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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactagttttttttctctcttagacgcatagttttgatccttgagctcttcaaaaatcaatccagGTGAATAGTTTTGAGACGGAGCTCGCTGTTCCGGCTCTGGCGGCGAGCGAAGGCGGTCCTCCAAGGTGCCGTGCAGTTTTTATTCGTGCTCCTGCCATCG

Basic information

species Selaginella moellendorffii
transcript EFJ33956
intron # 4
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|169065636|gb|FE474850.1|FE474850
EST:     TTCTGGGCGGATTAGACTGTACAGTTCATAGGAATTTCTTTGGAAGCCAG                         GTGAATAGTTTTGAGACGGAGCTCGCTGTTCCGGCTCTGGCGGCGAGCGAA
genomic: TTCTGGGCGGACTAGACTGTACAGTTCATAGGAATTTCTTTGGAAGCCAGgtactagttt ... atcaatccagGTGAATAGTTTTGAGACGGAGCTCGCTGTTCCGGCTCTGGCGGCGAGCGAA
EST: gi|169024035|gb|FE435143.1|FE435143
EST:     TTCTGGGCGGACTAGACTGTACAGTTCATAGGAATTTCTTTGGAAGCCAG                         GTGAATAGTTTTGAGACGGAGCTCGCTGTTCCGGCTCTGGCGGCGAGCGAA
genomic: TTCTGGGCGGACTAGACTGTACAGTTCATAGGAATTTCTTTGGAAGCCAGgtactagttt ... atcaatccagGTGAATAGTTTTGAGACGGAGCTCGCTGTTCCGGCTCTGGCGGCGAGCGAA
EST: gi|169024036|gb|FE435144.1|FE435144
EST:     TTCTGGGCGGACTAGACTGTACAGTTCATAGGAATTTCTTTGGAAGCCAG                         GTGAATAGTTTTGAGACGGAGCTCGCTGTTCCGGCTCTGGCGGCGAGCGAA
genomic: TTCTGGGCGGACTAGACTGTACAGTTCATAGGAATTTCTTTGGAAGCCAGgtactagttt ... atcaatccagGTGAATAGTTTTGAGACGGAGCTCGCTGTTCCGGCTCTGGCGGCGAGCGAA
EST: gi|169063023|gb|FE471129.1|FE471129
EST:     TTCTGGGCGGACTAGACTGTACAGTTCATAGGAATTTCTTTGGAAGCCAG                         GTGAATAGTTTTGAGACGGAGCTCGCTGTTCCGGCTCTGGCGGCGAGCGAA
genomic: TTCTGGGCGGACTAGACTGTACAGTTCATAGGAATTTCTTTGGAAGCCAGgtactagttt ... atcaatccagGTGAATAGTTTTGAGACGGAGCTCGCTGTTCCGGCTCTGGCGGCGAGCGAA
EST: gi|169065635|gb|FE474849.1|FE474849
EST:     TTCTGGGCGGATTAGACTGTACAGTTCATAGGAATTTCTTTGGAAGCCAG                         GTGAATAGTTTTGAGACGGAGCTCGCTGTTCCGGCTCTGGCGGCGAGCGAA
genomic: TTCTGGGCGGACTAGACTGTACAGTTCATAGGAATTTCTTTGGAAGCCAGgtactagttt ... atcaatccagGTGAATAGTTTTGAGACGGAGCTCGCTGTTCCGGCTCTGGCGGCGAGCGAA

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), 35 (downstream exon)
Score: 10

GGCTAAAGGATGGAGGACAAGAGCTTCTGGGCGGACTAGACTGTACAGTTCATAGGAATTTCTTTGGAAGCCAGgtactagttt ... atcaatccagGTGAATAGTTTTGAGACGGAGCTCGCTGTTCCGGCTCTGGCGGCGAGCGAAGGCGGTCCTCCAAGGTGCCGTGCAGTTTTTATTCGTGCTCCTGCCATCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctctcttagacgcatagttttgatccttgagctcttcaaaaatcaatccagGTGAATAGTTTTGAGACGGAGCTCGCTGTTCCGGCTCTGGCGGCGAGCGAAGGCGGTCCTCCAAGGTGCCGTGCAGTTTTTATTCGTGCTCCTGCCATCG
                     ttttgat  putative branch site (score: 10)
                                         aaaaatcaat  TA-rich tract