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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtactgtctacctcacatttcatggcactcacgcaaggtatcctagAGATGCGTTGTCGATCTTCCGGGTGGTCCACTGGAGATAGAGTGGAAAGAAGCAAACAACCACGTCTATATGACCGGACCTGCGAAACCAGTGTTCTCGG

Basic information

species Selaginella moellendorffii
transcript EFJ08289
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|169069071|gb|FE476723.1|FE476723
EST:     GAGCTTGCGCTGTCGTAGTAGCGGCAGTCTTGGAAGGACGAGCACAAAGG                         AGATGCGTTGTCGATCTTCCGGGTGGTCCACTGGAGATAGAGTGGAAAGAA
genomic: GAGCTTGCGCTGTCGTAGTAGCGGCAGTCTTGGAAGGACGAGCACAAAGGgtacgtactg ... ggtatcctagAGATGCGTTGTCGATCTTCCGGGTGGTCCACTGGAGATAGAGTGGAAAGAA
EST: gi|169110971|gb|FE512665.1|FE512665
EST:     GAGCTTGCGCTGTCGTAGTAGCGGCAGTCTTGGAAGGACGAGCACAAAGG                         AGATGCGTTGTCGATCTTCCGGGTGGTCCACTGGAGATAGAGTGGAAAGAA
genomic: GAGCTTGCGCTGTCGTAGTAGCGGCAGTCTTGGAAGGACGAGCACAAAGGgtacgtactg ... ggtatcctagAGATGCGTTGTCGATCTTCCGGGTGGTCCACTGGAGATAGAGTGGAAAGAA

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: 30 (upstream exon), 29 (downstream exon)
Score: 13

GTCCGACCTTGGCCTGTGGAACTGGAGCTTGCGCTGTCGTAGTAGCGGCAGTCTTGGAAGGACGAGCACAAAGGgtacgtactg ... ggtatcctagAGATGCGTTGTCGATCTTCCGGGTGGTCCACTGGAGATAGAGTGGAAAGAAGCAAACAACCACGTCTATATGACCGGACCTGCGAAACCAGTGTTCTCGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacgtactgtctacctcacatttcatggcactcacgcaaggtatcctagAGATGCGTTGTCGATCTTCCGGGTGGTCCACTGGAGATAGAGTGGAAAGAAGCAAACAACCACGTCTATATGACCGGACCTGCGAAACCAGTGTTCTCGG
                                  cactcac  putative branch site (score: 13)
                              atttcat  TA-rich tract