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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatctactgaacgaacagactcgatcggcacgaggttttgatttaccatccttccactgagttcagGAAAGGTTTCAGCAATTAGATTGCTTTCTAGCAG

Basic information

species Selaginella moellendorffii
transcript EFJ06979
intron # 6
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|169048834|gb|FE455301.1|FE455301
EST:     CTGCAACAAAGAGCTCTGTAGTATTTTGTCTCACGAATTTGCTTGGCAAG                         GAAAGGTTTCAGCAATTAGATTGCTTTCTAGCAGGCGATGATGT
genomic: CTGCAACAAAGAGCTCTGTAGTATTTTGTCTCACGAATTTGCTTGGCAAGgtaaatctac ... ctgagttcagGAAAGGTTTCAGCAATTAGATTGCTTTCTAGCAGGCGATGATGT
EST: gi|169104877|gb|FE505420.1|FE505420
EST:     CTGCAACAAAGAGCTCTGTAGTATTTTGTCTCACGAATTTGCTTGGCAAG                         GAAAGGTTTCAGCAATTAGATTGCTTTCTAGCAG
genomic: CTGCAACAAAGAGCTCTGTAGTATTTTGTCTCACGAATTTGCTTGGCAAGgtaaatctac ... ctgagttcagGAAAGGTTTCAGCAATTAGATTGCTTTCTAGCAG

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), 34 (downstream exon)
Score: 5

GGAATTAAGGTGGCTGTTTGCTCAGCTGCAACAAAGAGCTCTGTAGTATTTTGTCTCACGAATTTGCTTGGCAAGgtaaatctac ... ctgagttcagGAAAGGTTTCAGCAATTAGATTGCTTTCTAGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgaacagactcgatcggcacgaggttttgatttaccatccttccactgagttcagGAAAGGTTTCAGCAATTAGATTGCTTTCTAGCAG
                        ttttgat  putative branch site (score: 5)
                                     tccttccact  putative PPT
                        ttttgattta  TA-rich tract