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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaaaaaataaaacaagaagtcgacgagtttcctcactggtcctggcacagCTCGGATACTTTTCTTTCGGGGGAAGTACGTGCATTTGCGTCTTCCGCGCG

Basic information

species Selaginella moellendorffii
transcript EFJ07241
intron # 18
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|169028803|gb|FE438034.1|FE438034
EST:     GCATTACGTTCACTAAAAAAGAAGGATCCGTCGTCAAGAAGGGCGACGAG                         CTCGGATACTTTTCTTTCGGGGGAAGTACGTGCATTTGCGTCTTCCGCGCG
genomic: GCATTACGTTCACTAAAAAAGAAGGATCCGTCGTCAAGAAGGGCGACGAGgtatgaaaaa ... cctggcacagCTCGGATACTTTTCTTTCGGGGGAAGTACGTGCATTTGCGTCTTCCGCGCG
EST: gi|169105315|gb|FE506391.1|FE506391
EST:     GCATTACGTTCACTAAAAAAGAAGGATCCGTCGTCAAGAAGGGCGACGAG                         CTCGGATACTTTTCTTTCGGGGGAAGTACGTGCATTTGCGTCTTCCGCGCG
genomic: GCATTACGTTCACTAAAAAAGAAGGATCCGTCGTCAAGAAGGGCGACGAGgtatgaaaaa ... cctggcacagCTCGGATACTTTTCTTTCGGGGGAAGTACGTGCATTTGCGTCTTCCGCGCG

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: 32 (upstream exon), 35 (downstream exon)
Score: 7

GTGGCATTCGTGGCAATCGGAGCAACAATGGTGGGCAGCATTACGTTCACTAAAAAAGAAGGATCCGTCGTCAAGAAGGGCGACGAGgtatgaaaaa ... cctggcacagCTCGGATACTTTTCTTTCGGGGGAAGTACGTGCATTTGCGTCTTCCGCGCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatgaaaaaataaaacaagaagtcgacgagtttcctcactggtcctggcacagCTCGGATACTTTTCTTTCGGGGGAAGTACGTGCATTTGCGTCTTCCGCGCG
                                  tcctcac  putative branch site (score: 7)
       aaaaaataaaacaaga  TA-rich tract