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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtattttcttttacctcgcgtagtttctcacgagtgttcatcgcgctccagACGAAGGTGCGAAGTGGCTGAGGCGCTTGTGGAGAAAAACTTTGACTTGGCATTTCAAATAATCTATGACTTCGGACTTCCTG

Basic information

species Selaginella moellendorffii
transcript EFJ18188
intron # 31
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|169115116|gb|FE516689.1|FE516689
EST:     CCATGGAAACGCTCTCTTTTTGGAAATCCTAATGACAACGATACTTTCAA                         ACGAAGGTGCGAAGTGGCTGAGGCGCTTGTGGAGAAAAACTTTGACTTGGC
genomic: CCATGGAAACGCTCTCTTTTTGGAAATCCTAATGACAACGATACTTTCAAgtgcgtattt ... cgcgctccagACGAAGGTGCGAAGTGGCTGAGGCGCTTGTGGAGAAAAACTTTGACTTGGC
EST: gi|169083629|gb|FE494855.1|FE494855
EST:     CCATGGAAACGCTCTCTGTTTGGAAATCCTAATGACAACGATACTTTCAA                         ACGAAGGTGCGAAGTGGCTGAGGCGCTTGTGGAGAAAAACTTTGACTTGGC
genomic: CCATGGAAACGCTCTCTTTTTGGAAATCCTAATGACAACGATACTTTCAAgtgcgtattt ... cgcgctccagACGAAGGTGCGAAGTGGCTGAGGCGCTTGTGGAGAAAAACTTTGACTTGGC
EST: gi|169046677|gb|FE455419.1|FE455419
EST:     CCATGGAAACGCTCTCTTTTTGGAAATCCTAATGACAACGATACTTTCAA                         ACGAAGGTGCGAAGTGGCTGAGGCGCTTGTGGAGAAAAACTTTGACTTGGC
genomic: CCATGGAAACGCTCTCTTTTTGGAAATCCTAATGACAACGATACTTTCAAgtgcgtattt ... cgcgctccagACGAAGGTGCGAAGTGGCTGAGGCGCTTGTGGAGAAAAACTTTGACTTGGC

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: 26 (upstream exon), 34 (downstream exon)
Score: 6

ATGGAAGTGGTGAAATGCTTCAGCGACGCGGACGGCCCTCCATGGAAACGCTCTCTTTTTGGAAATCCTAATGACAACGATACTTTCAAgtgcgtattt ... cgcgctccagACGAAGGTGCGAAGTGGCTGAGGCGCTTGTGGAGAAAAACTTTGACTTGGCATTTCAAATAATCTATGACTTCGGACTTCCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcgtattttcttttacctcgcgtagtttctcacgagtgttcatcgcgctccagACGAAGGTGCGAAGTGGCTGAGGCGCTTGTGGAGAAAAACTTTGACTTGGCATTTCAAATAATCTATGACTTCGGACTTCCTG
                            ttctcac  putative branch site (score: 6)
     tattttctttta  TA-rich tract