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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcccgtcctagaatccccccttcatggcattaatccatgtacttggtgtctcagGCTGCTGCCCTTCAAGGATCGGAGCACAGGCGTGCAACTCCTGTGGCAGATCGTCTTGATGAACAACAAAAGCACTTAAAGCTTCCTATTCTGCCAACAA

Basic information

species Selaginella moellendorffii
transcript EFJ28889
intron # 6
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|169057672|gb|FE463723.1|FE463723
EST:     CCTCTAGGAAGACGTCTCCTAGAGTCCACAACGACGAAGTGAAGAAGGCG                         GCTGCTGCCCTTCAAGGATCGGAGCACAGGCGTGCAACTCCTGTGGCAGAT
genomic: CCTCTAGGAAGACGTCTCCTAGAGTCCACAACGACGAAGTGAAGAAGGCGgtaagcccgt ... ggtgtctcagGCTGCTGCCCTTCAAGGATCGGAGCACAGGCGTGCAACTCCTGTGGCAGAT
EST: gi|169053883|gb|FE460974.1|FE460974
EST:     CCTCTAGGAAGACGTCTCCTAGAGTCCACAACGACGAAGTGAAGAAGGCG                         GCTGCTGCCCTTCAAGGATCGGAGCACAGGCGTGCAACTCCTGTGGCAGAT
genomic: CCTCTAGGAAGACGTCTCCTAGAGTCCACAACGACGAAGTGAAGAAGGCGgtaagcccgt ... ggtgtctcagGCTGCTGCCCTTCAAGGATCGGAGCACAGGCGTGCAACTCCTGTGGCAGAT
EST: gi|169032658|gb|FE436931.1|FE436931
EST:     CCTCTAGGAAGACGTCTCCTAGAGTCCACAACGACGAAGTGAAGAAGGCG                         GCTGCTGCCCTTCAAGGATCGGAGCACAGGCGTGCAACTCCTGTGGCAGAT
genomic: CCTCTAGGAAGACGTCTCCTAGAGTCCACAACGACGAAGTGAAGAAGGCGgtaagcccgt ... ggtgtctcagGCTGCTGCCCTTCAAGGATCGGAGCACAGGCGTGCAACTCCTGTGGCAGAT
EST: gi|169027729|gb|FE434866.1|FE434866
EST:     CCTCTAGGAAGACGTCTCCTAGAGTCCACAACGACGAAGTGAAGAAGGCG                         GCTGCTGCCCTTCAAGGATCGGAGCACAGGCGTGCAACTCCTGTGGCAGAT
genomic: CCTCTAGGAAGACGTCTCCTAGAGTCCACAACGACGAAGTGAAGAAGGCGgtaagcccgt ... ggtgtctcagGCTGCTGCCCTTCAAGGATCGGAGCACAGGCGTGCAACTCCTGTGGCAGAT
EST: gi|169060120|gb|FE468106.1|FE468106
EST:     CCTCTAGGAAGACGTCTCCTAGAGTCCACAACGACGAAGTGAAGAAGGCG                         GCTGCTGCCCTTCAAGGATCGGAGCACAGGCGTGCAACTCCTGTGGCAGAT
genomic: CCTCTAGGAAGACGTCTCCTAGAGTCCACAACGACGAAGTGAAGAAGGCGgtaagcccgt ... ggtgtctcagGCTGCTGCCCTTCAAGGATCGGAGCACAGGCGTGCAACTCCTGTGGCAGAT
EST: gi|169061439|gb|FE469538.1|FE469538
EST:     CCTCTAGGAAGACGTCTCCTAGAGTCCACAACGACGAAGTGAAGAAGGCG                         GCTGCTGCCCTTCAAGGATCGGAGCACAGGCGTGCAACTCCTGTGGCAGAT
genomic: CCTCTAGGAAGACGTCTCCTAGAGTCCACAACGACGAAGTGAAGAAGGCGgtaagcccgt ... ggtgtctcagGCTGCTGCCCTTCAAGGATCGGAGCACAGGCGTGCAACTCCTGTGGCAGAT
EST: gi|169109744|gb|FE511815.1|FE511815
EST:     CCTCTAGGAAGACGTCTCCTAGAGTCCACAACGACGAAGTGAAGAAGGCG                         GCTGCTGCCCTTCAAGGATCGGAGCACAGGCGTGCAACTCCTGTGGCAGAT
genomic: CCTCTAGGAAGACGTCTCCTAGAGTCCACAACGACGAAGTGAAGAAGGCGgtaagcccgt ... ggtgtctcagGCTGCTGCCCTTCAAGGATCGGAGCACAGGCGTGCAACTCCTGTGGCAGAT

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), 34 (downstream exon)
Score: 134

GAGTTCTTTGCGGCCAATGCATCTGCTCAGGCCTCTAGGAAGACGTCTCCTAGAGTCCACAACGACGAAGTGAAGAAGGCGgtaagcccgt ... ggtgtctcagGCTGCTGCCCTTCAAGGATCGGAGCACAGGCGTGCAACTCCTGTGGCAGATCGTCTTGATGAACAACAAAAGCACTTAAAGCTTCCTATTCTGCCAACAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcccgtcctagaatccccccttcatggcattaatccatgtacttggtgtctcagGCTGCTGCCCTTCAAGGATCGGAGCACAGGCGTGCAACTCCTGTGGCAGATCGTCTTGATGAACAACAAAAGCACTTAAAGCTTCCTATTCTGCCAACAA
                            cattaat  putative branch site (score: 134)
                             attaat  TA-rich tract