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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcacccctaattcatgttggagtaaacaacactagaaggtaacaatctcactattttcttaattatatttcagGCCAGGACTATGGGGAAATGAAG

Basic information

species Arabidopsis thaliana
transcript AT1G06690.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G06690.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os07g04990.1 (Oryza sativa), 3'ss of exon 4
--------gtatgcac---ccctaattcatgttggagtaaacaacactagaaggtaacaatctca--ctattttcttaattatatttcagGCCAGGACTATGGGGAAATGAAG
        || ||| |   | || || |||  |    |    ||   | ||   |    ||||||  |  |||| ||  |    |||||||||||| ||||||||||||||||
gtcggcttgtctgctctttctctgatacatactttt-tctgtaaattttgagcattttgatctcagccgcttttgtttctctgttttcagGCCAGGGCTATGGGGAAATGAAG

upper sequence: AT1G06690.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv12s0028g01100.t01 (Vitis vinifera), 3'ss of exon 4
---------gtatgcaccccta-attcatgttggagtaaacaacactagaaggtaacaatctcactat--tttcttaattatatttcagGCCAGGACTATGGGGAAATGAAG
          ||||  ||  || | |    |     | |    |  |  |||  ||  | || |  |   | |||  |  |  ||||||||||||| |||||||||||||||
gtcagtgctttatgagcctttatactaccatctatctgagtttctgtcaaagaaaaatagctaatcaaagtgtctgtaccaattttcagGCCAGGAGTATGGGGAAATGAAG
















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|116456052|gb|EG498644.1|EG498644
EST:     TCCCTTTCCCGGCTTGAGCTTTCATCTGTTGATCTCTATCAACTGCATTG                         GCCAGGACTATGGGGAAATGAAG
genomic: TCCCTTTCCCGGCTTGAGCTTTCATCTGTTGATCTCTATCAACTGCATTGgtatgcaccc ... tatatttcagGCCAGGACTATGGGGAAATGAAG
EST: gi|116456053|gb|EG498645.1|EG498645
EST:     TCCCTTTCCCGGCTTGAGCTTTCATCTGTTGATCTCTATCAACTGCATTG                         GCCAGGACTATGGGGAAATGAAG
genomic: TCCCTTTCCCGGCTTGAGCTTTCATCTGTTGATCTCTATCAACTGCATTGgtatgcaccc ... tatatttcagGCCAGGACTATGGGGAAATGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggagtaaacaacactagaaggtaacaatctcactattttcttaattatatttcagGCCAGGACTATGGGGAAATGAAG
                                      tcttaat  putative branch site (score: 3)
                         aatctcactattttct  TA-rich tract