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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccattcttcctttctttgaaaactctctaaccggcgccttttttccaaccagACGACTTGCCGCTGTGGG

Basic information

species Selaginella moellendorffii
transcript EFJ37593
intron # 3
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|169087209|gb|FE493117.1|FE493117
EST:     GGAATTCAGAGCGGCCATCGAGGAAACATACTGGTTCGAGTTCTTTATGG                         ACGACTTGCCGCTGTGGG
genomic: GGAATTCAGAGCGGCCATCGAGGAAACATACTGGTTCGAGTTCTTTATGGgtaagccatt ... ttccaaccagACGACTTGCCGCTGTGGG
EST: gi|169088032|gb|FE492595.1|FE492595
EST:     GGAATTCAGAGCGGCCATCGAGGAAACATACTGGTTCGAGTTCTTTATGG                         ACGACTTGCCGCTGTGGG
genomic: GGAATTCAGAGCGGCCATCGAGGAAACATACTGGTTCGAGTTCTTTATGGgtaagccatt ... ttccaaccagACGACTTGCCGCTGTGGG
EST: gi|169095561|gb|FE498837.1|FE498837
EST:     GGAATTCAGAGCGGCCATCGAGGAAACATACTGGTTCGAGTTCTTTATGG                         ACGACTTGCCGCTGTGGG
genomic: GGAATTCAGAGCGGCCATCGAGGAAACATACTGGTTCGAGTTCTTTATGGgtaagccatt ... ttccaaccagACGACTTGCCGCTGTGGG

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: 34 (upstream exon), 35 (downstream exon)
Score: 24

GTTGACAAGGTTACGATATGCAAGCTGGATCTGAATCAGAGAAAAGCCATGGAATTCAGAGCGGCCATCGAGGAAACATACTGGTTCGAGTTCTTTATGGgtaagccatt ... ttccaaccagACGACTTGCCGCTGTGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagccattcttcctttctttgaaaactctctaaccggcgccttttttccaaccagACGACTTGCCGCTGTGGG
                           ctctaac  putative branch site (score: 24)
                                       ccttttttccaacc  putative PPT
                 tttgaaaa  TA-rich tract