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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctctgttttgtctacaaaattcgttttgtgcacattttttttatcatattactattttaatctgacacaggcttttcttctttttcttccatctcgcagATTACTCAGGTTTATGGATTTTATGATGAATGTCTACGAAA

Basic information

species Arabidopsis thaliana
transcript AT2G42500.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G42500.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G36510.1 (Glycine max), 3'ss of exon 5
tctctgttttgtctacaaaattcgttttgtgcacattttttttatcatattac-tattttaatctgacacaggcttttcttctttttcttccatct--cgcagATTACTCAGGTTTATGGATTTTATGATGAATGTCTACGAAA
  | | | |   |    |     ||  | || | | || | |       | |  | || | |||||    ||    || |||||||     | | |   |||||||||||| || |||||||||||||||||||| ||  ||||
--tgtttctaaacatttatggctgtgatttgaagacttatatgggtggttgatgttttcttatctgttg-agctaattgttcttttatcatcttttaatgcagATTACTCAAGTATATGGATTTTATGATGAATGCCTTAGAAA

upper sequence: AT2G42500.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G39170.1 (Glycine max), 3'ss of exon 5
-------------------------------------------------------------------------------------------tctctgt-tttgtctacaaaattcgt-tttgtgcacatttttt-ttatcatattactattttaat--ctgacacaggcttttcttctttttcttccatct--cgcagATTACTCAGGTTTATGGATTTTATGATGAATGTCTACGAAA
                                                                                            || ||| ||||| |   |||||  | ||| |  ||||||||   | | || | |  | ||  ||   ||    ||    || ||| |||     | | |   |||||||||||| || |||||||||||||||||||| ||  ||||
gtttgtgttttaactctttcagaactataaattactttctgaactgtagttatttatttgtgaatggcacataaattagctagtctgggaggctttgtatttgtatgataaattgttgtttctaaacatttttggctgtgatttgaagacttgtatgggtggttgagctaattgttcctttatcatcctttaatgcagATTACTCAAGTATATGGATTTTATGATGAATGCCTTAGAAA
















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|116476453|gb|EG519045.1|EG519045
EST:     GATATCCTCAGCGAATCACTATTCTTAGAGGAAACCATGAAAGTCGTCAG                         ATTACTCAGGTTTATGGATTTTATGATGAATGTCTACGAAA
genomic: GATATCCTCAGCGAATCACTATTCTTAGAGGAAACCATGAAAGTCGTCAGgtagactaat ... catctcgcagATTACTCAGGTTTATGGATTTTATGATGAATGTCTACGAAA
EST: gi|116427104|gb|EG469696.1|EG469696
EST:     GATATCCTCAGCGAATCACTATTCTTAGAGGAAACCATGAAAGTCGTCAG                         ATTACTCAGGTTTATGGATTTTATGATGAATGTCTACGAAA
genomic: GATATCCTCAGCGAATCACTATTCTTAGAGGAAACCATGAAAGTCGTCAGgtagactaat ... catctcgcagATTACTCAGGTTTATGGATTTTATGATGAATGTCTACGAAA
EST: gi|116476454|gb|EG519046.1|EG519046
EST:     GATATCCTCAGCGAATCACTATTCTTAGAGGAAACCATGAAAGTCGTCAG                         ATTACTCAGGTTTATGGATTTTATGATGAATGTCTACGAAA
genomic: GATATCCTCAGCGAATCACTATTCTTAGAGGAAACCATGAAAGTCGTCAGgtagactaat ... catctcgcagATTACTCAGGTTTATGGATTTTATGATGAATGTCTACGAAA
EST: gi|116427105|gb|EG469697.1|EG469697
EST:     GATATCCTCAGCGAATCACTATTCTTAGAGGAAACCATGAAAGTCGTCAG                         ATTACTCAGGTTTATGGATTTTATGATGAATGTCTACGAAA
genomic: GATATCCTCAGCGAATCACTATTCTTAGAGGAAACCATGAAAGTCGTCAGgtagactaat ... catctcgcagATTACTCAGGTTTATGGATTTTATGATGAATGTCTACGAAA
EST: gi|125191481|gb|EL206435.1|EL206435
EST:     GATATCCTCAGCGAATCACTATTCTTAGAGGAAACCATGAAAGTCGTCAG                         ATTACTCAGGTTTA
genomic: GATATCCTCAGCGAATCACTATTCTTAGAGGAAACCATGAAAGTCGTCAGgtagactaat ... catctcgcagATTACTCAGGTTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catattactattttaatctgacacaggcttttcttctttttcttccatctcgcagATTACTCAGGTTTATGGATTTTATGATGAATGTCTACGAAA
               atctgac  putative branch site (score: 3)
                           cttttcttctttttct  putative PPT
     tactattttaatct  TA-rich tract