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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaactaaaatccctttcgtcatcccttcaaacccttcatttcaagGTGGAGTGGCAAATACTTGGCCTAGGAGATCCAGCCAAACTCCCGCCATTTTCTTGTTTGAATTCAAAATAGTCGCGAATATTCATGAGGC

Basic information

species Selaginella moellendorffii
transcript EFJ26684
intron # 14
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|169049964|gb|FE458056.1|FE458056
EST:     ACCTACACTGCCAGGGAGCAAATTCAATTGCCTCTGGAAGGCGAGGAAAG                         GTGGAGTGGCAAATACTTGGCCTAGGAGATCCAGCCAAACTCCCGCCATTT
genomic: ACCTACACTGCCAGGGAGCAAATTCAATTGCCTCTGGAAGGCGAGGAAAGgtaaactaaa ... tcatttcaagGTGGAGTGGCAAATACTTGGCCTAGGAGATCCAGCCAAACTCCCGCCATTT
EST: gi|169038317|gb|FE445316.1|FE445316
EST:     ACCTACACTGCCAGGGAGCAAATTCAATTGCCTCTGGAAGGCGAGGAAAG                         GTGGAGTGGCAAATACTTGGCCTAGGAGATCCAGCCAAACTCCCGCCATTT
genomic: ACCTACACTGCCAGGGAGCAAATTCAATTGCCTCTGGAAGGCGAGGAAAGgtaaactaaa ... tcatttcaagGTGGAGTGGCAAATACTTGGCCTAGGAGATCCAGCCAAACTCCCGCCATTT

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: 5

CATCGACTCTTGCAGAAGTCACGGATGACATGGTAGAGATGATCTTGAACACCTACACTGCCAGGGAGCAAATTCAATTGCCTCTGGAAGGCGAGGAAAGgtaaactaaa ... tcatttcaagGTGGAGTGGCAAATACTTGGCCTAGGAGATCCAGCCAAACTCCCGCCATTTTCTTGTTTGAATTCAAAATAGTCGCGAATATTCATGAGGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaactaaaatccctttcgtcatcccttcaaacccttcatttcaagGTGGAGTGGCAAATACTTGGCCTAGGAGATCCAGCCAAACTCCCGCCATTTTCTTGTTTGAATTCAAAATAGTCGCGAATATTCATGAGGC
           aactaaa  putative branch site (score: 5)
                                         cccttcatttc  putative PPT
         taaactaaaat  TA-rich tract