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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGGTCTTGATGTAGACTCTCTCGTTGTCTCTCATATTCAAGTCAACCAGGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgctcctttgtcccacttttgtattgtcgtttcttcagttctcgattctctaggacgatcgtgaaagacgtatctgtgaaacttatgctaattctttattttgtgatgcag

Basic information

species Physcomitrella patens
transcript PP1S22_76V6.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S22_76V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: LOC_Os09g08430.1 (Oryza sativa), 5'ss of exon 5
AAGGGTCTTGATGTAGACTCTCTCGTTGTCTCTCATATTCAAGTCAACCAGGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgctcctttgtcccacttttgtattgtcgtttcttcagttct-cgattctctaggacgatcgtgaaagacgtatctgtgaaacttatgctaattctttattttgtgatgcag
|| ||||| ||||| ||  ||||   ||| || || |||||||| |||||||| || |||||| |  | ||||| |||||||| || ||||| |||||||||||||   |  |   | ||  ||||||||  || ||| |  |||||   ||| || |    |    |  || ||    | ||                                   
AAAGGTCTGGATGTTGATACTCTTTATGTGTCCCACATTCAAGTTAACCAGGCCCAGAAGCAGAGGCGCCGTACCTACCGTGCTCATGGACGCATCAACCgtaagt---ttgtcaatacc-tttttgtatgctc-tttgtagagttcggtgatgctttgtctcatgagcaaatgatac-tttgcag--------------------------------
















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|162262297|gb|FC437624.1|FC437624
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|67694098|gb|BJ954331.1|BJ954331
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|162270731|gb|FC446344.1|FC446344
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|162224836|gb|FC400836.1|FC400836
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|162227758|gb|FC402686.1|FC402686
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|18350710|gb|BJ182761.1|BJ182761
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|15728661|gb|BI740905.1|BI740905
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|162262298|gb|FC437625.1|FC437625
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|19781574|gb|BQ039741.1|BQ039741
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|162267059|gb|FC443290.1|FC443290
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|37830037|gb|BJ588049.1|BJ588049
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|37841076|gb|BJ599084.1|BJ599084
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|162273803|gb|FC449734.1|FC449734
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|162267060|gb|FC443291.1|FC443291
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|18365111|gb|BJ197185.1|BJ197185
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAG
EST: gi|18363914|gb|BJ195986.1|BJ195986
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|18361968|gb|BJ194035.1|BJ194035
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|37842317|gb|BJ600325.1|BJ600325
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|37845725|gb|BJ603733.1|BJ603733
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|162224837|gb|FC400837.1|FC400837
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|18364653|gb|BJ196726.1|BJ196726
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAG
EST: gi|67692927|gb|BJ953160.1|BJ953160
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|162205889|gb|FC381335.1|FC381335
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|162270730|gb|FC446343.1|FC446343
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|162272796|gb|FC447978.1|FC447978
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|37834233|gb|BJ592245.1|BJ592245
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|162205890|gb|FC381336.1|FC381336
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|37845346|gb|BJ603354.1|BJ603354
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|18365599|gb|BJ197676.1|BJ197676
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAANGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|18345004|gb|BJ177045.1|BJ177045
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|18352797|gb|BJ184852.1|BJ184852
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCC
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCC
EST: gi|15728104|gb|BI740621.1|BI740621
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|67571863|gb|BJ944687.1|BJ944687
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|37824207|gb|BJ582273.1|BJ582273
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|67569660|gb|BJ942484.1|BJ942484
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|18346488|gb|BJ178531.1|BJ178531
EST:     NGCGCAAAAGCAGCGTANACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTG
EST: gi|162273804|gb|FC449735.1|FC449735
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
EST: gi|162227744|gb|FC402685.1|FC402685
EST:     GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACC                         CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG
genomic: GGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGG

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: 144

AAGGGTCTTGATGTAGACTCTCTCGTTGTCTCTCATATTCAAGTCAACCAGGCGCAAAAGCAGCGTAGACGTACTTACCGTGCCCACGGACGTATCAACCgtaagtcgct ... tgtgatgcagCTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAG




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