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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgactcacactccttccaacttcttatcattgtaccattcttttcatctatagGACTCGTTACTTCTCGGCTCCTTGCAAGGGGCACAATCCACTACAAGGCAGAGCCTACTATCAACTGTTGGAATGCCTCGGG

Basic information

species Selaginella moellendorffii
transcript EFJ37404
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|169077607|gb|FE484869.1|FE484869
EST:     GACTCGGTGGATATGTATGGTTTTACGGTGGATCCAGGCTACACGGAATG                         GACTCGTTACTTCTCGGCTCCTCGCAAGGGACACAATCCACTACAAGGCAG
genomic: GACTCGGTGGATATGTATGGTTTTACGGTGGATCCAGGCTACACGGAATGgtattgactc ... tcatctatagGACTCGTTACTTCTCGGCTCCTTGCAAGGGGCACAATCCACTACAAGGCAG
EST: gi|169095779|gb|FE499705.1|FE499705
EST:     GACTCGGTGGATATGTATGGTTTTACGGTGGATCCAGGCTACACGGAATG                         GACTCGTTACTTCTCGGCTCCTCGCAAGGGACACAATCCACTACAAGGCAG
genomic: GACTCGGTGGATATGTATGGTTTTACGGTGGATCCAGGCTACACGGAATGgtattgactc ... tcatctatagGACTCGTTACTTCTCGGCTCCTTGCAAGGGGCACAATCCACTACAAGGCAG

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

GAGCGAAAGGGACAGGCATTAAGTCTTTGGAGCTCGCCTTGTCAATGTGTGACTCGGTGGATATGTATGGTTTTACGGTGGATCCAGGCTACACGGAATGgtattgactc ... tcatctatagGACTCGTTACTTCTCGGCTCCTTGCAAGGGGCACAATCCACTACAAGGCAGAGCCTACTATCAACTGTTGGAATGCCTCGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgactcacactccttccaacttcttatcattgtaccattcttttcatctatagGACTCGTTACTTCTCGGCTCCTTGCAAGGGGCACAATCCACTACAAGGCAGAGCCTACTATCAACTGTTGGAATGCCTCGGG
   gactcac  putative branch site (score: 24)
                                    ccattcttttcatct  putative PPT
                         ttatcatt  TA-rich tract