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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaagcagttgccttttgtcgagcttcgtttggtagcaaatagtagaatgatgagggttagaactgaattagagtgggcttctctatgtgagaattacagGAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTGAGATCTTTGACGTTGATCGCATGTCCGGTTTGATCCACGGACCGTCGTC

Basic information

species Physcomitrella patens
transcript PP1S120_79V6.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S120_79V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os05g22970.1 (Oryza sativa), 3'ss of exon 7
----ttaagcagttgccttttgtcgagcttcgtttggtagcaaatagtagaatgatgagggttagaactg-aattagagtgggcttctctatgtgagaattacagGAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTGAGATCTTTGACGTTGATCGCATGTCCGGTTTGATCCACGGACCGTCGTC
     | |  | || || | |||     || | |   | | ||     | ||||| ||   ||||| |   ||    | ||   |        |      | |||| |  ||||||||  ||||||||||||| ||||||||||| ||||||||||| || |||||| |  |  | ||    |   |||     | | | || | 
gcatcttatgaatttccatctgt---attttgctc--tcgtaatgttgaaaatgaagatatttagagcaacaacgtaaatgtattaacacggcttttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTGAAATATTTGACCTGAACAGAATTGGGGCGGTGACTGCGGAAGCATCATG
















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|67692817|gb|BJ953050.1|BJ953050
EST:     CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACG                         GAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
genomic: CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACGgtaagcggct ... agaattacagGAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
EST: gi|15327367|gb|BI487991.1|BI487991
EST:     CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACG                         GAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
genomic: CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACGgtaagcggct ... agaattacagGAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
EST: gi|37821833|gb|BJ579899.1|BJ579899
EST:     CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACG                         GAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
genomic: CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACGgtaagcggct ... agaattacagGAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
EST: gi|67694462|gb|BJ954695.1|BJ954695
EST:     CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACG                         GAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
genomic: CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACGgtaagcggct ... agaattacagGAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
EST: gi|15729599|gb|BI741396.1|BI741396
EST:     CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACG                         GAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
genomic: CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACGgtaagcggct ... agaattacagGAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
EST: gi|7583583|gb|AW699492.1|AW699492
EST:     CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACG                         GAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
genomic: CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACGgtaagcggct ... agaattacagGAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
EST: gi|67574192|gb|BJ947016.1|BJ947016
EST:     CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACG                         GAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
genomic: CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACGgtaagcggct ... agaattacagGAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
EST: gi|162210552|gb|FC386848.1|FC386848
EST:     CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACG                         GAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
genomic: CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACGgtaagcggct ... agaattacagGAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
EST: gi|67569549|gb|BJ942373.1|BJ942373
EST:     CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACG                         GAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
genomic: CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACGgtaagcggct ... agaattacagGAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
EST: gi|162221907|gb|FC398175.1|FC398175
EST:     CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACG                         GAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
genomic: CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACGgtaagcggct ... agaattacagGAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
EST: gi|7582951|gb|AW699115.1|AW699115
EST:     CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACG                         GAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
genomic: CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACGgtaagcggct ... agaattacagGAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
EST: gi|162227422|gb|FC403156.1|FC403156
EST:     CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACG                         GAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
genomic: CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACGgtaagcggct ... agaattacagGAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
EST: gi|162266890|gb|FC443004.1|FC443004
EST:     CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACG                         GAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
genomic: CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACGgtaagcggct ... agaattacagGAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
EST: gi|7583223|gb|AW699387.1|AW699387
EST:     CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACG                         GAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
genomic: CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACGgtaagcggct ... agaattacagGAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
EST: gi|15261229|gb|BI436539.1|BI436539
EST:     CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACG                         GAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
genomic: CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACGgtaagcggct ... agaattacagGAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
EST: gi|67691738|gb|BJ951971.1|BJ951971
EST:     CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACG                         GAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
genomic: CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACGgtaagcggct ... agaattacagGAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
EST: gi|67697592|gb|BJ957825.1|BJ957825
EST:     CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACG                         GAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG
genomic: CGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACGgtaagcggct ... agaattacagGAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTG

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: 29 (upstream exon), 13 (downstream exon)
Score: 2

GGCATATTGGAATTACTGTTGATGACGTCTACAAAGCATGCGAACGTTTTGAGAAGCTAGGAGTTGAATTCGTGAAGCGCCCAGATGACGgtaagcggct ... agaattacagGAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTGAGATCTTTGACGTTGATCGCATGTCCGGTTTGATCCACGGACCGTCGTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatgatgagggttagaactgaattagagtgggcttctctatgtgagaattacagGAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTGAGATCTTTGACGTTGATCGCATGTCCGGTTTGATCCACGGACCGTCGTC
                   tgaatta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaagcagttgccttttgtcgagcttcgtttggtagcaaatagtagaatgatgagggttagaactgaattagagtgggcttctctatgtgagaattacagGAAGGATGAAGGGACTTGCATTTATCAAGGACCCTGATGGTTACTGGATTGAGATCTTTGACGTTGATCGCATGTCCGGTTTGATCCACGGACCGTCGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC