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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatttgacctgattaagacggactttgatatacatgtctgggacttgttgttcttgagagctgtgtgtatcactgaaagtattaatgggtattttgcagGTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTGATATATGCAAATGTCACATATGAGGACATTTTACTCAAG

Basic information

species Physcomitrella patens
transcript PP1S165_105V6.1
intron # 5
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|162157574|gb|FC333832.1|FC333832
EST:     GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAG                         GTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
genomic: GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAGgtagtaatca ... tattttgcagGTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
EST: gi|100411604|gb|BY992247.1|BY992247
EST:     GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAG                         GTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
genomic: GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAGgtagtaatca ... tattttgcagGTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
EST: gi|100422280|gb|BY976296.1|BY976296
EST:     GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCCTGTATCAG                         GTTGCCAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATA
genomic: GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAGgtagtaatca ... tattttgcagGTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATA
EST: gi|208352513|gb|DC910213.1|DC910213
EST:     GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAG                         GTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
genomic: GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAGgtagtaatca ... tattttgcagGTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
EST: gi|162232093|gb|FC407695.1|FC407695
EST:     GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAG                         GTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
genomic: GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAGgtagtaatca ... tattttgcagGTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
EST: gi|100409366|gb|BY991976.1|BY991976
EST:     GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAN                         GTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
genomic: GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAGgtagtaatca ... tattttgcagGTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
EST: gi|100448582|gb|CJ972881.1|CJ972881
EST:     GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAG                         GTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAAACTAAAATATCTTTG
genomic: GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAGgtagtaatca ... tattttgcagGTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
EST: gi|100390506|gb|BY952914.1|BY952914
EST:     GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAG                         GTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
genomic: GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAGgtagtaatca ... tattttgcagGTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
EST: gi|208358223|gb|DC939391.1|DC939391
EST:     GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAG                         GTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
genomic: GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAGgtagtaatca ... tattttgcagGTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
EST: gi|162216664|gb|FC392730.1|FC392730
EST:     GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAG                         GTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
genomic: GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAGgtagtaatca ... tattttgcagGTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
EST: gi|7583600|gb|AW699509.1|AW699509
EST:     GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAG                         GTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
genomic: GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAGgtagtaatca ... tattttgcagGTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
EST: gi|208368598|gb|DC940019.1|DC940019
EST:     GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAG                         GTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAAATATCTTTG
genomic: GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAGgtagtaatca ... tattttgcagGTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
EST: gi|208365412|gb|DC950879.1|DC950879
EST:     GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAG                         GTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
genomic: GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAGgtagtaatca ... tattttgcagGTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
EST: gi|100375067|gb|BY949170.1|BY949170
EST:     AGAATTTGGAATGGTGGNCGGTGGNACTGGGTCT-ACTCCCATGTATCAG                         GTTTGCA-GAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTT
genomic: AGAATTTGGAATGGTGGCCGGTGGAACTGG-TCTTACTCCCATGTATCAGgtagtaatca ... tattttgcagGTT-GCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTT
EST: gi|100384199|gb|BY950585.1|BY950585
EST:     GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAG                         GTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
genomic: GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAGgtagtaatca ... tattttgcagGTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
EST: gi|208391805|gb|DC942339.1|DC942339
EST:     GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTGCTCCCATGTATCAG                         GTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
genomic: GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAGgtagtaatca ... tattttgcagGTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
EST: gi|100390026|gb|BY989106.1|BY989106
EST:     GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAG                         GTTGCAAGAGCGATTCTGGAGAACTCTCATGA
genomic: GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAGgtagtaatca ... tattttgcagGTTGCAAGAGCGATTCTGGAGAACTCTCATGA
EST: gi|162222464|gb|FC397198.1|FC397198
EST:     GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAG                         GTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
genomic: GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAGgtagtaatca ... tattttgcagGTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
EST: gi|208378861|gb|DC927563.1|DC927563
EST:     GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAG                         GTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
genomic: GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAGgtagtaatca ... tattttgcagGTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
EST: gi|208374639|gb|DC931978.1|DC931978
EST:     GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAG                         GTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
genomic: GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAGgtagtaatca ... tattttgcagGTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
EST: gi|208357969|gb|DC938840.1|DC938840
EST:     GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAG                         GTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG
genomic: GAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAGgtagtaatca ... tattttgcagGTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTG

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: 34 (upstream exon), 27 (downstream exon)
Score: 8

GGACGCTTTAAATACAAACCCAACCAAGTTAGAGAATTTGGAATGGTGGCCGGTGGAACTGGTCTTACTCCCATGTATCAGgtagtaatca ... tattttgcagGTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTGATATATGCAAATGTCACATATGAGGACATTTTACTCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttgttcttgagagctgtgtgtatcactgaaagtattaatgggtattttgcagGTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTGATATATGCAAATGTCACATATGAGGACATTTTACTCAAG
                                   tattaat  putative branch site (score: 8)
                               aaagtattaat  TA-rich tract