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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtttatcctatttaattgggcctgataatatcttttgaactgttccagagtgttattttgatactgtcgttactaacataatctttgttaacatgaaagGTTGCAAGAGATGAAGACCTTAAGGAACAAATTGGGAAGGATATATATTTTGATCTTGTGGATCATGACAAAGTTCGCAGTTTCCGTATCCAGAAACAGA

Basic information

species Arabidopsis thaliana
transcript AT5G06600.2
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G06600.3 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 10
gtttgtttatcctatttaattgggcctgataatatcttttgaact-gttccagagtgttattttgatactgtcgttactaacataatctttgttaacatgaa---agGTTGCAAGAGATGAAGACCTTAAGGAACAAATTGGGAAGGATATATATTTTGATCTTGTGGATCATGACAAAGTTCGCAGTTTCCGTATCCAGAAACAGA
      | | |  || | | |     |      |||  || | ||   ||  ||   |   | |||  ||||   |  ||      | ||||   | ||  |   |||| ||  |||||||  |  | ||||| |||||||| ||||||||||||||||| || ||||| ||||| |||||||| || ||||| || ||||| ||| 
-----gtcagc--atctgactactattatgttcatcacttcatctcagtctggaacctctctgtgaatctgtttctcatagtgctctgtttggacaaatatatctagGTGGCTCGAGATGAGAATTTGAAGGAGCAAATTGGCAAGGATATATATTTTGACCTGGTGGACCATGAAAAAGTTCGTAGCTTCCGAATTCAGAAGCAGT

upper sequence: AT5G06600.3 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 14
gtttgtttatcctatttaattgggcctgataatatcttttgaactgttccagagtgttattttgatactgtcgttactaacataatctttgttaacatgaaagGTTGCAAGAGATGAAGACCTTAAGGAACAAATTGGGAAGGATATATATTTTGATCTTGTGGATCATGACAAAGTTCGCAGTTTCCGTATCCAGAAACAGA
               |  ||  |  |   |  ||  |||  ||  |||    | | | ||| |||   | |  |||  |     || |    |  |   |  ||||||  ||||||| ||  | |||||||| ||||| ||| |||||||||||||||| ||||| ||||| || |||||||| ||||| || ||||| ||  
------------gtctggataagaacctgttttagtttt--aatggttt--aaatctcattgtgaacttttttttataatggctatgtgcaatgtcccta--gGTTGCCCGAGATGAGGATTTGAAGGAACAGATTGGTAAGAATATATATTTTGATCTGGTGGACCATGAAAAGGTTCGCAGCTTCCGCATACAGAAGCAAC

upper sequence: AT5G06600.3 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 14
gtttgtttatcctatttaattgggcctgataatatcttttgaactgttccagagtgttattttgatactgtcgttactaacataatctttgttaacatgaaagGTTGCAAGAGATGAAGACCTTAAGGAACAAATTGGGAAGGATATATATTTTGATCTTGTGGATCATGACAAAGTTCGCAGTTTCCGTATCCAGAAACAGA
              ||||  |   | | ||   ||   ||  | | |   | | || |||  |  ||  || | | || || || |  ||  |    |   |||||||  |||||   ||  ||   || |||||||| ||  ||||||||||||||||||||||| |||||||  | |  ||  | ||    |  |||||  
-------------gtttacct---ctttatttgatacgttacattatctgaaaatgctatcattcta--gttgctcctcacttagtgcttcattttct---agGTTGCCCGAGATTCTGATTTTGCAGAGCAAATTGGAAAACATATATATTTTGATCTTGTGGATTATGACAACATCCAAAGCCTTCGGGCACCTAAACATT

upper sequence: AT5G06600.3 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 4
gtttgtttatcctatttaat-tgggcctgataatatcttttgaactgttccagagtgttattttgat-actgtcgttactaacataatctttgttaacatgaa---agGTTGCAAGAGATGAAGACCTTAAGGAACAAATTGGGAAGGATATATATTTTGATCTTGTGGATCATGACAAAGTTCGCAGTTTCCGTATCCAGAAACAGA
              | | || | |      | ||| |    |    || ||  |||  | | ||| | |||    ||  ||  |   | | ||| || |||||   || | ||  |||| || ||| | ||||| ||||| || ||| |||||||||||||||| ||||| ||||| ||||||| ||||||||| || ||||| ||| 
-------------gtctgatcttgtttcagtcataccagcagctaagtgcctaagttctctcttggtgactcctcttgatagaactttttgtgtaaaaatgaaaatagATCGCTCGAGACGAGGACTTAAAGGAGCAAATCGGTAAGAATATATATTTTGATCTGGTGGACCATGAAAAAGTTCACAGTTTCCGCATTCAGAAGCAGT

upper sequence: AT5G06600.3 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 14
gtttgtttatcctatttaattgggcctgataatatcttttgaactgttccagagtgttattttgat-actgtcgttactaacataatctttgttaaca-tgaa---agGTTGCAAGAGATGAAGACCTTAAGGAACAAATTGGGAAGGATATATATTTTGATCTTGTGGATCATGACAAAGTTCGCAGTTTCCGTATCCAGAAACAGA
                       | ||| |  | | |     |      |||     | | ||| | |||    ||  ||  |   | ||||| || | ||||   || ||||  ||||  | ||  | ||||| |||||||| ||  ||||||||||||| || ||||| ||||| |||||| |||| ||||| || ||||| ||| 
-----------------------gtctggtcttgtttcagtcataccagcagctaactctcttggtgactcctcttgatagaactttatttgtaaaaaatgaaaatagATTGCTCGAGACAAGGATTTAAAGGAGCAAATTGGTAAAAATATATATTTTGACCTGGTGGACCATGAAAAAGTTTGCAGCTTCCGCATTCAGAAGCAGT

upper sequence: AT5G06600.3 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 14
-------gtttgtttatcctatt-taattgggcctgataatatcttttgaactgttccagag-tgttattt-tgatactgtcgttactaacataatctttgttaacatgaaagGTTGCAAGAGATGAAGACCTTAAGGAACAAATTGGGAAGGATATATATTTTGATCTTGTGGATCATGACAAAGTTCGCAGTTTCCGTATCCAGAAACAGA
       || | | | || |    | |||     || |||||  | | ||| ||      |  ||||  |  ||    | |  | ||||| ||||||  |     |||  | ||||||| | ||||||||||||   || |||||||| |||||||||||||||||||||||||||||||||||||| |||||||| || || ||||||||| 
gtaagtcgtgtttctttcttgccctcattttttgtggtaataggtctagaaatgactggaacctgttgctcatggggatcttttaactaaaataatcaatcgatgcatcta-gGTTGCACGGGATGAAGACCTTGCAGAGCAAATTGGAAAGGATATATATTTTGATCTTGTGGATCATGACAAAGTCCGCAGTTTTCGCATTCAGAAACAGT

upper sequence: AT5G06600.3 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: PP1S42_181V6.1 (Physcomitrella patens), 3'ss of exon 14
gtttgtttatcctatttaattgggcctgataatatcttttgaactgttccagagtgttattttgatactgtcgttactaacataatctttgttaacatgaaagGTTGCAAGAGATGAAGACCTTAAGGAACAAATTGGGAAGGATATATATTTTGATCTTGTGGATCATGACAAAGTTCGCAGTTTCCGTATCCAGAAACAGA
            ||   ||||     |     |   ||||    |||   |    ||   ||       ||  ||| | |  |  | |  ||||   | | ||||||   | |||||||| ||  || | || ||||| ||||| ||  |||||||| | ||||||||||| |||||||||||||| || |||||||| || |
-----------gtaaacaattaactgtatggtttattttttggttgtaggaagccgtagcttcag---agtaattaattat-tcgtttacgtta-tgt-atagGTTGGGCGCGATGAAGATCTCCAGAACCAGATTGGAAAGGACATTCATTTTGATTTGGTGGATCATGAGAAAGTTCGCAGTTTTCGCATCCAGAAGCAAA

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|125036372|gb|EL108641.1|EL108641
EST:     CTCACTTATATACCATAATTAAG                         GTTGCAAGAGATGAAGACCTTAAGGAACAAATTGGGAAGGATATATATTTT
genomic: CTCACTTATATACCATAATTAAGgtttgtttat ... aacatgaaagGTTGCAAGAGATGAAGACCTTAAGGAACAAATTGGGAAGGATATATATTTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccagagtgttattttgatactgtcgttactaacataatctttgttaacatgaaagGTTGCAAGAGATGAAGACCTTAAGGAACAAATTGGGAAGGATATATATTTTGATCTTGTGGATCATGACAAAGTTCGCAGTTTCCGTATCCAGAAACAGA
                                 ataatctttgttaa  TA-rich tract