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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattttgtccagaataggcattgtgagttacacaatccttcgtgaattaaggaacggaggtccttattctgtgctttgtgtggattgtgcaacttgttagTGCCAAAATATTCAATATTTATCCGCGGAAAGGAGCGGTGCTGCCAGGCTCTGATGCAGACATTATCATTTTGAACCCAAATGCAACTACTACTATATCC

Basic information

species Physcomitrella patens
transcript PP1S101_168V6.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S101_168V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA14G04030.1 (Glycine max), 3'ss of exon 11
-----tattttgtccagaataggcattgtgagttacacaatccttcgtgaattaaggaac--------ggaggtccttattctgtgctttgtgtg----gattgtgcaa-cttgttagTGCCAAAATATTCAATATTTATCCGCGGAAAGGAGCGGTGCTGCCAGGCTCTGATGCAGACATTATCATTTTGAACCCAAATGCAACTACTACTATATCC
     ||||  ||  |  | ||      | || | |    || |  |  ||| ||  | |          || | |  |   | |   |  |||       || | ||| | | | ||||| ||||| |||||||| |||||  |||||||||| || || ||||| ||||||||||| ||||||||  |||| |||||| | |    |   ||    
gtatatattcagttaatcaaagtgcaaattagcttctagttcttatggaaataaaaaagctttttggtaaagatgccaaaagtattactgatgttttttatttctacaatcatttcagTGCTAAAATCTTCAATATATATCCAAGGAAAGGAGCTGTTCTCCCAGGATCTGATGCAGATATTATCATCCTGAATCCAAATTCGAGCTTTGAGATGAGT

upper sequence: PP1S101_168V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA02G44690.1 (Glycine max), 3'ss of exon 11
-------------------------------------tattttgtccagaataggcattgtgagttacacaatccttcgtgaattaaggaacggaggtccttattctgtgctttgtgtggattgtgcaa-cttgttagTGCCAAAATATTCAATATTTATCCGCGGAAAGGAGCGGTGCTGCCAGGCTCTGATGCAGACATTATCATTTTGAACCCAAATGCAACTACTACTATATCC
                                       || |    |  |||          |||    ||   | |   ||   |  |    |  |   ||     |||||| |||   || | ||| | | | ||||| ||||| |||||||| |||||  ||||||||||  | || ||||| ||||||||||| ||||||||  | || |||||| | |    |   ||    
gtatattttcagttaatcaaagtgaaaattatctttcagttcttatgactataaaggaaaactgtttggtaaagatgccaaaaaccaaaagtataactgtataactgatgctttttgt---ttctacaatcatttcagTGCTAAAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTCCCAGGATCTGATGCAGATATTATCATCCTTAATCCAAATTCGAGCTTTGAGATGAGT

upper sequence: PP1S101_168V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA15G06100.1 (Glycine max), 3'ss of exon 11
-------------------------------------------------------------tattttgtccaga-ataggcattgtgagtt-acacaatccttcgtgaattaaggaacggaggtccttattctgtgctttgtgtggattgtgcaact-tgttagTGCCAAAATATTCAATATTTATCCGCGGAAAGGAGCGGTGCTGCCAGGCTCTGATGCAGACATTATCATTTTGAACCCAAATGCAACTACTACTATATCC
                                                              |   | |  |   ||    ||| | | || |   |   ||| ||  |      ||  |   | || ||| |    | | | |   || | |||   | ||||||| | ||| |||||||| |||||  ||||||||||  | || ||||| ||||||||||| ||||||||  | || |||||| ||||   |   ||| | 
gtatattttctgttaatcaaagtaaaattagcatccagttcttatagtaataaggagaattcagagtatttaattatttttattttaatttgatgaagctctttgtatagatgccaaaagtattactgatttttatttatttat---ttctacaatcattttagTGCTAGAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTTCCAGGATCTGATGCAGATATTATCATCCTCAATCCAAATTCAACCTTTGAGATAACT

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|37827807|gb|BJ585819.1|BJ585819
EST:     ACCGATGGACTATGTCCGCGTTACTAGCGCTGCATG                         TGCCAAAATATTCAATATTTATCCGCGGAAAGGAGCGGTGCTGCCAGGCTC
genomic: ACCGATGGACTATGTCCGCGTTACTAGCGCTGCATGgtgagtttat ... aacttgttagTGCCAAAATATTCAATATTTATCCGCGGAAAGGAGCGGTGCTGCCAGGCTC
EST: gi|37827078|gb|BJ585090.1|BJ585090
EST:     TCCGGCAAAATTTCACCGATGGACTATGTCCGCGTTACTAGCGCTGCATG                         TGCCAAAATATTCAATATTTATCCGCGGAAAGGAGCGGTGCTGCCAGGCTC
genomic: TCCGGCAAAATTTCACCGATGGACTATGTCCGCGTTACTAGCGCTGCATGgtgagtttat ... aacttgttagTGCCAAAATATTCAATATTTATCCGCGGAAAGGAGCGGTGCTGCCAGGCTC
EST: gi|37828630|gb|BJ586642.1|BJ586642
EST:     TCCGGCAAAATTTCACCGATGGACTATGTCCGCGTTACTAGCGCTGCATG                         TGCCAAAATATTCAATATTTATCCGCGGAAAGGAGCGGTGCTGCCAGGCTC
genomic: TCCGGCAAAATTTCACCGATGGACTATGTCCGCGTTACTAGCGCTGCATGgtgagtttat ... aacttgttagTGCCAAAATATTCAATATTTATCCGCGGAAAGGAGCGGTGCTGCCAGGCTC
EST: gi|208361856|gb|DC950128.1|DC950128
EST:     AATTTCACCGATGGACTATGTCCGCGTTACTAGCGCTGCATG                         TGCCAAAATATTCAATATTTATCCGCGGAAAGGAGCGGTGCTGCCAGGCTC
genomic: AATTTCACCGATGGACTATGTCCGCGTTACTAGCGCTGCATGgtgagtttat ... aacttgttagTGCCAAAATATTCAATATTTATCCGCGGAAAGGAGCGGTGCTGCCAGGCTC

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: 28 (upstream exon), 26 (downstream exon)
Score: 4

AATTCCGGCAAAATTTCACCGATGGACTATGTCCGCGTTACTAGCGCTGCATGgtgagtttat ... aacttgttagTGCCAAAATATTCAATATTTATCCGCGGAAAGGAGCGGTGCTGCCAGGCTCTGATGCAGACATTATCATTTTGAACCCAAATGCAACTACTACTATATCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaaggaacggaggtccttattctgtgctttgtgtggattgtgcaacttgttagTGCCAAAATATTCAATATTTATCCGCGGAAAGGAGCGGTGCTGCCAGGCTCTGATGCAGACATTATCATTTTGAACCCAAATGCAACTACTACTATATCC
                  ttattct  TA-rich tract