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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgagctttgattttccctgctttcgcttctcaccttttgttctctccagATCGTTCCAACTAGCACGGACCCGCTGCATCTTTGTATTAACGGGATGTCCTTCTCGAAACGTGCATCCAAGTGGGCAAATGCCGCTCTCGTCGTCAACG

Basic information

species Selaginella moellendorffii
transcript EFJ22253
intron # 8
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|169076380|gb|FE486008.1|FE486008
EST:     CCGACGAGCTCCGCTCGTGCTACTCTTTTTGCATGTGTCCCGGTGGCCAG                         ATCGTTCCAACTAGCACGGACCCGCTGCATCTTTGTATTAACGGGATGTCC
genomic: CCGACGAGCTCCGCTCGTGCTACTCTTTTTGCATGTGTCCCGGTGGCCAGgttgagcttt ... ttctctccagATCGTTCCAACTAGCACGGACCCGCTGCATCTTTGTATTAACGGGATGTCC
EST: gi|169054600|gb|FE462684.1|FE462684
EST:     CCGACGAGCTCCGCTCGTGCTACTCTTTTTGCATGTTTCCCGGTGGCCAG                         ATCGTTCCAACTAGCACGGACCCGCTGCATCTTTGTATTAACGGGATGTCC
genomic: CCGACGAGCTCCGCTCGTGCTACTCTTTTTGCATGTGTCCCGGTGGCCAGgttgagcttt ... ttctctccagATCGTTCCAACTAGCACGGACCCGCTGCATCTTTGTATTAACGGGATGTCC
EST: gi|169076379|gb|FE486007.1|FE486007
EST:     CCGACGAGCTCCGCTCGTGCTACTCTTTTTGCATGTGTCCCGGTGGCCAG                         ATCGTTCCAACTAGCACGGACCCGCTGCATCTTTGTATTAACGGGATGTCC
genomic: CCGACGAGCTCCGCTCGTGCTACTCTTTTTGCATGTGTCCCGGTGGCCAGgttgagcttt ... ttctctccagATCGTTCCAACTAGCACGGACCCGCTGCATCTTTGTATTAACGGGATGTCC

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: 23 (upstream exon), 31 (downstream exon)
Score: 4

CAAAGGAAAAGTCCCTGTGGCCGACTACAAGGTTGCTGCTTCGATAAATTCCGACGAGCTCCGCTCGTGCTACTCTTTTTGCATGTGTCCCGGTGGCCAGgttgagcttt ... ttctctccagATCGTTCCAACTAGCACGGACCCGCTGCATCTTTGTATTAACGGGATGTCCTTCTCGAAACGTGCATCCAAGTGGGCAAATGCCGCTCTCGTCGTCAACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgagctttgattttccctgctttcgcttctcaccttttgttctctccagATCGTTCCAACTAGCACGGACCCGCTGCATCTTTGTATTAACGGGATGTCCTTCTCGAAACGTGCATCCAAGTGGGCAAATGCCGCTCTCGTCGTCAACG
                                ttctcac  putative branch site (score: 4)
                ttttccctgctttcgc  CT-rich tract
           tttgatttt  TA-rich tract