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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggttccttctccgtatgtgtaatatcgcatgatagcttcaatggtgcacatgcagactggattttgcaagtaactttctcatgttcgtagctgcttatctgttcagGTATGGGAGAAGAGTGGTTACAACACTGTTGAATGGGTGCGCTACATCACAAGGGCCGGTTCTTATGAAATCCGGTGCTGA

Basic information

species Physcomitrella patens
transcript PP1S197_28V6.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S197_28V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 12
gtgggttccttctccgtatgtgtaatatcgcatgatagcttcaatggtgcacatgcagactggattttgcaagtaactttctcatgttcgtagctgcttatctgttcagGTATGGGAGAAGAGTGGTTACAACACTGTTGAATGGGTGCGCTACATCACAAGGGCCGGTTCTTATGAAATCCGGTGCTGA-------------------
            | |||    | |||        | | | |   |    || |  ||||| |   ||   ||        ||||||||   || ||| |||   | ||||| ||||||||||| ||||||||||| ||||| ||||| ||||||||||||||||| || || ||||| ||  |||| |                     
-----------gtacgtgcagggaatgctaatatagaacctttttaacacatac-cagacag---ttcagaa--------ctcatgttg--agatgcatat---tccagGTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACAAGGGCTGGATCATATGAGATAAGGTGTTAGCGATGAAGAAAAAAGTCCC

upper sequence: PP1S197_28V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GRMZM2G331032_T01 (Zea mays), 3'ss of exon 12
gtgggttccttctccgtatgtgtaatatcgcatgatagcttcaatggtgcacatgcagactggattttgcaagtaactttctcatgttcgtagctgcttatctgttcagGTATGGGAGAAGAGTGGTTACAACACTGTTGAATGGGTGCGCTACATCACAAGGGCCGGTTCTTATGAAATCCGGTGCTGA-------------------
                             | |||   ||  |||   |     || |   | |   | |||  | |  |    |   || |||      || | | ||||| ||||||||||||||||| ||||||||||| ||||| ||||||||||||||||| || || ||||| ||  |||| |                     
-----------------------------gtatgt--gcaccaagtcttggtttgaaactttg---tagcatctgagatggaaaatctcatagtgatacattt-tccagGTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACAAGGGCTGGATCATATGAGATAAGGTGTTAGCAACAAATCCATACAAGAT

upper sequence: PP1S197_28V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA17G16630.3 (Glycine max), 3'ss of exon 11
gtgggttccttctccgtatgtgtaatatcgcatgatagcttcaatggtgcacatgcagactggattttgcaagtaactttctcatgttcgtagctgcttatctgttcagGTATGGGAGAAGAGTGGTTACAACACTGTTGAATGGGTGCGCTACATCACAAGGGCCGGTTCTTATGAAATCCGGTGCTGA-------------------
               ||| || |    |||||   ||   |      | | | ||    ||    |    |||| | | | |  | ||  |      |  ||| ||||||| |||||||||||||| ||||| || ||||| ||||| || ||||| ||||  || || || || || ||  ||||||                     
---------------gtacgtatc-cgtcgcaacctactgttccattttcccctgttttctttcataactaagtgattctattttctttat-----ttactctcttcagGTGTGGGAGAAGAGTGGGTACAATACCGTTGAGTGGGTTCGTTACATTACAAAAGCAGGATCCTACGAGATTAGGTGCTAGACACAATTGGTATTTTGCT

upper sequence: PP1S197_28V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA05G23670.1 (Glycine max), 3'ss of exon 12
gtgggttccttctccgtatgtgtaatatcgcatgatagcttcaatggtgcacatgcagactggattttgcaagtaactttctcatgttcgtagctgcttatctgttcagGTATGGGAGAAGAGTGGTTACAACACTGTTGAATGGGTGCGCTACATCACAAGGGCCGGTTCTTATGAAATCCGGTGCTGA-------------------
                   || |   ||||||   || | |      |   | ||||  ||    |    | || | | | |  | ||  |      |  ||| ||||||| |||||||||||||| ||||| || ||||| ||||| || ||||| ||||  || || || || || ||  ||||||                     
-------------------gtatc-catcgcaacctaccgttcccctttttcctgcattctctcataactaggtgattctattttctttat-----ttactctcttcagGTGTGGGAGAAGAGTGGGTACAATACCGTTGAGTGGGTTCGTTACATTACAAAAGCTGGATCCTACGAGATTAGGTGCTAGACAGAGTTTGTATTACTGG

upper sequence: PP1S197_28V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: Vv02s0012g00910.t01 (Vitis vinifera), 3'ss of exon 12
gtgggttccttctccgtatgtgtaatatcgcatgatagcttcaatggtgcacatgcagactggattttgcaagtaactttctcatgttcgtagctgcttatctgttcagGTATGGGAGAAGAGTGGTTACAACACTGTTGAATGGGTGCGCTACATCACAAGGGCCGGTTCTTATGAAATCCGGTGCTGA-------------------
               ||||||   ||   | |   |||    ||||   | |||||  |   | ||||| ||| | |||   | |     || |  |||   | | ||||| ||||||||||| || ||||| || ||||| ||||||||||| || || |  |||||||| ||||||||  ||||||                     
---------------gtatgt---atgctgaac--tagtcagaatg---cccatgccaat--gtttttgaaagcagcttcaccct-----taccaactt---tctacagGTCTGGGAGAAGAGCGGGTACAATACCGTTGAGTGGGTGCGCTATATTACCAAAGCCGGTTCATATGAAATTAGGTGCTAGAGTTGTGAAATGCAGGTGT

upper sequence: PP1S197_28V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: EFJ22278 (Selaginella moellendorffii), 3'ss of exon 12
gtgggttccttctccgtatgtgtaatatcgcatgatagcttcaatggtgcacatgcagactggattttgcaagtaactttctcatgttcgtagctgcttatctgttcagGTATGGGAGAAGAGTGGTTACAACACTGTTGAATGGGTGCGCTACATCACAAGGGCCGGTTCTTATGAAATCCGGTGCTGA-------------------
                                              ||   ||  |     |   ||    || || | |   ||| |     ||   |  ||  |||||| ||||| |||||||| |||| ||| || |||||||| |||||||||||||| || || || || |||||  |||||| |                   
----------------------------------------------gtaagcaaactcgtcgcgattgtttaggaattctggaatgatt---tctttctggctcctcagGTGTGGGAAAAGAGTGGATACAGCACAGTGGAATGGGTACGCTACATCACAAGAGCTGGATCGTACGAAATAAGGTGCTAAAAAAACGTGAGGGAAGGGA

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), 31 (downstream exon)
Score: 3

AACCATGGTTGATAAAAAGACTTGGACTAGACCGCCCATCCAGATGGAGTTCCAGGTCCCCATGTTTACTGCTTCCGGCCTAAGGGTCCGTTTTTTGAAGgtgggttcct ... atctgttcagGTATGGGAGAAGAGTGGTTACAACACTGTTGAATGGGTGCGCTACATCACAAGGGCCGGTTCTTATGAAATCCGGTGCTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcagactggattttgcaagtaactttctcatgttcgtagctgcttatctgttcagGTATGGGAGAAGAGTGGTTACAACACTGTTGAATGGGTGCGCTACATCACAAGGGCCGGTTCTTATGAAATCCGGTGCTGA
                aagtaac  putative branch site (score: 3)
                                          cttatct  putative PPT
                   taacttt  TA-rich tract