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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTAGTGCGAACTCAGTGTATGGATTCACAGGCGCAACAGTTGGCCAGCTTCCTTGCCTTGAAATTTCATCCAGCGTAACTAGCTATGgtacaatctcatccgttttgttttgttggttttaatagaacgagagttgcag

Basic information

species Selaginella moellendorffii
transcript EFJ15982
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ15982 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: PP1S14_182V6.1 (Physcomitrella patens), 5'ss of exon 19
GTTAGTGCGAACTCAGTGTATGGATTCACAGGCGCAACAGTTGGCCAGCTTCCTTGCCTTGAAATTTCATCCAGCGTAACTAGCTATGgtacaatc--tcatcc---gttttgttttgttggt--tttaatagaacgagagttgcag-----------------------------------------
 | ||||||||||| |||||||||||||| || |||||  | || ||||| || ||||||||||| || ||||| || || |||| ||||| | ||  | | ||    |||         | |  ||| ||    |   | | | ||                                         
ATCAGTGCGAACTCGGTGTATGGATTCACGGGGGCAACTATAGGGCAGCTGCCATGCCTTGAAATCTCCTCCAGTGTCACCAGCTTTGgtaaagtcaataaccctgaatttaaagcaacagctaatttcattcctcacaactggaagttttttatatccaataattttatcccttctccaactactgg

upper sequence: EFJ15982 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: PP1S54_271V6.1 (Physcomitrella patens), 5'ss of exon 19
GTTAGTGCGAACTCAGTGTATGGATTCACAGGCGCAACAGTTGGCCAGCTTCCTTGCCTTGAAATTTCATCCAGCGTAACTAGCTATGgtacaatctcatccgttttgttttgttggttttaatagaacgagagttgcag--------------------------------------------------
|| ||||| ||||||||||||||||| || || ||||||||||| ||||| || || ||||| || || ||||| || || || | ||||| | ||  |  | |    |    || ||   ||| ||       || |                                                    
GTGAGTGCCAACTCAGTGTATGGATTTACGGGGGCAACAGTTGGGCAGCTGCCATGTCTTGAGATCTCTTCCAGTGTTACGAGTTTTGgta-agtcagaaacttgacatcc-attagtcgcaattgattttttttttcttgttactcttcatcagaaagtgttctaagtttcgaaagtatcaacacttaa
















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|169106879|gb|FE505486.1|FE505486
EST:     AGTTGGCCAGCTTCCTTGCCTTGAAATTTCATCCAGCGTAACTAGCTATG                         GAAGGCAGATGATTGAACACACCAAAACCCTCGTGGAAGGACGTTTCAACA
genomic: AGTTGGCCAGCTTCCTTGCCTTGAAATTTCATCCAGCGTAACTAGCTATGgtacaatctc ... agagttgcagGAAGGCAGATGATTGAACACACCAAAACCCTCGTGGAAGGACGTTTCAACA
EST: gi|169049692|gb|FE459318.1|FE459318
EST:     AGTTGGCCAGCTTCCTTGCCTTGAAATTTCATCCAGCGTAACTAGCTATG                         GAAGGCAGATGATTGAACACACCAAAACCCTCGTGGAAGGACGTTTCAACA
genomic: AGTTGGCCAGCTTCCTTGCCTTGAAATTTCATCCAGCGTAACTAGCTATGgtacaatctc ... agagttgcagGAAGGCAGATGATTGAACACACCAAAACCCTCGTGGAAGGACGTTTCAACA
EST: gi|169019789|gb|FE426876.1|FE426876
EST:     AGTTGGCCAGCTTCCTTGCCTTGAAATTTCATCCAGCGTAACTAGCTATG                         GAAGGCAGATGATTGAA
genomic: AGTTGGCCAGCTTCCTTGCCTTGAAATTTCATCCAGCGTAACTAGCTATGgtacaatctc ... agagttgcagGAAGGCAGATGATTGAA

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: 34 (upstream exon), 9 (downstream exon)
Score: 2

GTTAGTGCGAACTCAGTGTATGGATTCACAGGCGCAACAGTTGGCCAGCTTCCTTGCCTTGAAATTTCATCCAGCGTAACTAGCTATGgtacaatctc ... agagttgcagGAAGGCAGATGATTGAACACACCAAAACCCTCGTGGAAGGACGTTTCAACACAAGCAACAAATATGACAACAATGCAGAA




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