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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgtctcttattatgcagagcagtatgtgatctggattgtgaatatcatgccgaaattgcttttaattgaccagcttgtggagtcggtgattttggcagGTACCTGATAGCGTCACATACAACCGACTATAGGAACCCAAACCTCTTCCTCAATACGATTGCGGTCTGCTGGTTGGTGATTGCCAAGTTTCCGAATATG

Basic information

species Physcomitrella patens
transcript PP1S123_9V6.1
intron # 2
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|162208070|gb|FC384239.1|FC384239
EST:     CGCCAGCTCACTCGCAACCGGAAGTTTTTGACCGTCGTTCCTGTCGTCCT                         GTACCTGAGAGCGTCACATACAACCGACTATAGGAACCCAAACTTCTTCCT
genomic: CGCCAGCTCACTCGCAACCGGAAGTTTTTGACCGTCGTTCCTGTCGTCCTgtgagtagct ... attttggcagGTACCTGATAGCGTCACATACAACCGACTATAGGAACCCAAACCTCTTCCT
EST: gi|208347824|gb|DC921137.1|DC921137
EST:     CGCCAGCTCACTCGCAACCGGAAGTTTTTGACCGTCGTTCCTGTCGTCCT                         GTACCTGATAGCGTCACATACAACCGACTATAGGAACCCAAACCTCTTCCT
genomic: CGCCAGCTCACTCGCAACCGGAAGTTTTTGACCGTCGTTCCTGTCGTCCTgtgagtagct ... attttggcagGTACCTGATAGCGTCACATACAACCGACTATAGGAACCCAAACCTCTTCCT
EST: gi|67693578|gb|BJ953811.1|BJ953811
EST:     CGCCAGCTCACTCGCAACCGGAAGTTTTTGACCGTCGTTCCTGTCGTCCT                         GTACCTGATAGCGTCACATACAACCGACTATAGGAACCCAAACCTCTTCCT
genomic: CGCCAGCTCACTCGCAACCGGAAGTTTTTGACCGTCGTTCCTGTCGTCCTgtgagtagct ... attttggcagGTACCTGATAGCGTCACATACAACCGACTATAGGAACCCAAACCTCTTCCT
EST: gi|162251000|gb|FC426342.1|FC426342
EST:     CGCCAGCTCACTCGCAACCGGAAGTTTTTGACCGTCGTTCCTGTCGTCCT                         GTACCTGATAGCGTCACATACAACCGACTATAGGAACCCAAACCTCTTCCT
genomic: CGCCAGCTCACTCGCAACCGGAAGTTTTTGACCGTCGTTCCTGTCGTCCTgtgagtagct ... attttggcagGTACCTGATAGCGTCACATACAACCGACTATAGGAACCCAAACCTCTTCCT
EST: gi|208387217|gb|DC945516.1|DC945516
EST:     CGCCAGCTCACTCGCAACCGGAAG-TTTTGACCGTCGTTCCTGTCGTCCT                         GTACCTGATAGCGTCACATACAACCGACTATAGGAACCCAAACCTCTTCCT
genomic: CGCCAGCTCACTCGCAACCGGAAGTTTTTGACCGTCGTTCCTGTCGTCCTgtgagtagct ... attttggcagGTACCTGATAGCGTCACATACAACCGACTATAGGAACCCAAACCTCTTCCT
EST: gi|67570276|gb|BJ943100.1|BJ943100
EST:     CGCCAGCTCACTCGCAACCGGAAGTTTTTGACCGTCGTTCCTGTCGTCCT                         GTACCTGATAGCGTCACATACAACCGACTATAGGAACCCAAACCTCTTCCT
genomic: CGCCAGCTCACTCGCAACCGGAAGTTTTTGACCGTCGTTCCTGTCGTCCTgtgagtagct ... attttggcagGTACCTGATAGCGTCACATACAACCGACTATAGGAACCCAAACCTCTTCCT
EST: gi|208380086|gb|DC914636.1|DC914636
EST:     CGCCAGCTCACTCGCAACCGGAAGTTTTTGACCGTCGTTCCTGTCGTCCT                         GTACCTGATAGCGTCACATACAACCGACTATAGGAACCCAAACCTCTTCCT
genomic: CGCCAGCTCACTCGCAACCGGAAGTTTTTGACCGTCGTTCCTGTCGTCCTgtgagtagct ... attttggcagGTACCTGATAGCGTCACATACAACCGACTATAGGAACCCAAACCTCTTCCT
EST: gi|67570307|gb|BJ943131.1|BJ943131
EST:     CGCCAGCTCACTCGCAACCGGAAGTTTTTGACCGTCGTTCCTGTCGTCCT                         GTACCTGATAGCGTCACATACAACCGACTATAGGAACCCAAACCTCTTCCT
genomic: CGCCAGCTCACTCGCAACCGGAAGTTTTTGACCGTCGTTCCTGTCGTCCTgtgagtagct ... attttggcagGTACCTGATAGCGTCACATACAACCGACTATAGGAACCCAAACCTCTTCCT
EST: gi|208366110|gb|DC955211.1|DC955211
EST:     CGCCAGCTCACTCGCAACCGGAAGTTTTTGACCGTCGTTCCTGTCGTCCT                         GTACCTGATAGCGTCACATACAACCGACTATAGGAACCCAAACCTCTTCCT
genomic: CGCCAGCTCACTCGCAACCGGAAGTTTTTGACCGTCGTTCCTGTCGTCCTgtgagtagct ... attttggcagGTACCTGATAGCGTCACATACAACCGACTATAGGAACCCAAACCTCTTCCT
EST: gi|208374713|gb|DC948671.1|DC948671
EST:     CGCCAGCTCACTCGCAACCGGAAGTTTTTGACCGTCGTTCCTGTCGTCCT                         GTACCTGATAGCGTCACATACAACCGACTATAGGAACCCAAACCTCTTCCT
genomic: CGCCAGCTCACTCGCAACCGGAAGTTTTTGACCGTCGTTCCTGTCGTCCTgtgagtagct ... attttggcagGTACCTGATAGCGTCACATACAACCGACTATAGGAACCCAAACCTCTTCCT
EST: gi|208358318|gb|DC934539.1|DC934539
EST:     CGCCAGCTCACTCGCAACCGGAAGTTTTTGACCGTCGTTCCTGTCGTCCT                         GTACCTGATAGCGTCACATACAACCGACTATAGGAACCCAAACCTCTTCCT
genomic: CGCCAGCTCACTCGCAACCGGAAGTTTTTGACCGTCGTTCCTGTCGTCCTgtgagtagct ... attttggcagGTACCTGATAGCGTCACATACAACCGACTATAGGAACCCAAACCTCTTCCT
EST: gi|208390884|gb|DC942216.1|DC942216
EST:     CGCCAGCTCACTCGCAACCGGAAGTTTTTGACCGTCGTTCCTGTCGTCCT                         GTACCTGATAGCGTCACATACAACCGACTATAGGAACCCAAACCTCTTCCT
genomic: CGCCAGCTCACTCGCAACCGGAAGTTTTTGACCGTCGTTCCTGTCGTCCTgtgagtagct ... attttggcagGTACCTGATAGCGTCACATACAACCGACTATAGGAACCCAAACCTCTTCCT
EST: gi|67693546|gb|BJ953779.1|BJ953779
EST:     CGCCAGCTCACTCGCAACCGGAAGTTTTTGACCGTCGTTCCTGTCGTCCT                         GTACCTGATAGCGTCACATACAACCGACTATAGGAACCCAAACCTCTTCCT
genomic: CGCCAGCTCACTCGCAACCGGAAGTTTTTGACCGTCGTTCCTGTCGTCCTgtgagtagct ... attttggcagGTACCTGATAGCGTCACATACAACCGACTATAGGAACCCAAACCTCTTCCT
EST: gi|208381726|gb|DC928389.1|DC928389
EST:     CGCCAGCTCACTCGCAACCGGAAGTTTTTGACCGTCGTTCCTGTCGTCCT                         GTACCTGATAGCGTCACATACAACCGACTATAGGAACCCAAACCTCTTCCT
genomic: CGCCAGCTCACTCGCAACCGGAAGTTTTTGACCGTCGTTCCTGTCGTCCTgtgagtagct ... attttggcagGTACCTGATAGCGTCACATACAACCGACTATAGGAACCCAAACCTCTTCCT
EST: gi|162208071|gb|FC384240.1|FC384240
EST:     CGCCAGCTCACTCGCAACCGGAAGTTTTTGACCGTCGTTCCTGTCGTCCT                         GTACCTGATAGCGTCACATACAACCGACTATAGGAACCCAAACCTCTTCCT
genomic: CGCCAGCTCACTCGCAACCGGAAGTTTTTGACCGTCGTTCCTGTCGTCCTgtgagtagct ... attttggcagGTACCTGATAGCGTCACATACAACCGACTATAGGAACCCAAACCTCTTCCT

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), 33 (downstream exon)
Score: 32

ACCAAGGTGATTATGGGAAGCTTACATGGTGGGAGCAAGTGGACGATGGGCGCCAGCTCACTCGCAACCGGAAGTTTTTGACCGTCGTTCCTGTCGTCCTgtgagtagct ... attttggcagGTACCTGATAGCGTCACATACAACCGACTATAGGAACCCAAACCTCTTCCTCAATACGATTGCGGTCTGCTGGTTGGTGATTGCCAAGTTTCCGAATATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcatgccgaaattgcttttaattgaccagcttgtggagtcggtgattttggcagGTACCTGATAGCGTCACATACAACCGACTATAGGAACCCAAACCTCTTCCTCAATACGATTGCGGTCTGCTGGTTGGTGATTGCCAAGTTTCCGAATATG
                    aattgac  putative branch site (score: 32)
         aaattgcttttaatt  TA-rich tract