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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcagcgatcagtcgtaaagtccctccctgtttcttagttttcttgttgctttgcccagGTACTTTTGAGGGGTCGCAAGTCCGCTCGGGAGGCCGTGAAGCACTTTGGGCCGGCTCCTGGTGTGCCACACAGCCACACCAAGCCGTACGTGCGCTCCA

Basic information

species Selaginella moellendorffii
transcript EFJ22685
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ22685 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: Vv05s0077g02060.t01 (Vitis vinifera), 3'ss of exon 1
---------------------------------gtaagcagcgatcagtcgtaaagtccctccct---gtttcttagttttcttgttgctttgc--ccagGTACTTTTGAGGGGTCGCAAGTCCGCTCGGGAGGCCGTGAAGCACTTTGGGCCGGCTCCTGGTGTGCCACACAGCCACACCAAGCCGTACGTGCGCTCCA
                                 | ||     |   |    | || ||  |       ||||   |  ||   | ||  ||||   |||||| ||  |||| || |  |||   ||||| || || || || ||||||||    |||||||||||||||||||||||||| || || || || || || |
ttattttgatcattattccaattcttttttgctgaaaattcaggcaataaatgaattctgtaaaagaggtttaacaaattaaatatttatttgatgccagGTTCTGCTGAGAGGCCCAAAGAATGCTCGTGAAGCAGTAAAACACTTTGGTAAAGCTCCTGGTGTGCCACACAGCCACACTAAACCATATGTTCGATCAA
















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|169052996|gb|FE460711.1|FE460711
EST:     GCCTCACCTTTGACGAGCTCGCGCTCCTGGCACCCACTGGATGCAACACG                         GTACTTTTGAGGGGTCGCAAGTCCGCTCGGGAGGCCGTGAAGCACTTTGGG
genomic: GCCTCACCTTTGACGAGCTCGCGCTCCTGGCACCCACTGGATGCAACACGgtaagcagcg ... ctttgcccagGTACTTTTGAGGGGTCGCAAGTCCGCTCGGGAGGCCGTGAAGCACTTTGGG
EST: gi|169099479|gb|FE500510.1|FE500510
EST:     GCCTCACCTTTGACGAGCTCGCGCTCCTGGCACCCACTGGATGCAACACG                         GTACTTTTGAGGGGTCGCAAGTCCGCTCGGGAGGCCGTGAAGCACTTTGGG
genomic: GCCTCACCTTTGACGAGCTCGCGCTCCTGGCACCCACTGGATGCAACACGgtaagcagcg ... ctttgcccagGTACTTTTGAGGGGTCGCAAGTCCGCTCGGGAGGCCGTGAAGCACTTTGGG
EST: gi|70671039|gb|DN839616.1|DN839616
EST:     GCCTCACCTTTGACGAGCTCGCGCTCCTGGCACCCACTGGATGCAACACG                         GTACTTTTGAGGGGTCGCAAGTCCGCTCGGGAGGCCGTGAAGCACTTTGGG
genomic: GCCTCACCTTTGACGAGCTCGCGCTCCTGGCACCCACTGGATGCAACACGgtaagcagcg ... ctttgcccagGTACTTTTGAGGGGTCGCAAGTCCGCTCGGGAGGCCGTGAAGCACTTTGGG
EST: gi|169076248|gb|FE485694.1|FE485694
EST:     GCCTCACCTTTGACGAGCTCGCGCTCCTGGCACCCACTGGATGCAACACG                         GTACTTTTGAGGGGTCGCAAGTCCGCTCGGGAGGCCGTGAAGCACTTTGGG
genomic: GCCTCACCTTTGACGAGCTCGCGCTCCTGGCACCCACTGGATGCAACACGgtaagcagcg ... ctttgcccagGTACTTTTGAGGGGTCGCAAGTCCGCTCGGGAGGCCGTGAAGCACTTTGGG
EST: gi|169099478|gb|FE500509.1|FE500509
EST:     GCCTCACCTTTGACGAGCTCGCGCTCCTGGCACCCACTGGATGCAACACG                         GTACTTTTGAGGGGTCGCAAGTCCGCTCGGGAGGCCGTGAAGCACTTTGGG
genomic: GCCTCACCTTTGACGAGCTCGCGCTCCTGGCACCCACTGGATGCAACACGgtaagcagcg ... ctttgcccagGTACTTTTGAGGGGTCGCAAGTCCGCTCGGGAGGCCGTGAAGCACTTTGGG
EST: gi|169035084|gb|FE445920.1|FE445920
EST:     GCCTCACCTTTGACGAGCTCGCGCTCCTGGCACCCACTGGATGCAACACG                         GTACTTTTGAGGGGTCGCAAGTCCGCTCGGGAGGCCGTGAAGCACTTTGGG
genomic: GCCTCACCTTTGACGAGCTCGCGCTCCTGGCACCCACTGGATGCAACACGgtaagcagcg ... ctttgcccagGTACTTTTGAGGGGTCGCAAGTCCGCTCGGGAGGCCGTGAAGCACTTTGGG

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), 24 (downstream exon)
Score: 40

GCGCTTCACCCGGACTGCCCGCGCCAGGATCACCAACGCCGGAGGGAAATGCCTCACCTTTGACGAGCTCGCGCTCCTGGCACCCACTGGATGCAACACGgtaagcagcg ... ctttgcccagGTACTTTTGAGGGGTCGCAAGTCCGCTCGGGAGGCCGTGAAGCACTTTGGGCCGGCTCCTGGTGTGCCACACAGCCACACCAAGCCGTACGTGCGCTCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgatcagtcgtaaagtccctccctgtttcttagttttcttgttgctttgcccagGTACTTTTGAGGGGTCGCAAGTCCGCTCGGGAGGCCGTGAAGCACTTTGGGCCGGCTCCTGGTGTGCCACACAGCCACACCAAGCCGTACGTGCGCTCCA
                                  ttttcttgttgcttt  CT-rich tract
                              ttagtttt  TA-rich tract