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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttccaaagggactacttctctgcgctaattctgtgcctcgacagCATTTTTGGATATCTGTTTCGATGGTTTTCTTTGTGGCTGCGACCGTTCTTACCTTGTTAAAATTAACTG

Basic information

species Selaginella moellendorffii
transcript EFJ05219
intron # 5
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|169066919|gb|FE473673.1|FE473673
EST:     CGGCAGACGAAGAAAGTTTAACTGATGATATAATCTGGGAAACACTTCCG                         CATTTTTGGATATCTGTTTCGATGGTCTTCTTTGTGGCTGCGACCGTTCTT
genomic: CGGCAGACGAAGAAAGTTTAACTGATGATATAATCTGGGAAACACTTCCGgtaagtttcc ... gcctcgacagCATTTTTGGATATCTGTTTCGATGGTTTTCTTTGTGGCTGCGACCGTTCTT
EST: gi|169096245|gb|FE497831.1|FE497831
EST:     CGGCAGACGAAGAAAGTTTAACTGATGATATAATCTGGGAAACACTTCCG                         CATTTTTGGATATCTGTTTCGATGGTCTTCTTTGTGGCTGCGACCGTTCTT
genomic: CGGCAGACGAAGAAAGTTTAACTGATGATATAATCTGGGAAACACTTCCGgtaagtttcc ... gcctcgacagCATTTTTGGATATCTGTTTCGATGGTTTTCTTTGTGGCTGCGACCGTTCTT
EST: gi|169099242|gb|FE502067.1|FE502067
EST:     CGGCAGACGAAGAAAGTTTAACTGATGATATAATCTGGGAAACACTTCCG                         CATTTTTGGATATCTGTTTCGATGGTCTTCTTTGTGGCTGCGACCGTTCTT
genomic: CGGCAGACGAAGAAAGTTTAACTGATGATATAATCTGGGAAACACTTCCGgtaagtttcc ... gcctcgacagCATTTTTGGATATCTGTTTCGATGGTTTTCTTTGTGGCTGCGACCGTTCTT
EST: gi|169095753|gb|FE498366.1|FE498366
EST:     CGGCAGACGAAGAAAGTTTAACTGATGATATAATCTGGGAAACACTTCCG                         CATTTTTGGATATCTGTTTCGATGGTTTTCTTTGTGGCTGCGACCGTTCTT
genomic: CGGCAGACGAAGAAAGTTTAACTGATGATATAATCTGGGAAACACTTCCGgtaagtttcc ... gcctcgacagCATTTTTGGATATCTGTTTCGATGGTTTTCTTTGTGGCTGCGACCGTTCTT

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), 35 (downstream exon)
Score: 47

GATGTGCAGGGCTCTGATGCCGGCAGACGAAGAAAGTTTAACTGATGATATAATCTGGGAAACACTTCCGgtaagtttcc ... gcctcgacagCATTTTTGGATATCTGTTTCGATGGTTTTCTTTGTGGCTGCGACCGTTCTTACCTTGTTAAAATTAACTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagtttccaaagggactacttctctgcgctaattctgtgcctcgacagCATTTTTGGATATCTGTTTCGATGGTTTTCTTTGTGGCTGCGACCGTTCTTACCTTGTTAAAATTAACTG
                                 cgctaat  putative branch site (score: 47)
           taagttt  TA-rich tract