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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacatttttttgtcatctggaagcttttggtggatctcttgtatgaaggataagctctgttgcaacttgaatctggcaataactgacttctttgtgcctggtcaccttttcagGAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGGGTCGCAGTTATTGATTTGGTAGTTATGAGAGTATCTTCTGCTTTCAGTG

Basic information

species Physcomitrella patens
transcript PP1S7_175V6.1
intron # 10
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|18339632|gb|BJ171659.1|BJ171659
EST:     GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAG                         GAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
genomic: GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAGgtaacatttt ... accttttcagGAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
EST: gi|162238449|gb|FC414587.1|FC414587
EST:     GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACTCACTTCCTGAAG                         GAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
genomic: GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAGgtaacatttt ... accttttcagGAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
EST: gi|37829899|gb|BJ587911.1|BJ587911
EST:     GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAGG                         GAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
genomic: GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAGgtaacatttt ... accttttcagGAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
EST: gi|162173416|gb|FC349795.1|FC349795
EST:     GCCATTCGAGCAGGATACCCTTCCAATGGTGTGGAACTCACTTCCTGAAG                         GAACCAAGTGTTTGGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
genomic: GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAGgtaacatttt ... accttttcagGAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
EST: gi|162224268|gb|FC399514.1|FC399514
EST:     GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACTCACTTCCTGAAG                         GAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
genomic: GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAGgtaacatttt ... accttttcagGAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
EST: gi|37841561|gb|BJ599569.1|BJ599569
EST:     GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAG                         GAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
genomic: GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAGgtaacatttt ... accttttcagGAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
EST: gi|67699791|gb|BJ960024.1|BJ960024
EST:     GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAG                         GAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
genomic: GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAGgtaacatttt ... accttttcagGAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
EST: gi|37823266|gb|BJ581332.1|BJ581332
EST:     GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAG                         GAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
genomic: GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAGgtaacatttt ... accttttcagGAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
EST: gi|37828261|gb|BJ586273.1|BJ586273
EST:     GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAG                         GAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
genomic: GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAGgtaacatttt ... accttttcagGAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
EST: gi|162168455|gb|FC344119.1|FC344119
EST:     GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACTCACTTCCTGAAG                         GAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
genomic: GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAGgtaacatttt ... accttttcagGAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
EST: gi|208351458|gb|DC926304.1|DC926304
EST:     GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAG                         GAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
genomic: GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAGgtaacatttt ... accttttcagGAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
EST: gi|162250112|gb|FC427421.1|FC427421
EST:     GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACTCACTTCCTGAAG                         GAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
genomic: GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAGgtaacatttt ... accttttcagGAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
EST: gi|162258850|gb|FC434857.1|FC434857
EST:     GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAG                         GAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
genomic: GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAGgtaacatttt ... accttttcagGAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
EST: gi|162237814|gb|FC413923.1|FC413923
EST:     GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACTCACTTCCTGAAG                         GAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
genomic: GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAGgtaacatttt ... accttttcagGAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
EST: gi|37827562|gb|BJ585574.1|BJ585574
EST:     GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAG                         GAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
genomic: GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAGgtaacatttt ... accttttcagGAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
EST: gi|162158159|gb|FC333954.1|FC333954
EST:     GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACTCACTTCCTGAAG                         GAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
genomic: GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAGgtaacatttt ... accttttcagGAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
EST: gi|37825576|gb|BJ583642.1|BJ583642
EST:     GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAG                         GAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
genomic: GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAGgtaacatttt ... accttttcagGAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
EST: gi|37826374|gb|BJ584386.1|BJ584386
EST:     GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAG                         GAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
genomic: GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAGgtaacatttt ... accttttcagGAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
EST: gi|37853519|gb|BJ611527.1|BJ611527
EST:     GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAG                         GAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
genomic: GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAGgtaacatttt ... accttttcagGAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
EST: gi|162224254|gb|FC399513.1|FC399513
EST:     GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACTCACTTCCTGAAG                         GAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
genomic: GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAGgtaacatttt ... accttttcagGAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
EST: gi|162264775|gb|FC440342.1|FC440342
EST:     GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAG                         GAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
genomic: GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAGgtaacatttt ... accttttcagGAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
EST: gi|162215795|gb|FC390860.1|FC390860
EST:     GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACTCACTTCCTGAAG                         GAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG
genomic: GCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAGgtaacatttt ... accttttcagGAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGG

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: 11

GTCAAGGCTCGCACAAAGGGTGAAGCTGGTGCTGCTAAAACCCTATGCATGCCATTCGAGCAGGATACCCTTCCAATGGTGTCGAACACACTTCCTGAAGgtaacatttt ... accttttcagGAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGGGTCGCAGTTATTGATTTGGTAGTTATGAGAGTATCTTCTGCTTTCAGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgcaacttgaatctggcaataactgacttctttgtgcctggtcaccttttcagGAACCAAGTGTTTCGTATCAGGCAAACCTGCGAAGAAATGGGCTTTGTGGGGTCGCAGTTATTGATTTGGTAGTTATGAGAGTATCTTCTGCTTTCAGTG
                      aactgac  putative branch site (score: 11)
                                           tcaccttttc  putative PPT
                   aataact  TA-rich tract