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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtgtacgagtgactggctgtaaactggtttgaagcgctgtgggactttgttttgtagATCAAGATTCACTGAGACTTTCGGCGGTAGAAGGCTGTGCTGCGTTGGGCAAGCTACTTGAGCCTCAAGATTGCATAGCCAATATTCTTCCAGTTATTGT

Basic information

species Selaginella moellendorffii
transcript EFJ15458
intron # 2
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|169028897|gb|FE438596.1|FE438596
EST:     TCATCTGAAATCTGATATAATGTCGTTTTTCAAAGACCTCACACAAGATG                         ATCAAGATTCACTGAGACTTTCGGCGGTAGAAGGCTGTGCTGCGTTGGGCA
genomic: TCATCTGAAATCTGATATAATGTCGTTTTTCAAAGACCTCACACAAGATGgtaagtgtgt ... tgttttgtagATCAAGATTCACTGAGACTTTCGGCGGTAGAAGGCTGTGCTGCGTTGGGCA
EST: gi|169030962|gb|FE439829.1|FE439829
EST:     TCATCTGAAATCTGATATAATGTCGTTTTTCAAAGACCTCACACAAGATG                         ATCAAGATTCACTGAGACTTTCGGCGGTAGAAGGCTGTGCTGCGTTGGGCA
genomic: TCATCTGAAATCTGATATAATGTCGTTTTTCAAAGACCTCACACAAGATGgtaagtgtgt ... tgttttgtagATCAAGATTCACTGAGACTTTCGGCGGTAGAAGGCTGTGCTGCGTTGGGCA
EST: gi|169030963|gb|FE439830.1|FE439830
EST:     TCATCTGAAATCTGATATAATGTCGTTTTTCAAAGACCTCACACAAGATG                         ATCAAGATTCACTGAGACTTTCGGCGGTAGAAGGCTGTGCTGCGTTGGGCA
genomic: TCATCTGAAATCTGATATAATGTCGTTTTTCAAAGACCTCACACAAGATGgtaagtgtgt ... tgttttgtagATCAAGATTCACTGAGACTTTCGGCGGTAGAAGGCTGTGCTGCGTTGGGCA
EST: gi|169028896|gb|FE438595.1|FE438595
EST:     TCATCTGAAATCTGATATAATGTCGTTTTTCAAAGACCTCACACAAGATG                         ATCAAGATTCACTGAGACTTTCGGCGGTAGAAGGCTGTGCTGCGTTGGGCA
genomic: TCATCTGAAATCTGATATAATGTCGTTTTTCAAAGACCTCACACAAGATGgtaagtgtgt ... tgttttgtagATCAAGATTCACTGAGACTTTCGGCGGTAGAAGGCTGTGCTGCGTTGGGCA

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: 33 (upstream exon), 34 (downstream exon)
Score: 11

CGGTCGGCGGCTTCGAATCTGGCAAAGTTTGCAGCCACCGTGGAGCCGGCTCATCTGAAATCTGATATAATGTCGTTTTTCAAAGACCTCACACAAGATGgtaagtgtgt ... tgttttgtagATCAAGATTCACTGAGACTTTCGGCGGTAGAAGGCTGTGCTGCGTTGGGCAAGCTACTTGAGCCTCAAGATTGCATAGCCAATATTCTTCCAGTTATTGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacgagtgactggctgtaaactggtttgaagcgctgtgggactttgttttgtagATCAAGATTCACTGAGACTTTCGGCGGTAGAAGGCTGTGCTGCGTTGGGCAAGCTACTTGAGCCTCAAGATTGCATAGCCAATATTCTTCCAGTTATTGT
                                          ctttgtttt  CT-rich tract
                                           tttgtttt  TA-rich tract