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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtactgtatgagcgaggcattgaagatttttcaatacagaacctctatattgtgttcttcggtgcatacatgtacatcaagtgtgtttggaatgtgtagGTGCAACTGATACGGATAAGGTTTCGCGCTCCAGAGTATGGTTGGACTACACAGAAAGTCTTCCATCTCTTGAATTTCATCGTTAATGGAG

Basic information

species Physcomitrella patens
transcript PP1S295_28V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S295_28V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv10s0116g00020.t01 (Vitis vinifera), 3'ss of exon 1
---------tgtactgt-atgagcgaggcattgaagatttttcaatacagaacctctatattgtgttcttcggtgcatacatgtacatcaagtgtgtttggaatgtgtagGTGCAACTGATACGGATAAGGTTTCGCGCTCCAGAGTATGGTTGGACTACACAGAAAGTCTTCCATCTCTTGAATTTCATCGTTAATGGAG
         |  |||||  |||     | | |  || ||  |   |    || || ||| |||||   ||    |  ||    | |||  |     | || | || | || | ||||||||| ||||     |  | |  ||||||||||||||||| || ||||| || ||||||||  |||| |||||||| |||||||
gaattgtttttcactgtcgtgatttgtggagttgagcttgattgttgagaaatct-tatgttgtgcggtt----gactaagatttcattga-----tgtgcactgcgcagATTCAACTGATAAGGATTGAACTGAGAGTGCCAGAGTATGGTTGGACGACGCAGAAGGTTTTCCATCTTATGAACTTCATCGTCAATGGAG

upper sequence: PP1S295_28V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv00s2255g00010.t01 (Vitis vinifera), 3'ss of exon 1
----tgtactgtatgagcgaggcattgaagatttttcaatacagaacctctatattgtgttcttcggtgcatacatgtacatcaagtgtgtttggaatgtgtagGTGCAACTGATACGGATAAGGTTTCGCGCTCCAGAGTATGGTTGGACTACACAGAAAGTCTTCCATCTCTTGAATTTCATCGTTAATGGAG
    |||  |  |    || |   |      ||   |   |  |       || || |||| | ||||  |   |  |        ||||     | || | || | ||||||||| ||||     |  | |  ||||||||||||||||| || ||||| || ||||||||  |||| |||||||| |||||||
gaattgtttttcactgccgtgatttgtggagttgagcttgattgttgagaaatcttatgttgtgcggttgactaagatttcattgatgtgc----actgcgcagATTCAACTGATAAGGATTGAACTGAGAGTGCCAGAGTATGGTTGGACGACGCAGAAGGTTTTCCATCTTATGAACTTCATCGTCAATGGAG
















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|100358043|gb|BY965443.1|BY965443
EST:     TCTGGCTGGGACTGGCGATTGCGTACGCTGTGATCGCCGTGATCGCGCTG                         GTGCAACTGATACGGATAAGGTTTCGCGCTCCAGAGTATGGTTGGACTACA
genomic: TCTGGCTGGGACTGGCGATTGCGTACGCTGTGATCGCCGTGATCGCGCTGgtacctgcgg ... gaatgtgtagGTGCAACTGATACGGATAAGGTTTCGCGCTCCAGAGTATGGTTGGACTACA
EST: gi|67716278|gb|BJ966538.1|BJ966538
EST:     TCTGGCTGGGACTGGCGATTGCGTACGCTGTGATCGCCGTGATCGCGCTG                         GTGCAACTGATACGGATAAGGTTTCGCGCTCCAGAGTATGGTTGGACTACA
genomic: TCTGGCTGGGACTGGCGATTGCGTACGCTGTGATCGCCGTGATCGCGCTGgtacctgcgg ... gaatgtgtagGTGCAACTGATACGGATAAGGTTTCGCGCTCCAGAGTATGGTTGGACTACA
EST: gi|67704141|gb|BJ964374.1|BJ964374
EST:     TCTGGCTGGNACTGGCGATTGCGTACGCTGTGATCGCCGTGATCGCGCTG                         GTGCAACTGATACGGATAAGGNTTCGCGCTCCANAGTATGGTTGGACTACA
genomic: TCTGGCTGGGACTGGCGATTGCGTACGCTGTGATCGCCGTGATCGCGCTGgtacctgcgg ... gaatgtgtagGTGCAACTGATACGGATAAGGTTTCGCGCTCCAGAGTATGGTTGGACTACA
EST: gi|208372289|gb|DC936447.1|DC936447
EST:     TCTGGCTGGGACTGGCGATTGCGTACGCTGTGATCGCCGTGATCGCGCTG                         GTGCAACTGATACGGATAAGGTTTCGCGCTCCAGAGTATGGTTGGACTACA
genomic: TCTGGCTGGGACTGGCGATTGCGTACGCTGTGATCGCCGTGATCGCGCTGgtacctgcgg ... gaatgtgtagGTGCAACTGATACGGATAAGGTTTCGCGCTCCAGAGTATGGTTGGACTACA
EST: gi|100377699|gb|BY986358.1|BY986358
EST:     TCTGGCTGGGACTGGCGATTGCATACGCTGTGATCGCCGTGATCGCGCTG                         GTGCAACTGATACGGATAAGGTTTCTCGCTCCAGAGTATGGTTGGACTACA
genomic: TCTGGCTGGGACTGGCGATTGCGTACGCTGTGATCGCCGTGATCGCGCTGgtacctgcgg ... gaatgtgtagGTGCAACTGATACGGATAAGGTTTCGCGCTCCAGAGTATGGTTGGACTACA
EST: gi|100356111|gb|BY946202.1|BY946202
EST:     TCTGGCTGGGACTGGCGATTGCGTACGCTGTGATCGCCGTGATCGCGCTG                         GTGCAACTGATACGGATAAGGTTTCGCGCTCCAGAGTATGGTTGGACTACA
genomic: TCTGGCTGGGACTGGCGATTGCGTACGCTGTGATCGCCGTGATCGCGCTGgtacctgcgg ... gaatgtgtagGTGCAACTGATACGGATAAGGTTTCGCGCTCCAGAGTATGGTTGGACTACA
EST: gi|67508414|gb|BJ941281.1|BJ941281
EST:     TCTGGCTGGGACTGGCGATTGCGTACGCTGTGATCGCCGTGATCGCGCTG                         GTGCAACTGATACGGATAAGGTTTCGCGCTCCAGAGTATGGTTGGACTACA
genomic: TCTGGCTGGGACTGGCGATTGCGTACGCTGTGATCGCCGTGATCGCGCTGgtacctgcgg ... gaatgtgtagGTGCAACTGATACGGATAAGGTTTCGCGCTCCAGAGTATGGTTGGACTACA
EST: gi|208355715|gb|DC910613.1|DC910613
EST:     TCTGGCTGGGACTGGCGATTGCGTACGCTGTGATCGCCGTGATCGCGCTG                         GTGCAACTGATACGGATAAGGTTTCGCGCTCCAGAGTATGGTTGGACTACA
genomic: TCTGGCTGGGACTGGCGATTGCGTACGCTGTGATCGCCGTGATCGCGCTGgtacctgcgg ... gaatgtgtagGTGCAACTGATACGGATAAGGTTTCGCGCTCCAGAGTATGGTTGGACTACA
EST: gi|208374316|gb|DC940673.1|DC940673
EST:     TCTGGCTGGGACTGGCGATTGCGTACGCTGTGATCGCCGTGATCGCGCTG                         GTGCAACTGATACGGATAAGGTTTCGCGCTCCAGAGTATGGTTGGACTACA
genomic: TCTGGCTGGGACTGGCGATTGCGTACGCTGTGATCGCCGTGATCGCGCTGgtacctgcgg ... gaatgtgtagGTGCAACTGATACGGATAAGGTTTCGCGCTCCAGAGTATGGTTGGACTACA

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), 34 (downstream exon)
Score: 9

TGCGGATTGGTGGCGTCGGGTGGACTCGTCCGTGCTCTGGCAGGAGCGCATCTGGCTGGGACTGGCGATTGCGTACGCTGTGATCGCCGTGATCGCGCTGgtacctgcgg ... gaatgtgtagGTGCAACTGATACGGATAAGGTTTCGCGCTCCAGAGTATGGTTGGACTACACAGAAAGTCTTCCATCTCTTGAATTTCATCGTTAATGGAG




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