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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttagtttttgtcaggctgttggtctgataaaatatttttgctgttccagGAAATTCGTAAGAGAGGAGTTAAAGTTGCCGTGGCTGGCATTCCAAAAACCATAGACAACGATATCGCG

Basic information

species Selaginella moellendorffii
transcript EFJ21599
intron # 6
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|169049154|gb|FE457142.1|FE457142
EST:     ACATTATCGGTGGAGATGGCACACAGAAAGGAGTGAATGCTATCTACGAA                         GAAATTCGTAAGAGAGGAGTTAAAGTTGCCGTGGCTGGCATTCCAAAAACC
genomic: ACATTATCGGTGGAGATGGCACACAGAAAGGAGTGAATGCTATCTACGAAgtgagtttag ... gctgttccagGAAATTCGTAAGAGAGGAGTTAAAGTTGCCGTGGCTGGCATTCCAAAAACC
EST: gi|70669058|gb|DN837635.1|DN837635
EST:     ACATTATCGGTGGAGATGGCACACAGAAAGGAGTGAATGCTATCTACGAA                         GAAATTCGTAAGAGAGGAGTTAAAGTTGCCGTGGCTGGCATTCCAAAAACC
genomic: ACATTATCGGTGGAGATGGCACACAGAAAGGAGTGAATGCTATCTACGAAgtgagtttag ... gctgttccagGAAATTCGTAAGAGAGGAGTTAAAGTTGCCGTGGCTGGCATTCCAAAAACC
EST: gi|169028988|gb|FE438128.1|FE438128
EST:     ACATTATCGGTGGAGATGGCACACAGAAAGGAGTGAATGCTATCTACGAA                         GAAAT-CGTAAGAGAGGAG
genomic: ACATTATCGGTGGAGATGGCACACAGAAAGGAGTGAATGCTATCTACGAAgtgagtttag ... gctgttccagGAAATTCGTAAGAGAGGAG

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: 42

GTTTACATTATCGGTGGAGATGGCACACAGAAAGGAGTGAATGCTATCTACGAAgtgagtttag ... gctgttccagGAAATTCGTAAGAGAGGAGTTAAAGTTGCCGTGGCTGGCATTCCAAAAACCATAGACAACGATATCGCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgagtttagtttttgtcaggctgttggtctgataaaatatttttgctgttccagGAAATTCGTAAGAGAGGAGTTAAAGTTGCCGTGGCTGGCATTCCAAAAACCATAGACAACGATATCGCG
                           gtctgat  putative branch site (score: 42)
                                        tttttgct  putative PPT
                            tctgataaaatatttt  TA-rich tract