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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgatgcctatgttagtgattctttcctttgacgacttcttcttcttgcttttttttttttatcaaaatacgcagCAAGCAATTGCCCAAGGCATCGTTGATACTGGCTTGGACGTTGTTTTGTACGG

Basic information

species Selaginella moellendorffii
transcript EFJ15375
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|169055219|gb|FE462419.1|FE462419
EST:     TACGGGTCTCAATCGGCCACGATTCAAGAATATCTGCGAGCTCCCTCGAG                         CAAGCAATTGCCCAAGGCATCGTTGATACTGGCTTGGACGTTGTTTTGTAC
genomic: TACGGGTCTCAATCGGCCACGATTCAAGAATATCTGCGAGCTCCCTCGAGgtctgatgcc ... aaatacgcagCAAGCAATTGCCCAAGGCATCGTTGATACTGGCTTGGACGTTGTTTTGTAC
EST: gi|169094540|gb|FE494505.1|FE494505
EST:     TACGGGTCTCAATCGGCCACGATTCAAGAATATCTGCGAGCTCCCTCGAG                         CAAGCAATTGCCCAAGGCATCGTTGATACTGGCTTGGACGTTGTTTTGTAC
genomic: TACGGGTCTCAATCGGCCACGATTCAAGAATATCTGCGAGCTCCCTCGAGgtctgatgcc ... aaatacgcagCAAGCAATTGCCCAAGGCATCGTTGATACTGGCTTGGACGTTGTTTTGTAC
EST: gi|169074927|gb|FE482782.1|FE482782
EST:     GCGAGCTCCCTCGAG                         CAAGCAATTGCTCAAGGCATCGGTGATACTGGCTTGGACGTTGTTTTGTAC
genomic: GCGAGCTCCCTCGAGgtctgatgcc ... aaatacgcagCAAGCAATTGCCCAAGGCATCGTTGATACTGGCTTGGACGTTGTTTTGTAC
EST: gi|169026292|gb|FE432655.1|FE432655
EST:     TACGCGTCTCAATCGGCCACGATTCAAGAATATCTGCGAGCTCCCTCGAG                         CAAGCAATTGCTCAAGGCATCGGTGATACTGGCTTGGACGTTGTTTTGTAC
genomic: TACGGGTCTCAATCGGCCACGATTCAAGAATATCTGCGAGCTCCCTCGAGgtctgatgcc ... aaatacgcagCAAGCAATTGCCCAAGGCATCGTTGATACTGGCTTGGACGTTGTTTTGTAC

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: 29 (upstream exon), 29 (downstream exon)
Score: 4

ATTTGCGCAATGGCTGGCTGATAAGAAAAAAGAATCCACGTCCAGTGCTTTACGGGTCTCAATCGGCCACGATTCAAGAATATCTGCGAGCTCCCTCGAGgtctgatgcc ... aaatacgcagCAAGCAATTGCCCAAGGCATCGTTGATACTGGCTTGGACGTTGTTTTGTACGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttcctttgacgacttcttcttcttgcttttttttttttatcaaaatacgcagCAAGCAATTGCCCAAGGCATCGTTGATACTGGCTTGGACGTTGTTTTGTACGG
      ctttgac  putative branch site (score: 4)
               cttcttcttcttgctt  putative PPT
                      ttcttgcttttttttt  TA-rich tract