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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatttataaagatctctcttcctcgattcttggatcgatccctttttttttgtttctttgatcttctctacagTGCACCGTGTGCTTCTTATCTCTTGAGAAAGCGGGCCCTTCACAACGACATGTCCAG

Basic information

species Selaginella moellendorffii
transcript EFJ37190
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|169109931|gb|FE511079.1|FE511079
EST:     CATTTTGCTGCTTTGCCGCCTTCTG                         TGCACCGTGTGCTTCTTATCTCTTGAGAAAGCGGGCCCTTCACAACGACAT
genomic: CATTTTGCTGCTTTGCCGCCTTCTGgtgagattta ... ttctctacagTGCACCGTGTGCTTCTTATCTCTTGAGAAAGCGGGCCCTTCACAACGACAT
EST: gi|169109930|gb|FE511078.1|FE511078
EST:     CATTTTGCTGCTTTGCCGCCTTCTG                         TGCACCGTGTGCTTCTTATCTCTTGAGAAAGCGGGCCCTTCACAACGACAT
genomic: CATTTTGCTGCTTTGCCGCCTTCTGgtgagattta ... ttctctacagTGCACCGTGTGCTTCTTATCTCTTGAGAAAGCGGGCCCTTCACAACGACAT
EST: gi|169048544|gb|FE454426.1|FE454426
EST:     CATTTTGCTGCTTTGCCGCCTTCTGATCTTCTCTACAG             
genomic: CATTTTGCTGCTTTGCCG----C----C-T-TCT---Ggtgagattta ..

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: 19 (upstream exon), 35 (downstream exon)
Score: 4

TTTGCTGCTTTGCCGCCTTCTGgtgagattta ... ttctctacagTGCACCGTGTGCTTCTTATCTCTTGAGAAAGCGGGCCCTTCACAACGACATGTCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctcgattcttggatcgatccctttttttttgtttctttgatcttctctacagTGCACCGTGTGCTTCTTATCTCTTGAGAAAGCGGGCCCTTCACAACGACATGTCCAG
                                     ctttgat  putative branch site (score: 4)
                tcgatccctttttttt  CT-rich tract
                        tttttttttgtttctt  TA-rich tract