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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagagcagtttatagcttccattgtttttcttctccgagtttgatcaactgagagctcttgcagGGATTTGGCAATGTTGGTCACCATACTGCCCAGTTCCTGTTCGAGGCCAAAGGAAGAGTCAAGGCGGTAAGCGACATAACTGGAGCGATAAAGAACGATG

Basic information

species Selaginella moellendorffii
transcript EFJ06181
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|169073033|gb|FE483683.1|FE483683
EST:     TGCTTGCCGACCATGGCAAGTCTCTCTCGAACCAAACTTTTGTGATCCAG                         GGATTTGGCAATGTTGGTCACCATACTGCCCAGTTCCTCTTCGAGGCCAAA
genomic: TGCTTGCCGACCATGGCAAGTCTCTCTCGAACCAAACTTTTGTGATCCAGgtagagcagt ... gctcttgcagGGATTTGGCAATGTTGGTCACCATACTGCCCAGTTCCTGTTCGAGGCCAAA
EST: gi|169029682|gb|FE437353.1|FE437353
EST:     TGCTTGCCGACCATGGCAAGTCTCTCTCGAACCAAACTTTTGTGATCCAG                         GGATTTGGCAATGTTGGTCACCATACTGCCCAGTTCCTCTTCGAGGCCAAA
genomic: TGCTTGCCGACCATGGCAAGTCTCTCTCGAACCAAACTTTTGTGATCCAGgtagagcagt ... gctcttgcagGGATTTGGCAATGTTGGTCACCATACTGCCCAGTTCCTGTTCGAGGCCAAA
EST: gi|169034524|gb|FE444571.1|FE444571
EST:     TGCTTGCCGACCATGGCAAGTCTCTCTCGAACCAAACTTTTGTGATCCAG                         GGATTTGGCAATGTTGGTCACCATACTGCCCAGTTCCTCTTCGAGGCCAAA
genomic: TGCTTGCCGACCATGGCAAGTCTCTCTCGAACCAAACTTTTGTGATCCAGgtagagcagt ... gctcttgcagGGATTTGGCAATGTTGGTCACCATACTGCCCAGTTCCTGTTCGAGGCCAAA
EST: gi|169046220|gb|FE456379.1|FE456379
EST:     TGCTTGCCGACCATGGCAAGTCTCTCTCGAACCAAACTTTTGTGATCCAG                         GGATTTGGCAATGTTGGTCACCATACTGCCCAGTTCCTCTTCGAGGCCAAA
genomic: TGCTTGCCGACCATGGCAAGTCTCTCTCGAACCAAACTTTTGTGATCCAGgtagagcagt ... gctcttgcagGGATTTGGCAATGTTGGTCACCATACTGCCCAGTTCCTGTTCGAGGCCAAA
EST: gi|169067884|gb|FE474755.1|FE474755
EST:     TGCTTGCCGACCATGGCAAGTCTCTCTCGAACCAAACTTTTGTGATCCAG                         GGATTTGGCAATGTTGGTCACCATACTGCCCAGTTCCTGTTCGAGGCCAAA
genomic: TGCTTGCCGACCATGGCAAGTCTCTCTCGAACCAAACTTTTGTGATCCAGgtagagcagt ... gctcttgcagGGATTTGGCAATGTTGGTCACCATACTGCCCAGTTCCTGTTCGAGGCCAAA
EST: gi|169022697|gb|FE429724.1|FE429724
EST:     TGCTTGCCGACCATGGCAAGTCTCTCTCGAACCAAACTTTTGTGATCCAG                         GGATTTGGCAATGTTGGTCACCATACTGCCCAGTTCCTGTTCGAGGCCAAA
genomic: TGCTTGCCGACCATGGCAAGTCTCTCTCGAACCAAACTTTTGTGATCCAGgtagagcagt ... gctcttgcagGGATTTGGCAATGTTGGTCACCATACTGCCCAGTTCCTGTTCGAGGCCAAA
EST: gi|169030555|gb|FE437888.1|FE437888
EST:     TGCTTGCCGACCATGGCAAGTCTCTCTCGAACCAAACTTTTGTGATCCAG                         GGATTTGGCAATGTTGGTCACCATACTGCCCAGTTCCTGTTCGAGGCCAAA
genomic: TGCTTGCCGACCATGGCAAGTCTCTCTCGAACCAAACTTTTGTGATCCAGgtagagcagt ... gctcttgcagGGATTTGGCAATGTTGGTCACCATACTGCCCAGTTCCTGTTCGAGGCCAAA

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: 59

AGGACGTGAGGCTGCCACTGGAAGAGGAGTTGTATACGTGACTGAAGCATTGCTTGCCGACCATGGCAAGTCTCTCTCGAACCAAACTTTTGTGATCCAGgtagagcagt ... gctcttgcagGGATTTGGCAATGTTGGTCACCATACTGCCCAGTTCCTGTTCGAGGCCAAAGGAAGAGTCAAGGCGGTAAGCGACATAACTGGAGCGATAAAGAACGATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatagcttccattgtttttcttctccgagtttgatcaactgagagctcttgcagGGATTTGGCAATGTTGGTCACCATACTGCCCAGTTCCTGTTCGAGGCCAAAGGAAGAGTCAAGGCGGTAAGCGACATAACTGGAGCGATAAAGAACGATG
                             gtttgat  putative branch site (score: 59)
                                              ctcttgc  putative PPT
           attgttttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagagcagtttatagcttccattgtttttcttctccgagtttgatcaactgagagctcttgcagGGATTTGGCAATGTTGGTCACCATACTGCCCAGTTCCTGTTCGAGGCCAAAGGAAGAGTCAAGGCGGTAAGCGACATAACTGGAGCGATAAAGAACGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC