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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgtttcttctcttttgttgtcatacaatgttctttaaaaatgcgggtttgcagCTGAAATATCATGAAACGGGTAGAGAAAAGGATTGCTTGCCTCAAGACGGGACCTGGAATATGATGAACAAG

Basic information

species Selaginella moellendorffii
transcript EFJ14095
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ19862 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 9
-------------------gtttgtgtttcttct---cttttgttgtcatacaatgttctttaa--aaatgcgg----gtttgcagCTGAAATATCATGAAACGGGTAGAGAAAAGGATTGCTTGCCTCAAGACGGGACCTGGAATATGATGAACAAG
                    ||| | | | |         | | | | | ||| ||| | | |    | | |       | |||||||||||||||||||||| || |  ||||||||||| |||||||||| |||    ||||||||||||||||| 
gtaatattcaccatcctaaatttatatatgtgaaagatgataggtattacacattgtgcctgatctgacttctattttatctgcagCTGAAATATCATGAAACTGGGAAGGAAAAGGATTGTTTGCCTCAAGTCGGTCAGTGGAATATGATGAACAAA
















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|169021774|gb|FE430421.1|FE430421
EST:     TCAGTGACAGACTGGCTCTCGTGGAAGCTAGAATACTGCCTGCCCCATGG                         CTGAAATATCATGAAACGGGTAGAGAAAAGGATTGCTTGCCTCAAGACGGG
genomic: TCAGTGACAGACTGGCTCTCGTGGAAGCTAGAATACTGCCTGCCCCATGGgtttgtgttt ... gggtttgcagCTGAAATATCATGAAACGGGTAGAGAAAAGGATTGCTTGCCTCAAGACGGG
EST: gi|169027234|gb|FE435092.1|FE435092
EST:     TCAGTGACAGACTGGCTCTCGTGGAAGCTAGAATACTGCCTGCCCCATGG                         CTGAAATATCATGAAACGGGTAGAGAAAAGGATTGCTTGCCTCAAGACGGG
genomic: TCAGTGACAGACTGGCTCTCGTGGAAGCTAGAATACTGCCTGCCCCATGGgtttgtgttt ... gggtttgcagCTGAAATATCATGAAACGGGTAGAGAAAAGGATTGCTTGCCTCAAGACGGG
EST: gi|169052413|gb|FE462247.1|FE462247
EST:     TCAGTGACAGACTGGCTCTCGTGGAAGCTAGAATACTGCCTGCCCCATGG                         CTGAAATATCATGAAACGGGTAGAGAAAAGGATTGCTTGCCTCAAGACGGG
genomic: TCAGTGACAGACTGGCTCTCGTGGAAGCTAGAATACTGCCTGCCCCATGGgtttgtgttt ... gggtttgcagCTGAAATATCATGAAACGGGTAGAGAAAAGGATTGCTTGCCTCAAGACGGG
EST: gi|169078634|gb|FE487066.1|FE487066
EST:     TCAGTGACAGACTGGCTCTCGTGGAAGCTAGAATACTGCCTGCCCCATGG                         CTGAAATATCATGAAACGGGTAGAGAAAAGGATTGCTTGCCTCAAGACGGG
genomic: TCAGTGACAGACTGGCTCTCGTGGAAGCTAGAATACTGCCTGCCCCATGGgtttgtgttt ... gggtttgcagCTGAAATATCATGAAACGGGTAGAGAAAAGGATTGCTTGCCTCAAGACGGG
EST: gi|169025754|gb|FE433664.1|FE433664
EST:     TCAGTGACAGACTGGCTCTCGTGGAAGCTAGAATACTGCCTGCCCCATGG                         CTGAAATATCATGAAACGGGTAGAGAAAAGGATTGCTTGCCTCAAGACGGG
genomic: TCAGTGACAGACTGGCTCTCGTGGAAGCTAGAATACTGCCTGCCCCATGGgtttgtgttt ... gggtttgcagCTGAAATATCATGAAACGGGTAGAGAAAAGGATTGCTTGCCTCAAGACGGG
EST: gi|169094790|gb|FE492941.1|FE492941
EST:     TCAGTGACAGACTGGCTCTCGTGGAAGCTAGAATACTGCCTGCCCCATGG                         CTGAAATATCATGAAACGGGTAGAGAAAAGGATTGCTTGCCTCAAGACGGG
genomic: TCAGTGACAGACTGGCTCTCGTGGAAGCTAGAATACTGCCTGCCCCATGGgtttgtgttt ... gggtttgcagCTGAAATATCATGAAACGGGTAGAGAAAAGGATTGCTTGCCTCAAGACGGG
EST: gi|169077160|gb|FE484539.1|FE484539
EST:     TCAGTGACAGACTGGCTCTCGTGGAAGCTAGAATACTGCCTGCCCCATGG                         CTGAAATATCATGAAACGGGTAGAGAAAAGGATTGCTTGCCTCAAGACGGG
genomic: TCAGTGACAGACTGGCTCTCGTGGAAGCTAGAATACTGCCTGCCCCATGGgtttgtgttt ... gggtttgcagCTGAAATATCATGAAACGGGTAGAGAAAAGGATTGCTTGCCTCAAGACGGG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 35 (downstream exon)
Score: 44

TCATAATGCATATAATCAGGACCCATACGCCCAGGAGTTTGGGATACGTATCAGTGACAGACTGGCTCTCGTGGAAGCTAGAATACTGCCTGCCCCATGGgtttgtgttt ... gggtttgcagCTGAAATATCATGAAACGGGTAGAGAAAAGGATTGCTTGCCTCAAGACGGGACCTGGAATATGATGAACAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtttcttctcttttgttgtcatacaatgttctttaaaaatgcgggtttgcagCTGAAATATCATGAAACGGGTAGAGAAAAGGATTGCTTGCCTCAAGACGGGACCTGGAATATGATGAACAAG
                           aatgttctttaaaaat  TA-rich tract