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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaagattgtactcagtgttaaaagtttctatccctgaatgtttgtcattcaattcagaaataagtcttactgaccacatagtttgttttcaatccatagACAGAGTTCATGGTGGACATGAAATGTGACGGATGCGTCAAGTCAGTGCGCACTAAGTTAGAACCCCTTGCTG

Basic information

species Physcomitrella patens
transcript PP1S19_254V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S19_254V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G175728_T01 (Zea mays), 3'ss of exon 2
gcaagattg-tactcagtgttaaaagtttctatccctgaa--tgtttgtcattcaattcagaaataagtc--ttactgaccacatagtttgttttcaatccatagACAGAGTTCATGGTGGACATGAAATGTGACGGATGCGTCAAGTCAGTGCGCACTAAGTTAGAACCCCTTGCTG
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gctggttcacttcatgattctttgtgcattttctttagaaattgtttatgtcccaat---gaaacgagttagttaataatcttgtgcttgatat--gatctgaagACGGAATTCATGGTGGACATGAAATGTGAGGGATGTGTAACAGCTGTGAAAAACAAGCTGCAAACTCTTGAAG
















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|100357957|gb|BY965399.1|BY965399
EST:     GACAAAAATGGGGGAGAAGTTAAGGCGCAACTACCTGACTTGATG                         ACAGAGTTCATGGTGGACATGAAATGTGACGGATGCGTCAAGTCAGTGCGC
genomic: GACAAAAATGGGGGAGAAGTTAAGGCGCAACTACCTGACTTGATGgtaagaatta ... caatccatagACAGAGTTCATGGTGGACATGAAATGTGACGGATGCGTCAAGTCAGTGCGC
EST: gi|100421658|gb|BY976252.1|BY976252
EST:     GACAAAAATGGGGGAGAAGTTAAGGCGCAACTACCTGACTTGATG                         ACAGAGTTCATGGTGGACATGAAATGTGACGGATGCGTCAAGTCAGTGCGC
genomic: GACAAAAATGGGGGAGAAGTTAAGGCGCAACTACCTGACTTGATGgtaagaatta ... caatccatagACAGAGTTCATGGTGGACATGAAATGTGACGGATGCGTCAAGTCAGTGCGC
EST: gi|18325651|gb|BJ157648.1|BJ157648
EST:     GACAAAAATGGGGGAGAAGTTAAGGCGCAACTACCTGACTTGATG                         ACAGAGTTCATGGTGGACATGAAATGTGACGGATGCGTCAAGTCAGTGCGC
genomic: GACAAAAATGGGGGAGAAGTTAAGGCGCAACTACCTGACTTGATGgtaagaatta ... caatccatagACAGAGTTCATGGTGGACATGAAATGTGACGGATGCGTCAAGTCAGTGCGC
EST: gi|100440610|gb|BY962297.1|BY962297
EST:     GACAAAAATGGGGGAGAAGTTAAGGCGCAACTACCTGACTTGATG                         ACAGAGTTCATGGTGGACATGAAATGTGACGGATGCGTCAAGTCAGTGCGC
genomic: GACAAAAATGGGGGAGAAGTTAAGGCGCAACTACCTGACTTGATGgtaagaatta ... caatccatagACAGAGTTCATGGTGGACATGAAATGTGACGGATGCGTCAAGTCAGTGCGC
EST: gi|100405311|gb|BY955462.1|BY955462
EST:     GACAAAAATGGGGGAGAAGTTAAGGCGCAACTACCTGACTTGATG                         ACAGAGTTCATGGTGGACATGANATGTGACGGATGCGTCAAGTCAGTGCGC
genomic: GACAAAAATGGGGGAGAAGTTAAGGCGCAACTACCTGACTTGATGgtaagaatta ... caatccatagACAGAGTTCATGGTGGACATGAAATGTGACGGATGCGTCAAGTCAGTGCGC
EST: gi|100410559|gb|BY992161.1|BY992161
EST:     GACAAAAATGGGGGAGAAGTTAAGGCGCAACTACCTGACTTGATG                         ACAGAGTTCATGGTGGACATGAAATGTGACGGATGCGTCAAGTCAGTGCGC
genomic: GACAAAAATGGGGGAGAAGTTAAGGCGCAACTACCTGACTTGATGgtaagaatta ... caatccatagACAGAGTTCATGGTGGACATGAAATGTGACGGATGCGTCAAGTCAGTGCGC
EST: gi|162279579|gb|FC455344.1|FC455344
EST:     GACAAAAATGGGGGAGAAGTTAAGGCGCAACTACCTGACTTGATG                         ACAGAGTTCATGGTGGACATGAAATGTGACGGATGCGTCAAGTCAGTGCGC
genomic: GACAAAAATGGGGGAGAAGTTAAGGCGCAACTACCTGACTTGATGgtaagaatta ... caatccatagACAGAGTTCATGGTGGACATGAAATGTGACGGATGCGTCAAGTCAGTGCGC
EST: gi|100440335|gb|BY962181.1|BY962181
EST:     GACAAAAATGGGGGAGAAGTTAAGGCGCAACTACCTGACTTGATG                         ACAGAGTTCATGGTGGACATGAAATGTGACGGATGCGTCAAGTCAGTGCGC
genomic: GACAAAAATGGGGGAGAAGTTAAGGCGCAACTACCTGACTTGATGgtaagaatta ... caatccatagACAGAGTTCATGGTGGACATGAAATGTGACGGATGCGTCAAGTCAGTGCGC
EST: gi|162192045|gb|FC367258.1|FC367258
EST:     AGTTAAGGCGCAACTACCTGACTTGATG                         ACAGAGTTCATGGTGGACATGAAATGTGACGGATGCGTCAAGTCAGTGCGC
genomic: AGTTAAGGCGCAACTACCTGACTTGATGgtaagaatta ... caatccatagACAGAGTTCATGGTGGACATGAAATGTGACGGATGCGTCAAGTCAGTGCGC

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: 32 (upstream exon), 23 (downstream exon)
Score: 3

GACAAAAATGGGGGAGAAGTTAAGGCGCAACTACCTGACTTGATGgtaagaatta ... caatccatagACAGAGTTCATGGTGGACATGAAATGTGACGGATGCGTCAAGTCAGTGCGCACTAAGTTAGAACCCCTTGCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattcaattcagaaataagtcttactgaccacatagtttgttttcaatccatagACAGAGTTCATGGTGGACATGAAATGTGACGGATGCGTCAAGTCAGTGCGCACTAAGTTAGAACCCCTTGCTG
                       tactgac  putative branch site (score: 3)
                                     tttgttttc  putative PPT
           agaaataa  TA-rich tract