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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcaaagctttcttcttcttttcggtcgctctcttttcttacgagtggccttttctttttcgtgctaccgcagGGGATTCTTGTGTTTGCTTCCGTGATGGCGACTTTGGGACTACAAATTCTCCTTGAATCCGGGCGGAAGCTCATCAACAAT

Basic information

species Selaginella moellendorffii
transcript EFJ22209
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|169094578|gb|FE492450.1|FE492450
EST:     GGCCGAATCCATATCTCTATCCCATTGGGAAGAAGCGAATGCAACCACTG                         GGGATTCTTGTGTTTGCTTCCGTGATGGCGACTTTGGGACTACAAATTCTC
genomic: GGCCGAATCCATATCTCTATCCCATTGGGAAGAAGCGAATGCAACCACTGgtgagcaaag ... gctaccgcagGGGATTCTTGTGTTTGCTTCCGTGATGGCGACTTTGGGACTACAAATTCTC
EST: gi|169115734|gb|FE517320.1|FE517320
EST:     GGCCGAATCCATATCTCTATCCCATTGGGAAGAAGCGAATGCAACCACTG                         GGGATTCTTGTGTTTGCTTCCGTGATGGCGACTTTGGGACTACAAATTCTC
genomic: GGCCGAATCCATATCTCTATCCCATTGGGAAGAAGCGAATGCAACCACTGgtgagcaaag ... gctaccgcagGGGATTCTTGTGTTTGCTTCCGTGATGGCGACTTTGGGACTACAAATTCTC
EST: gi|169094521|gb|FE494499.1|FE494499
EST:     GGCCGAATCCATATCTCTATCCCATTGGGAAGAAGCGAATGCAACCACTG                         GGGATTCTTGTGTTTGCTTCCGTGATGGCGACTTTGGGACTACAAATTCTC
genomic: GGCCGAATCCATATCTCTATCCCATTGGGAAGAAGCGAATGCAACCACTGgtgagcaaag ... gctaccgcagGGGATTCTTGTGTTTGCTTCCGTGATGGCGACTTTGGGACTACAAATTCTC
EST: gi|169018700|gb|FE426677.1|FE426677
EST:     GGCCGAATCCATATCTCTATCNCATGGGGAAGAAGCGAATGCAACCACTG                         GGGATTCTTGTGTTTGCTTCCGTGATGGCGACTTTGGGACTACAAATTCTC
genomic: GGCCGAATCCATATCTCTATCCCATTGGGAAGAAGCGAATGCAACCACTGgtgagcaaag ... gctaccgcagGGGATTCTTGTGTTTGCTTCCGTGATGGCGACTTTGGGACTACAAATTCTC
EST: gi|169101381|gb|FE502524.1|FE502524
EST:     GGCCGAATCCATATCTCTATCCCATTGNGAAGAAGCGAATGCAACCACTG                         GGGATTCTTGTGTTTGCTTCCGTGATGGCGACTTTGGGACTAC
genomic: GGCCGAATCCATATCTCTATCCCATTGGGAAGAAGCGAATGCAACCACTGgtgagcaaag ... gctaccgcagGGGATTCTTGTGTTTGCTTCCGTGATGGCGACTTTGGGACTAC
EST: gi|169103985|gb|FE504296.1|FE504296
EST:     GGCCGAATCCATATCTCTATCCCATTGGGAAGAAGCGAATGCAACCACTG                         GGGATTCTTGTGTTTGCTTCCGTGATGGCGACTTTGGGACTACAAATTCTC
genomic: GGCCGAATCCATATCTCTATCCCATTGGGAAGAAGCGAATGCAACCACTGgtgagcaaag ... gctaccgcagGGGATTCTTGTGTTTGCTTCCGTGATGGCGACTTTGGGACTACAAATTCTC
EST: gi|169056828|gb|FE465418.1|FE465418
EST:     GGCCGAATCCATATCTCTATCCCATTGGGAAGAAGCGAATGCAACCACTG                         GGGATTCTTGTGTTTGCTTCCGTGATGGCGACTTTGGGACTACAAATTCTC
genomic: GGCCGAATCCATATCTCTATCCCATTGGGAAGAAGCGAATGCAACCACTGgtgagcaaag ... gctaccgcagGGGATTCTTGTGTTTGCTTCCGTGATGGCGACTTTGGGACTACAAATTCTC
EST: gi|169101380|gb|FE502523.1|FE502523
EST:     TGCAACCACTG                         GGGATTCTTGTGTTTGCTTCCGTGATGGCGACTTTGGGACTACAAATTCTC
genomic: TGCAACCACTGgtgagcaaag ... gctaccgcagGGGATTCTTGTGTTTGCTTCCGTGATGGCGACTTTGGGACTACAAATTCTC
EST: gi|169068129|gb|FE476886.1|FE476886
EST:     GGCCGAATCCATATCTCTATCCCATTGGGAAGAAGCGAATGCAACCACTG                         GGGATTCTTGTGTTTGCTTCCGTGATGGCGACTTTGGGACTACAAATTCTC
genomic: GGCCGAATCCATATCTCTATCCCATTGGGAAGAAGCGAATGCAACCACTGgtgagcaaag ... gctaccgcagGGGATTCTTGTGTTTGCTTCCGTGATGGCGACTTTGGGACTACAAATTCTC
EST: gi|169054285|gb|FE460730.1|FE460730
EST:     GGCCGAATCCATATCTCTATCCCATTGGGAAGAAGCGAATGCAACCACTG                         GGGATTCTTGTGTTTGCTTCCGTGATGGCGACTTTGGGACTACAAATTCTC
genomic: GGCCGAATCCATATCTCTATCCCATTGGGAAGAAGCGAATGCAACCACTGgtgagcaaag ... gctaccgcagGGGATTCTTGTGTTTGCTTCCGTGATGGCGACTTTGGGACTACAAATTCTC
EST: gi|169022152|gb|FE430981.1|FE430981
EST:     GGCCGAATCCATATCTCTATCCCATTGGGAAGAAGCGAATGCAACCACTG                         GGGATTCTTGTGTTTGCTTCCGTGATGGCGACTTTGGGACTACAAATTCTC
genomic: GGCCGAATCCATATCTCTATCCCATTGGGAAGAAGCGAATGCAACCACTGgtgagcaaag ... gctaccgcagGGGATTCTTGTGTTTGCTTCCGTGATGGCGACTTTGGGACTACAAATTCTC
EST: gi|169042485|gb|FE453670.1|FE453670
EST:     GGCCGAATCCATATCTCTATCCCATTGGGAAGAAGCGAATGCAACCACTG                         GGGATTCTTGTGTTTGCTTCCGTGATGGCGACTTTGGGACTACAAATTCTC
genomic: GGCCGAATCCATATCTCTATCCCATTGGGAAGAAGCGAATGCAACCACTGgtgagcaaag ... gctaccgcagGGGATTCTTGTGTTTGCTTCCGTGATGGCGACTTTGGGACTACAAATTCTC
EST: gi|169028596|gb|FE440739.1|FE440739
EST:     GGCCGAATCCATATCTCTATCCCATTGGGAAGAAGCGAATGCAACCACTG                         GGGATTCTTGTGTTTGCTTCCGTGATGGCGACTTTGGGACTACAAATTCTC
genomic: GGCCGAATCCATATCTCTATCCCATTGGGAAGAAGCGAATGCAACCACTGgtgagcaaag ... gctaccgcagGGGATTCTTGTGTTTGCTTCCGTGATGGCGACTTTGGGACTACAAATTCTC
EST: gi|169109635|gb|FE510069.1|FE510069
EST:     GCCGAATCCATATCTCTATCCCATTGGGAAGAAGCGAATGNCA-CCACTG                         GGGATTCTTGTGTTTGCTTCCGTGATGGCGACTTTGGGACTACAAATTCT
genomic: GCCGAATCCATATCTCTATCCCATTGGGAAGAAGCGAATG-CAACCACTGgtgagcaaag ... gctaccgcagGGGATTCTTGTGTTTGCTTCCGTGATGGCGACTTTGGGACTACAAATTCT

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: 43

GGATCTCTTGTCCGGCTTCATCCTTTGGTTCACTGCCTTTTCGATGCAACGGCCGAATCCATATCTCTATCCCATTGGGAAGAAGCGAATGCAACCACTGgtgagcaaag ... gctaccgcagGGGATTCTTGTGTTTGCTTCCGTGATGGCGACTTTGGGACTACAAATTCTCCTTGAATCCGGGCGGAAGCTCATCAACAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcggtcgctctcttttcttacgagtggccttttctttttcgtgctaccgcagGGGATTCTTGTGTTTGCTTCCGTGATGGCGACTTTGGGACTACAAATTCTCCTTGAATCCGGGCGGAAGCTCATCAACAAT
                 ttcttac  putative branch site (score: 43)
                              ccttttctttttcgtg  putative PPT
                                ttttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcaaagctttcttcttcttttcggtcgctctcttttcttacgagtggccttttctttttcgtgctaccgcagGGGATTCTTGTGTTTGCTTCCGTGATGGCGACTTTGGGACTACAAATTCTCCTTGAATCCGGGCGGAAGCTCATCAACAAT

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