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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagctctgatgaagcattctgttctttaaatttatttaattgcgatcacttttttgtagGACACGGATGAAATTATAAGTTCGTGGAATTTGCGTAAGTGCAGTGCGGCTGGACTGGACACTCTATCGACATTATTTGGCGACGATATTTTACCTCTCC

Basic information

species Selaginella moellendorffii
transcript EFJ11805
intron # 10
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|169098376|gb|FE497730.1|FE497730
EST:     CTAGATTTCATCAATCACGAGTTCATGGAAATGAAACTGATGATGATGAG                         GACACGGATGAAATTATAAGTTCGTGGAATTTGCGTAAGTGCAGTGCGGCT
genomic: CTAGATTTCATCAATCACGAGTTCATGGAAATGAAACTGATGATGATGAGgtagctctga ... ttttttgtagGACACGGATGAAATTATAAGTTCGTGGAATTTGCGTAAGTGCAGTGCGGCT
EST: gi|169050437|gb|FE459570.1|FE459570
EST:     CATCAATCACGAGTTCATGGAAATGAAACTGATGATGATGAG                         GACACGGATGAAATTATAAGTTCGTGGAATTTGCGCAAGTGCAGTGCCGCT
genomic: CATCAATCACGAGTTCATGGAAATGAAACTGATGATGATGAGgtagctctga ... ttttttgtagGACACGGATGAAATTATAAGTTCGTGGAATTTGCGTAAGTGCAGTGCGGCT
EST: gi|169077651|gb|FE484913.1|FE484913
EST:     GATTTCATCAATCACGAGTTCATGGAAATGAAACTGATGATGATGAG                         GACACGGATGAAATTATAAGTTCGTGGAATTTGCGCAAGTGCAGTGCCGCT
genomic: GATTTCATCAATCACGAGTTCATGGAAATGAAACTGATGATGATGAGgtagctctga ... ttttttgtagGACACGGATGAAATTATAAGTTCGTGGAATTTGCGTAAGTGCAGTGCGGCT
EST: gi|169019859|gb|FE426946.1|FE426946
EST:     CTAGATTTCATCAATCACGAGTTCATGGAAATGAAACTGATGATGATGAG                         GACACGGATGAAATTATAAGTTCGTGGAATTTGCGCAAGTGCAGTGCCGCT
genomic: CTAGATTTCATCAATCACGAGTTCATGGAAATGAAACTGATGATGATGAGgtagctctga ... ttttttgtagGACACGGATGAAATTATAAGTTCGTGGAATTTGCGTAAGTGCAGTGCGGCT
EST: gi|169081293|gb|FE489283.1|FE489283
EST:     CTAGATTTCATCAATCACGAGTTCATGGAAATGAAACTGATGATGATGAG                         GACACGGATGAAATTATAAGTTCGTGGAATTTGCGTAAGTGCAGTGCGGCT
genomic: CTAGATTTCATCAATCACGAGTTCATGGAAATGAAACTGATGATGATGAGgtagctctga ... ttttttgtagGACACGGATGAAATTATAAGTTCGTGGAATTTGCGTAAGTGCAGTGCGGCT
EST: gi|169080569|gb|FE490522.1|FE490522
EST:     CTAGATTTCATCAATCACGAGTTCATGGAAATGAAACTGATGATGATGAG                         GACACGGATGAAATTATAAGTTCGTGGAATTTGCGTAAGTGCAGTGCGGCT
genomic: CTAGATTTCATCAATCACGAGTTCATGGAAATGAAACTGATGATGATGAGgtagctctga ... ttttttgtagGACACGGATGAAATTATAAGTTCGTGGAATTTGCGTAAGTGCAGTGCGGCT
EST: gi|169072892|gb|FE480773.1|FE480773
EST:     CTAGATTTCATCAATCACGAGTTCATGGAAATGAAACTGATGATGATGAG                         GACACGGATGAAATTATAAGTTCGTGGAATTTGCGCAAGTGCAGTGCCGCT
genomic: CTAGATTTCATCAATCACGAGTTCATGGAAATGAAACTGATGATGATGAGgtagctctga ... ttttttgtagGACACGGATGAAATTATAAGTTCGTGGAATTTGCGTAAGTGCAGTGCGGCT

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: 19

AACTTAAAGCCTAGATTTCATCAATCACGAGTTCATGGAAATGAAACTGATGATGATGAGgtagctctga ... ttttttgtagGACACGGATGAAATTATAAGTTCGTGGAATTTGCGTAAGTGCAGTGCGGCTGGACTGGACACTCTATCGACATTATTTGGCGACGATATTTTACCTCTCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgatgaagcattctgttctttaaatttatttaattgcgatcacttttttgtagGACACGGATGAAATTATAAGTTCGTGGAATTTGCGTAAGTGCAGTGCGGCTGGACTGGACACTCTATCGACATTATTTGGCGACGATATTTTACCTCTCC
                             atttaat  putative branch site (score: 19)
                                         tcactttttt  putative PPT
           attctgttctttaaat  TA-rich tract