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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccttggaagttttcaccttttcgttttcttcttggtgctcatgatattctttccactgacagGTGTTCTTTGCTATCATCTTCACTGCTCTTAGTGTCTCCCAGACACTGGGACTAGCTCCAGATCTTTCAAAGGTGAAAGCTTCCGTCGCTTCGATCTTCG

Basic information

species Selaginella moellendorffii
transcript EFJ21083
intron # 11
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|169087212|gb|FE493120.1|FE493120
EST:     GTGCCCGCCTCGTCCGCCAGGGAAAGACAGAATTTAAGAACGTTTTTAAG                         GTGTTCTTTGCTATCATCTTCACTGCTCTTAGTGTCTCCCAGACACTGGGA
genomic: GTGCCCGCCTCGTCCGCCAGGGAAAGACAGAATTTAAGAACGTTTTTAAGgtccttggaa ... ccactgacagGTGTTCTTTGCTATCATCTTCACTGCTCTTAGTGTCTCCCAGACACTGGGA
EST: gi|169102241|gb|FE503631.1|FE503631
EST:     GTGCCCGCCTCGTCCGCCAGGGAAAGACAGAATTTAAGAACGTTTTTAAG                         GTGTTCTTTGCTATCATCTTCACTG
genomic: GTGCCCGCCTCGTCCGCCAGGGAAAGACAGAATTTAAGAACGTTTTTAAGgtccttggaa ... ccactgacagGTGTTCTTTGCTATCATCTTCACTG
EST: gi|169093495|gb|FE496556.1|FE496556
EST:     GTGCCCGCCTCGTCCGCCAGGGAAAGACAGAATTTAAGAACGTTTT-AAG                         GTGTTCTTTGCTATCATCTTCACTGCTNCT-AGTGTCTCCCAGACACTGNG
genomic: GTGCCCGCCTCGTCCGCCAGGGAAAGACAGAATTTAAGAACGTTTTTAAGgtccttggaa ... ccactgacagGTGTTCTTTGCTATCATCTTCACTGCT-CTTAGTGTCTCCCAGACACTGGG
EST: gi|169070586|gb|FE479863.1|FE479863
EST:     GTGCCCGCCTCGTCCGCCAGGGAAAGACAGAATTTAAGAACGTTTTTAAG                         GTGTTCTTTGCTATCATCTTCACTGCTCTTAGTGTCTCCCAGACACTGGGA
genomic: GTGCCCGCCTCGTCCGCCAGGGAAAGACAGAATTTAAGAACGTTTTTAAGgtccttggaa ... ccactgacagGTGTTCTTTGCTATCATCTTCACTGCTCTTAGTGTCTCCCAGACACTGGGA
EST: gi|70671149|gb|DN839726.1|DN839726
EST:     GTGCCCGCCTCGTCCGCCAGGGAAAGACAGAATTTAAGAACGTTTTTAAG                         GTGTTCTTTGCTATCATCTTCACTGCTCTTAGTGTCTCCCAGACACTGGGA
genomic: GTGCCCGCCTCGTCCGCCAGGGAAAGACAGAATTTAAGAACGTTTTTAAGgtccttggaa ... ccactgacagGTGTTCTTTGCTATCATCTTCACTGCTCTTAGTGTCTCCCAGACACTGGGA
EST: gi|169038939|gb|FE449656.1|FE449656
EST:     GTGCCCGCCTCGTCCGCCAGGGAAAGACAGAATTTAAGAACGTTTTTAAG                         GTGTTCTTTGCTATCATCTTCACTGCTCTTAGTGTCTCCCAGACACTGGGA
genomic: GTGCCCGCCTCGTCCGCCAGGGAAAGACAGAATTTAAGAACGTTTTTAAGgtccttggaa ... ccactgacagGTGTTCTTTGCTATCATCTTCACTGCTCTTAGTGTCTCCCAGACACTGGGA
EST: gi|169099202|gb|FE502053.1|FE502053
EST:     GTGCCCGCCTCGTCCGCCAGGGAAAGACAGAATTTAAGAACGTTTTTAAG                         GTGTTCTTTGCTATCATCTTCACTGCTCTTAGTGTCT
genomic: GTGCCCGCCTCGTCCGCCAGGGAAAGACAGAATTTAAGAACGTTTTTAAGgtccttggaa ... ccactgacagGTGTTCTTTGCTATCATCTTCACTGCTCTTAGTGTCT

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: 15 (upstream exon), 23 (downstream exon)
Score: 5

CATCTCCACTCTCGTGCAGTTCGGTTCGCAAGCTCTCATCTTCTGGTATGGTGCCCGCCTCGTCCGCCAGGGAAAGACAGAATTTAAGAACGTTTTTAAGgtccttggaa ... ccactgacagGTGTTCTTTGCTATCATCTTCACTGCTCTTAGTGTCTCCCAGACACTGGGACTAGCTCCAGATCTTTCAAAGGTGAAAGCTTCCGTCGCTTCGATCTTCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttttcaccttttcgttttcttcttggtgctcatgatattctttccactgacagGTGTTCTTTGCTATCATCTTCACTGCTCTTAGTGTCTCCCAGACACTGGGACTAGCTCCAGATCTTTCAAAGGTGAAAGCTTCCGTCGCTTCGATCTTCG
                                       ttctttccact  CT-rich tract
                                    atattcttt  TA-rich tract