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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgtgtagcgttgtgctgacatttcctatctaactttcttctttgcagCTTGGACCAGTACGCGATAAGAAAGTTTGCTCAGAGCTTCGAAGTTGTGCCTCGAACTCTGGCTGAAAATGCGGGTCTAAACTCTACTGATGTGATCTCG

Basic information

species Selaginella moellendorffii
transcript EFJ21647
intron # 9
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|169071329|gb|FE479605.1|FE479605
EST:     GAGATTGAGTTAGCCAAACAGTTAAACGACATTGCTTCCAAGGAGACAGG                         CTTGGACCAGTACGCGATAAGAAAGTTTGCTCAGAGCTTCGAAGTTGTGCC
genomic: GAGATTGAGTTAGCCAAACAGTTAAACGACATTGCTTCCAAGGAGACAGGgtactgtgta ... ttctttgcagCTTGGACCAGTACGCGATAAGAAAGTTTGCTCAGAGCTTCGAAGTTGTGCC
EST: gi|169034405|gb|FE446376.1|FE446376
EST:     GAGATTGAGTTAGCCAAACAGTTAAACGACATTGCTTCCAAGGAGACAGG                         CTTGGACCAGTACGCGATAAGAAAGTTTGCTCAGAGCTTCGAAGTTGTGCC
genomic: GAGATTGAGTTAGCCAAACAGTTAAACGACATTGCTTCCAAGGAGACAGGgtactgtgta ... ttctttgcagCTTGGACCAGTACGCGATAAGAAAGTTTGCTCAGAGCTTCGAAGTTGTGCC
EST: gi|169036843|gb|FE443829.1|FE443829
EST:     GAGATTGAGTTAGCCAAACAGTTAAATGACATTGCTTCCAAGGAGACAGG                         CTTGGACCAGTACGCGATAAGAAAGTTTGCTCAGAGCTTCGAAGTTGTGCC
genomic: GAGATTGAGTTAGCCAAACAGTTAAACGACATTGCTTCCAAGGAGACAGGgtactgtgta ... ttctttgcagCTTGGACCAGTACGCGATAAGAAAGTTTGCTCAGAGCTTCGAAGTTGTGCC
EST: gi|169070714|gb|FE477313.1|FE477313
EST:     GAGATTGAGTTAGCCAAACAGTTAAATGACATTGCTTCCAAGGAGACAGG                         CTTGGACCAGTACGCGATAAGAAAGTTTGCTCAGAGCTTCGAAGTTGTGCC
genomic: GAGATTGAGTTAGCCAAACAGTTAAACGACATTGCTTCCAAGGAGACAGGgtactgtgta ... ttctttgcagCTTGGACCAGTACGCGATAAGAAAGTTTGCTCAGAGCTTCGAAGTTGTGCC
EST: gi|169072127|gb|FE479883.1|FE479883
EST:     GAGATTGAGTTAGCCAAACAGTTAAATGACATTGCTTCCAAGGAGACAGG                         CTTGGACCAGTACGCGATAAGAAAGTTTGCTCAGAGCTTCGAAGTTGTGCC
genomic: GAGATTGAGTTAGCCAAACAGTTAAACGACATTGCTTCCAAGGAGACAGGgtactgtgta ... ttctttgcagCTTGGACCAGTACGCGATAAGAAAGTTTGCTCAGAGCTTCGAAGTTGTGCC
EST: gi|169034975|gb|FE444836.1|FE444836
EST:     GAGATTGAGTTAGCCAAACAGTTAAACGACATTGCTTCCAAGGAGACAGG                         CTTGGACCAGTACGCGATAAGAAAGTTTGCTCAGAGCTTCGAAGTTGTGCC
genomic: GAGATTGAGTTAGCCAAACAGTTAAACGACATTGCTTCCAAGGAGACAGGgtactgtgta ... ttctttgcagCTTGGACCAGTACGCGATAAGAAAGTTTGCTCAGAGCTTCGAAGTTGTGCC

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: 13

GCTATGTGCAAGGATAGCCGTACAGTTCCTGGTGCGGGTGCAACGGAGATTGAGTTAGCCAAACAGTTAAACGACATTGCTTCCAAGGAGACAGGgtactgtgta ... ttctttgcagCTTGGACCAGTACGCGATAAGAAAGTTTGCTCAGAGCTTCGAAGTTGTGCCTCGAACTCTGGCTGAAAATGCGGGTCTAAACTCTACTGATGTGATCTCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtactgtgtagcgttgtgctgacatttcctatctaactttcttctttgcagCTTGGACCAGTACGCGATAAGAAAGTTTGCTCAGAGCTTCGAAGTTGTGCCTCGAACTCTGGCTGAAAATGCGGGTCTAAACTCTACTGATGTGATCTCG
                                  atctaac  putative branch site (score: 13)
                            tttcctatctaacttt  CT-rich tract
                                 tatctaa  TA-rich tract