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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttctagcttggaagtttgtcttgcttccagcggactctaacaggacaagtttctatcattctagCTTGCAGAAGACTTGGACGCATTGCCAATATGGGTATTCAACAATG

Basic information

species Selaginella moellendorffii
transcript EFJ11809
intron # 7
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|169054491|gb|FE462159.1|FE462159
EST:     TGTGGGGGTACTGGTCCGACGATGGAATCGGCTACTTTGAGTTCCTCCAA                         CTTGCAGAAGACTTGGACGCATTGCCAATATGGGTATTCAACAATG
genomic: TGTGGGGGTACTGGTCCGACGATGGAATCGGCTACTTTGAGTTCCTCCAAgtaagttttc ... atcattctagCTTGCAGAAGACTTGGACGCATTGCCAATATGGGTATTCAACAATG
EST: gi|169029632|gb|FE437303.1|FE437303
EST:     TGTGGGGGTACTGGTCCGACGATGGAATCGGCTACTTTGAGTTCCTCCAA                         CTTGCAGAAGACTTGGACGCATTGCCAATATGGGTATTCAACAATG
genomic: TGTGGGGGTACTGGTCCGACGATGGAATCGGCTACTTTGAGTTCCTCCAAgtaagttttc ... atcattctagCTTGCAGAAGACTTGGACGCATTGCCAATATGGGTATTCAACAATG
EST: gi|169104839|gb|FE508710.1|FE508710
EST:     TGTGGGGGTACTGGTCCGACGATGGAATCGGCTACTTTGAGTTCCTCCAA                         CTTGCAGAAGACTTGGACGCA
genomic: TGTGGGGGTACTGGTCCGACGATGGAATCGGCTACTTTGAGTTCCTCCAAgtaagttttc ... atcattctagCTTGCAGAAGACTTGGACGCA

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: 40

GCGAGCCTCGGTTGGTCCATGGGAAGAAAGGCCCGGCCATCTCGGCGACGTGTGGGGGTACTGGTCCGACGATGGAATCGGCTACTTTGAGTTCCTCCAAgtaagttttc ... atcattctagCTTGCAGAAGACTTGGACGCATTGCCAATATGGGTATTCAACAATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaagtttgtcttgcttccagcggactctaacaggacaagtttctatcattctagCTTGCAGAAGACTTGGACGCATTGCCAATATGGGTATTCAACAATG
                         ctctaac  putative branch site (score: 40)
                                        tttctatc  putative PPT
                                        tttctat  TA-rich tract