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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttctttattttcgtttccatccttgttcttttggaagtaacttttgcgtatagATCTGCTGCAGTGGACTCCAGCGGCAGAGAACTTAATCGTAATCGCTTAATTGCACTTATTTCTGCCATTGTTTTGGCCGAG

Basic information

species Selaginella moellendorffii
transcript EFJ15375
intron # 8
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|169032008|gb|FE440682.1|FE440682
EST:     GACACGGATGTTGACAG                         ATCTGCTGCAGTGGACTCCAGCGGCAGAGAACTTAATCGTAATCGCTTAAT
genomic: GACACGGATGTTGACAGgtttctttat ... ttgcgtatagATCTGCTGCAGTGGACTCCAGCGGCAGAGAACTTAATCGTAATCGCTTAAT
EST: gi|169074927|gb|FE482782.1|FE482782
EST:     CTCAAGCACAAGGCGGACTTGGGGATCATATTTGACACGGATGTTGACAG                         ATCTGCTGCAGTGGACTCCAGCGGCAGAGAACTTAATCGTAATCGCTTAAT
genomic: CTCAAGCACAAGGCGGACTTGGGGATCATATTTGACACGGATGTTGACAGgtttctttat ... ttgcgtatagATCTGCTGCAGTGGACTCCAGCGGCAGAGAACTTAATCGTAATCGCTTAAT
EST: gi|169094539|gb|FE494504.1|FE494504
EST:     ACACGGATGTTGACAG                         ATCTGCTGCAGTGGACTCCAGCGGCAGAGAACTTAATCGTAATCGCTTAAT
genomic: ACACGGATGTTGACAGgtttctttat ... ttgcgtatagATCTGCTGCAGTGGACTCCAGCGGCAGAGAACTTAATCGTAATCGCTTAAT

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: 33 (upstream exon), 32 (downstream exon)
Score: 15

TTCCCAATCCTGAGGACAAGAAAGCAATGGAAGCCGTGACAAGTGCTGTTCTCAAGCACAAGGCGGACTTGGGGATCATATTTGACACGGATGTTGACAGgtttctttat ... ttgcgtatagATCTGCTGCAGTGGACTCCAGCGGCAGAGAACTTAATCGTAATCGCTTAATTGCACTTATTTCTGCCATTGTTTTGGCCGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttctttattttcgtttccatccttgttcttttggaagtaacttttgcgtatagATCTGCTGCAGTGGACTCCAGCGGCAGAGAACTTAATCGTAATCGCTTAATTGCACTTATTTCTGCCATTGTTTTGGCCGAG
                                    aagtaac  putative branch site (score: 15)
 cttttgc  CT-rich tract
 tttatttt  TA-rich tract