGAACAG
     ctttaat  putative branch site (score: 4)
                                       tattttttt  putative PPT
                              aacattatgtattttt  TA-rich tract