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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtttttcctctttttcctctcttttttctcattaaaggaaaaaaggctctgaccactttacttttcttctcgcagCTACTATACCGTGTTGTTTGGCGTCTCTCGGGCCTTAGGCGTTCTTGCACAG

Basic information

species Selaginella moellendorffii
transcript EFJ29959
intron # 17
splice site 3'
intron type U2

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|169033440|gb|FE441793.1|FE441793
EST:     GATGCGCATAGCGGAGTGCTTCTACAATACTTCGGGTTGACTGAAGAGAA                         CTACTATACCGTGTTGTTTGGCGTCTCTCGGGCCTTAGGCGTTCTTGCACA
genomic: GATGCGCATAGCGGAGTGCTTCTACAATACTTCGGGTTGACTGAAGAGAAgtacgttttt ... cttctcgcagCTACTATACCGTGTTGTTTGGCGTCTCTCGGGCCTTAGGCGTTCTTGCACA
EST: gi|169051940|gb|FE459044.1|FE459044
EST:     GATGCGCATAGCGGAGTACTTCTACAATACTTCGGGTTGACTGAAGAGAA                         CTACTACACCGTGTTGTTTGGCGTCTCTCGGGCCTTAGGCGTTCTCGCACA
genomic: GATGCGCATAGCGGAGTGCTTCTACAATACTTCGGGTTGACTGAAGAGAAgtacgttttt ... cttctcgcagCTACTATACCGTGTTGTTTGGCGTCTCTCGGGCCTTAGGCGTTCTTGCACA
EST: gi|169064916|gb|FE475612.1|FE475612
EST:     GATGCGCATAGCGGAGTGCTTCTACAATACTTCGGGTTGACTGAAGAGAA                         CTACTATACCGTGTTGTTTGGCGTCTCTCGGGCCTTAGGCGTTCTTGCACA
genomic: GATGCGCATAGCGGAGTGCTTCTACAATACTTCGGGTTGACTGAAGAGAAgtacgttttt ... cttctcgcagCTACTATACCGTGTTGTTTGGCGTCTCTCGGGCCTTAGGCGTTCTTGCACA
EST: gi|169065764|gb|FE476213.1|FE476213
EST:     GATGCGCATAGCGGAGTACTTCTACAATACTTCGGGTTGACTGAAGAGAA                         CTACTACACCGTGTTGTTTGGCGTCTCTCGGGCCTTAGGCGTTCTCGCACA
genomic: GATGCGCATAGCGGAGTGCTTCTACAATACTTCGGGTTGACTGAAGAGAAgtacgttttt ... cttctcgcagCTACTATACCGTGTTGTTTGGCGTCTCTCGGGCCTTAGGCGTTCTTGCACA

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), 34 (downstream exon)
Score: 13

GTGAAAAATCCTTGGCCTAACGTGGATGCGCATAGCGGAGTGCTTCTACAATACTTCGGGTTGACTGAAGAGAAgtacgttttt ... cttctcgcagCTACTATACCGTGTTGTTTGGCGTCTCTCGGGCCTTAGGCGTTCTTGCACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttttctcattaaaggaaaaaaggctctgaccactttacttttcttctcgcagCTACTATACCGTGTTGTTTGGCGTCTCTCGGGCCTTAGGCGTTCTTGCACAG
                          ctctgac  putative branch site (score: 13)
                                ccactttacttttctt  CT-rich tract
          attaaaggaaaaaa  TA-rich tract