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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcagaaatggtgtatttagcacagccataatcgcagagttatcaagatataaccttgccgatgggcttcctgactttgtgctcgtaaatctctgcacagCTATTAGCTTATCATCTGACAGTTCTGCGCGGCTTCAACGTGGACCAACCTCGGAACTTAGCCAAGAGTGTGACGACGTCATGA

Basic information

species Physcomitrella patens
transcript PP1S304_37V6.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S304_37V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: EDP02705 (Chlamydomonas reinhardtii), 3'ss of exon 17
--ttcagaaatgg-tgtatttagcac-agccataatcgcagagttatcaagatataacctt---gccgatgggcttcctgactttgtgctcgtaaatct---------ctgcacagCTATTAGCTTATCATCTGACAGTTCTGCGCGGCTTCAACG-TGGACCAACCTCGGAACTTAGCCAAGAGTGTGACGACGTCATGA-------------------------------------------
     ||   ||| || ||   |    ||   |    | | |  | |||        ||      ||| |  ||   |  || |  ||   | ||| |          |  | | ||| |  ||    |  ||| | |      | | |    ||| |||||   |  | |    |   ||| |  ||| ||  |                                                 
gtgggaggggtgggtgaatgaggtgggaggggtgggtgaataagtgtcatctccccccccctgccccgctccgcgctcccacctattgactgcaaagcctcaccccacccaccccgctctccgcgcgcctgctgcctgccgcagGTGCCCGAGACGGTGGACTGCCTGCAGCCGGTGATCAACATCGTGCCGCTGCAGCTGCTGTCGTACCACCTCACAGTGCTGCGCGGCTTCAACGTGGACC
















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: 27 (upstream exon), 33 (downstream exon)
Score: 2

CGACGCTAATCTCATGTGCCCGAATGGTGGTTGCCGTGTTATTGAGGTTCCGCAACTTCAGGATTGCCTACAGCCCATCATCAACATTGTTCCCTTTCAGgtacatttca ... ctctgcacagCTATTAGCTTATCATCTGACAGTTCTGCGCGGCTTCAACGTGGACCAACCTCGGAACTTAGCCAAGAGTGTGACGACGTCATGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatataaccttgccgatgggcttcctgactttgtgctcgtaaatctctgcacagCTATTAGCTTATCATCTGACAGTTCTGCGCGGCTTCAACGTGGACCAACCTCGGAACTTAGCCAAGAGTGTGACGACGTCATGA
                       tcctgac  putative branch site (score: 2)
                                            tctctgc  putative PPT
                                        taaatct  TA-rich tract