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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcttgaatttattggctaaccttctactccctcttgcactattaagggctgtattgtgttgtattgggtgtatgtttgacacattgtttgcttttgcagTTCTACGATCTTCTCAATATCTTTGAGCTTAATGGCCTCCCTTCGGAGGAGAACCCATACCTATTTAATGGCGACTTTGTGGACAGAGGCTCATTCTCCG

Basic information

species Arabidopsis thaliana
transcript AT2G42810.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G42810.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G42380.1 (Glycine max), 3'ss of exon 7
-atcttgaatttattggctaaccttctactcc-ctcttgcactattaagggctgtattgtgttgtattgggtgtatgtttg-acacattgtttg-cttttgcagTTCTACGATCTTCTCAATATCTTTGAGCTTAATGGCCTCCCTTCGGAGGAGAACCCATACCTATTTAATGGCGACTTTGTGGACAGAGGCTCATTCTCCG
  ||||  ||    | || | | || | ||   || ||| | | ||     || || | | |    |||    |   || | |    || |    ||| |||||| ||| |||||||| ||||| |||||||||||||| || ||||| || ||||| || || ||||||||||| ||||||||||| || || || || ||  
cttcttttatcctgttgc-atcattttgcttggcttttgaattttttt---ctttaatttttaaccttgcaatttcattagtatttgttttccatcttctgcagTACTATGATCTTCTGAATATTTTTGAGCTTAATGGGCTTCCTTCAGAAGAGAATCCGTATCTATTTAATGGTGACTTTGTGGATAGGGGATCTTTTTCAT

upper sequence: AT2G42810.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA18G12440.1 (Glycine max), 3'ss of exon 7
----atcttgaatttattggctaaccttctactccctcttgcactattaagggctgtattgtgttgtattgggtgtatgtt-tgacacattgtttg-cttttgcagTTCTACGATCTTCTCAATATCTTTGAGCTTAATGGCCTCCCTTCGGAGGAGAACCCATACCTATTTAATGGCGACTTTGTGGACAGAGGCTCATTCTCCG-
     || |  ||  ||||     | ||    |   | ||| | | |||    || || | | |    |||    |   || | |    || | || ||| |||||| ||| |||||||| ||||| |||||||||||||| || ||||| || ||||| || || ||||||||||| ||||||||||| || || || || ||   
gaaggtcctccatc-attgcagggcatttgtat---ttttgtatttttat---ctttaatttttaactttgcaaattcattattatttgttttctgtcttctgcagtACTATGATCTTCTGAATATTTTTGAGCTTAATGGGCTTCCTTCAGAAGAGAATCCGTATCTATTTAATGGTGACTTTGTGGATAGGGGATCCTTTTCATT

upper sequence: AT2G42810.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv12s0142g00720.t01 (Vitis vinifera), 3'ss of exon 1
atcttgaatttattggctaaccttctactccctcttgcactattaagggctgtattgtgttgtattgggtgtatgtttgacacattgtttgcttttgcagTTCTACGATCTTCTCAATATCTTTGAGCTTAATGGCCTCCCTTCGGAGGAGAACCCATACCTATTTAATGGCGACTTTGTGGACAGAGGCTCATTCTCCG------------------------------------------------
                                                                                    |  | |||||  ||||||||| |||||  | ||||| ||||| || ||||| || || || || |||||||| || ||||||||||| || |||||||| ||||| || || ||                                                  
------------------------------------------------------------------------------------tgatatgctt--gcagttctatgatctattaaatatttttgacctcaatggacttccctcagaagagaacccctatctatttaatggtgattttgtggatagAGGATCCTTTTCTTTAGAGGTCATCCTCACACTGTTTGCATTTAAGTGCATGTCTCCATCAG

upper sequence: AT2G42810.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S87_139V6.2 (Physcomitrella patens), 3'ss of exon 7
--------atcttgaatttattggctaaccttctactccctcttgcactattaagggctgtattgtgttgtattgggtgtatgtttgacacattgtttgcttt--tgcagTTCTACGATCTTCTCAATATCTTTGAGCTTAATGGCCTCCCTTCGGAGGAGAACCCATACCTATTTAATGGCGACTTTGTGGACAGAGGCTCATTCTCCG
        |  ||   | ||  ||| |  |||    |    | ||   || |    |   |  ||| |   ||  | | | |   |   |   || | |  ||   ||||| ||| ||  | || || || ||  |||||||||| ||||| ||||| ||||| || || || ||||||||||||||||| ||  | |||||||| || |
gtactataaaattctttgtaggggcaatgctttgtattttccgtgtgttacttcatgacttggtgtttgacat--gatttctaactaggaggatgatggaattgacgcagTACTATGACTTGCTGAACATTTTCAAGCTTAATGGTCTCCCCTCGGAAGAGAATCCTTATCTCTTTAATGGCGACTTTGTTGATCGTGGCTCATTTTCGG

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|124982622|gb|EL055414.1|EL055414
EST:     GTGTTCCACATGGCAAACATATCACTGTTTGCGGTGACGTTCATGGTCAG                         TTCTACGATCTTCTCAATA
genomic: GTGTTCCACATGGCAAACATATCACTGTTTGCGGTGACGTTCATGGTCAGgtatgctttg ... gcttttgcagTTCTACGATCTTCTCAATA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agggctgtattgtgttgtattgggtgtatgtttgacacattgtttgcttttgcagTTCTACGATCTTCTCAATATCTTTGAGCTTAATGGCCTCCCTTCGGAGGAGAACCCATACCTATTTAATGGCGACTTTGTGGACAGAGGCTCATTCTCCG
                             gtttgac  putative branch site (score: 4)
                                          tttgctttt  putative PPT
              ttgtatt  TA-rich tract