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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgctgttgcccttcaactctctttcttcaaaagcttgttaatctggtgctttctctgcagGGATATTCTAGAAATACAGCAATCAGAATGTAGAGCTCGAGCCCAAATACAACGTTTACAGGAGGCCTTGGATGAACACAGCCTTGAACTTCGCGTAAAG

Basic information

species Selaginella moellendorffii
transcript EFJ11831
intron # 12
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|169045078|gb|FE452794.1|FE452794
EST:     GAGTTGAAGCTTATACTAGATATGTATGAAAAGGAGTCAATAGAAAGCAG                         GGATATTCTAGAAATACAGCAATCAGAATGTAGAGCTCGAGCCCAAATACA
genomic: GAGTTGAAGCTTATACTAGATATGTATGAAAAGGAGTCAATAGAAAGCAGgtgtgctgtt ... ttctctgcagGGATATTCTAGAAATACAGCAATCAGAATGTAGAGCTCGAGCCCAAATACA
EST: gi|169115605|gb|FE517815.1|FE517815
EST:     GAGTTGAAGCTTATACTAGATATGTATGAAAAGGAGTCAATAGAAAGCAG                         GGATATTCTAGAAATACAGCAATCAGAATGTAGAGCTCGAGCCCAAATACA
genomic: GAGTTGAAGCTTATACTAGATATGTATGAAAAGGAGTCAATAGAAAGCAGgtgtgctgtt ... ttctctgcagGGATATTCTAGAAATACAGCAATCAGAATGTAGAGCTCGAGCCCAAATACA
EST: gi|169106191|gb|FE507957.1|FE507957
EST:     GAGTTGAAGCTTATACTAGATATGTATGAAAAGGAGTCAATAGAAAGCAG                         GGATATTCTAGAAATACAGCAAT
genomic: GAGTTGAAGCTTATACTAGATATGTATGAAAAGGAGTCAATAGAAAGCAGgtgtgctgtt ... ttctctgcagGGATATTCTAGAAATACAGCAAT
EST: gi|169031780|gb|FE440610.1|FE440610
EST:     GAGTTGAAGCTTATACTAGATATGTATGAAAAGGAGTCAATAGAAAGCAG                         GGATATTCTAGAAATACAGCAATCAGAATGTAGAGCTCGAGCCCAAATACA
genomic: GAGTTGAAGCTTATACTAGATATGTATGAAAAGGAGTCAATAGAAAGCAGgtgtgctgtt ... ttctctgcagGGATATTCTAGAAATACAGCAATCAGAATGTAGAGCTCGAGCCCAAATACA
EST: gi|169067313|gb|FE473898.1|FE473898
EST:     GAGTTGAAGCTTATACTAGATATGTATGAAAAGGAGTCAATAGAAAGCAG                         GGATATTCTAGAAATACAGCAATCAGAATGTAGAGCTCGAGCCCAAATACA
genomic: GAGTTGAAGCTTATACTAGATATGTATGAAAAGGAGTCAATAGAAAGCAGgtgtgctgtt ... ttctctgcagGGATATTCTAGAAATACAGCAATCAGAATGTAGAGCTCGAGCCCAAATACA

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), 26 (downstream exon)
Score: 21

ATTCGCGTTCTCAAAGAAAGCGAGCAGGAGTTGAAGCTTATACTAGATATGTATGAAAAGGAGTCAATAGAAAGCAGgtgtgctgtt ... ttctctgcagGGATATTCTAGAAATACAGCAATCAGAATGTAGAGCTCGAGCCCAAATACAACGTTTACAGGAGGCCTTGGATGAACACAGCCTTGAACTTCGCGTAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcccttcaactctctttcttcaaaagcttgttaatctggtgctttctctgcagGGATATTCTAGAAATACAGCAATCAGAATGTAGAGCTCGAGCCCAAATACAACGTTTACAGGAGGCCTTGGATGAACACAGCCTTGAACTTCGCGTAAAG
                              tgttaat  putative branch site (score: 21)
                                         tgctttctct  putative PPT
                             ttgttaat  TA-rich tract