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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgtgtgtacgtgtgtttgtgtgggctgaaagattcctcgaggggagttttgggcagagtgggattgatgtgtagaatttgaatgtttttattttgtagGTGTTGAAAAGGGATATTCCATGGGAGATGTACATGACAGCCAAGCTGATCAATAGCACTGGGTTGCAACTGCTGAGGCGATATGACCACCGTCCCGAAA

Basic information

species Physcomitrella patens
transcript PP1S51_320V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S51_320V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT3G42050.1 (Arabidopsis thaliana), 3'ss of exon 2
-tgtgtgtgtacgtgtgtttgtgtgggctgaaagattcctcgaggggagttttg-ggcagagtgggattgatgtgtagaatttgaatgtt--tttattttgtagGTGTTGAAAAGGGATATTCCATGGGAGATGTACATGACAGCCAAGCTGATCAATAGCACTGGGTTGCAACTGCTGAGGCGATATGACCACCGTCCCGAAA
      ||  |  |   | | |||    |     | |  |  | |    |  || ||    ||  ||||    |||| | ||  | ||||  |||| |||| |||| ||||||||||| |||||||||||||  |||||||   | |||||| |       |  ||  | || ||  | ||||| |||||  |    || ||||
caaaccgtcaatatagatctttgtaactttggctacttataaatgtttatcatgtggttttgtcagattt---tgta-atttctattgttggtttactttgcagGTATTGAAAAGGGACATTCCATGGGAGACTTACATGAACACTAAGCTGGTTTCAGCTAAAGGTCTCCAGCTCTTAAGGCGCTATGATAAAAAACCTGAAA
















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|208391479|gb|DC937627.1|DC937627
EST:     GAGGGGGATTGGAAGCCATGACGACGGACACTGAGCTCACTAGAGAGGAG                         GTGTTGAAAAGGGATATTCCATGGGAGATGTACATGACAGCCAAGCTGATC
genomic: GAGGGGGATTGGAAGCCATGACGACGGACACTGAGCTCACTAGAGAGGAGgtagggtggt ... tattttgtagGTGTTGAAAAGGGATATTCCATGGGAGATGTACATGACAGCCAAGCTGATC
EST: gi|100396694|gb|BY953780.1|BY953780
EST:     GAGGGGGATTGGAAGCCATGACGACGGACACTGAGCTCACTAGAGAGGAG                         GTGTTGAAAAGGGATATTCCATGGGAGATGTACATGACAGCCAAGCTGATC
genomic: GAGGGGGATTGGAAGCCATGACGACGGACACTGAGCTCACTAGAGAGGAGgtagggtggt ... tattttgtagGTGTTGAAAAGGGATATTCCATGGGAGATGTACATGACAGCCAAGCTGATC
EST: gi|100434945|gb|BY960883.1|BY960883
EST:     GAGGGGGATTGGAAGCCATGACGACGGACACTGAGCTCACTAGAGAGGAG                         GTGTTGAAAAGGGATATTCCATGGGAGATGTACATGACAGCCAAGCTGATC
genomic: GAGGGGGATTGGAAGCCATGACGACGGACACTGAGCTCACTAGAGAGGAGgtagggtggt ... tattttgtagGTGTTGAAAAGGGATATTCCATGGGAGATGTACATGACAGCCAAGCTGATC
EST: gi|162201234|gb|FC378469.1|FC378469
EST:     GAGGGGGATTGGAAGCCATGACGACGGACACTGAGCTCACTAGAGAGGAG                         GTGTTGAAAAGGGATATTCCATGGGAGATGTACATGACAGCCAAGCTGATC
genomic: GAGGGGGATTGGAAGCCATGACGACGGACACTGAGCTCACTAGAGAGGAGgtagggtggt ... tattttgtagGTGTTGAAAAGGGATATTCCATGGGAGATGTACATGACAGCCAAGCTGATC
EST: gi|100448937|gb|CJ973236.1|CJ973236
EST:     GAGGGGGATTGGAAGCCATGACGACGGACACTGAGCTCACTAGAGAGGAG                         GTGTTGAAAAGGGATATTCCATGGGAGATGTACATGACAGCCAAGCTGATC
genomic: GAGGGGGATTGGAAGCCATGACGACGGACACTGAGCTCACTAGAGAGGAGgtagggtggt ... tattttgtagGTGTTGAAAAGGGATATTCCATGGGAGATGTACATGACAGCCAAGCTGATC
EST: gi|100411612|gb|BY992251.1|BY992251
EST:     GAGGGGGATTGGAAGCCATGACGACGGACACTGAGCTCACTAGAGAGGAG                         GTGTTGAAAAGGGATATTCCATGGGAGATGTACATGACAGCCAAGCTGATC
genomic: GAGGGGGATTGGAAGCCATGACGACGGACACTGAGCTCACTAGAGAGGAGgtagggtggt ... tattttgtagGTGTTGAAAAGGGATATTCCATGGGAGATGTACATGACAGCCAAGCTGATC
EST: gi|162194589|gb|FC369980.1|FC369980
EST:     GCCATGACGACGGACACTGAGCTCACTAGAGAGGAG                         GTGTTGAAAAGGGATATTCCATGGGAGATGTACATGACAGCCAAGCTGATC
genomic: GCCATGACGACGGACACTGAGCTCACTAGAGAGGAGgtagggtggt ... tattttgtagGTGTTGAAAAGGGATATTCCATGGGAGATGTACATGACAGCCAAGCTGATC

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: 33 (upstream exon), 33 (downstream exon)
Score: 11

GCAGGAGGGGCAGATTTGGTACTGCTGATTGCGTTTCGACCGGAAGAGGAGAGGGGGATTGGAAGCCATGACGACGGACACTGAGCTCACTAGAGAGGAGgtagggtggt ... tattttgtagGTGTTGAAAAGGGATATTCCATGGGAGATGTACATGACAGCCAAGCTGATCAATAGCACTGGGTTGCAACTGCTGAGGCGATATGACCACCGTCCCGAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagttttgggcagagtgggattgatgtgtagaatttgaatgtttttattttgtagGTGTTGAAAAGGGATATTCCATGGGAGATGTACATGACAGCCAAGCTGATCAATAGCACTGGGTTGCAACTGCTGAGGCGATATGACCACCGTCCCGAAA
                  gattgat  putative branch site (score: 11)
                                         tttttatttt  putative PPT
                            tagaatttgaatgttt  TA-rich tract