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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgcagttttcgtaggcatgcaacgaactaagttcatttttggctgattaacagGTCTGCAAGATTGTGGAAGGACAAAGGTATACTAAACGTCTCAACGAGCGTCAAGTGACAGCCCTTCTAAAAGTAACATGCCAACGGCCCAGGGAAAGAG

Basic information

species Selaginella moellendorffii
transcript EFJ14095
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|169021774|gb|FE430421.1|FE430421
EST:     CTTGTTTAC-AGTTGGAAATCAAGAAAGACCAAATTATCTGCCAATGGAG                         GTCTGCAAGATTGTGGAAGGACAAAGGTATACTAAACGTCTCAACGAGCGT
genomic: CTTGTTTACAAGTTGGAAATCAAGAAAGACCAAATTATCTGCCAATGGAGgtgtgcagtt ... tgattaacagGTCTGCAAGATTGTGGAAGGACAAAGGTATACTAAACGTCTCAACGAGCGT
EST: gi|169027234|gb|FE435092.1|FE435092
EST:     CTTGTTTGCAAGTTGGAAATCAAGAAAGACCAAATTATCTGCCAATGGAG                         GTCTGCAAGATTGTGGAAGGACAAAGGTATACTAAACGTCTCAACGAGCGT
genomic: CTTGTTTACAAGTTGGAAATCAAGAAAGACCAAATTATCTGCCAATGGAGgtgtgcagtt ... tgattaacagGTCTGCAAGATTGTGGAAGGACAAAGGTATACTAAACGTCTCAACGAGCGT
EST: gi|169052413|gb|FE462247.1|FE462247
EST:     CTTGTTTGCAAGTTGGAAATCAAGAAAGACCAAATTATCTGCCAATGGAG                         GTCTGCAAGATTGTGGAAGGACAAAGGTATACTAAACGTCTCAACGAGCGT
genomic: CTTGTTTACAAGTTGGAAATCAAGAAAGACCAAATTATCTGCCAATGGAGgtgtgcagtt ... tgattaacagGTCTGCAAGATTGTGGAAGGACAAAGGTATACTAAACGTCTCAACGAGCGT
EST: gi|169078634|gb|FE487066.1|FE487066
EST:     CTTGTTTGCAAGTTGGAAATCAAGAAAGACCAAATTATCTGCCAATGGAG                         GTCTGCAAGATTGTGGAAGGACAAAGGTATACTAAACGTCTCAACGAGCGT
genomic: CTTGTTTACAAGTTGGAAATCAAGAAAGACCAAATTATCTGCCAATGGAGgtgtgcagtt ... tgattaacagGTCTGCAAGATTGTGGAAGGACAAAGGTATACTAAACGTCTCAACGAGCGT
EST: gi|169025754|gb|FE433664.1|FE433664
EST:     GAAAGACCAAATTATCTGCCAATGGAG                         GTCTGCAAGATTGTGGAAGGACAAAGGTATACTAAACGTCTCAACGAGCGT
genomic: GAAAGACCAAATTATCTGCCAATGGAGgtgtgcagtt ... tgattaacagGTCTGCAAGATTGTGGAAGGACAAAGGTATACTAAACGTCTCAACGAGCGT
EST: gi|169094790|gb|FE492941.1|FE492941
EST:     CTTGTTTGCAAGTTGGAAATCAAGAAAGACCAAATTATCTGCCAATGGAG                         GTCTGCAAGATTGTGGAAGGACAAAGGTATACTAAACGTCTCAACGAGCGT
genomic: CTTGTTTACAAGTTGGAAATCAAGAAAGACCAAATTATCTGCCAATGGAGgtgtgcagtt ... tgattaacagGTCTGCAAGATTGTGGAAGGACAAAGGTATACTAAACGTCTCAACGAGCGT
EST: gi|169077160|gb|FE484539.1|FE484539
EST:     CTTGTTTGCAAGTTGGAAATCAAGAAAGACCAAATTATCTGCCAATGGAG                         GTCTGCAAGATTGTGGAAGGACAAAGGTATACTAAACGTCTCAACGAGCGT
genomic: CTTGTTTACAAGTTGGAAATCAAGAAAGACCAAATTATCTGCCAATGGAGgtgtgcagtt ... tgattaacagGTCTGCAAGATTGTGGAAGGACAAAGGTATACTAAACGTCTCAACGAGCGT

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: 31 (upstream exon), 35 (downstream exon)
Score: 13

GGAGTATTTCCGAGATACATATCACTACACTATACGAAGCCCATCTTTACCTTGTTTACAAGTTGGAAATCAAGAAAGACCAAATTATCTGCCAATGGAGgtgtgcagtt ... tgattaacagGTCTGCAAGATTGTGGAAGGACAAAGGTATACTAAACGTCTCAACGAGCGTCAAGTGACAGCCCTTCTAAAAGTAACATGCCAACGGCCCAGGGAAAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgcagttttcgtaggcatgcaacgaactaagttcatttttggctgattaacagGTCTGCAAGATTGTGGAAGGACAAAGGTATACTAAACGTCTCAACGAGCGTCAAGTGACAGCCCTTCTAAAAGTAACATGCCAACGGCCCAGGGAAAGAG
                                          ggctgat  putative branch site (score: 13)
                                 ttcattttt  TA-rich tract