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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgggagcgccttcatctttgtatgctttatcacttccataaacatttttatgaccagctgcgttgtgacgcttttccctcatatgttatttcatgactttgattatcgtggggtatagggtttttgacgttgttgcctgcatttattttgtcacgtttctgtattgcagGTGCATTTTTTCCGACCTGTGCCTAAAGAGTATTTGCATTCAGCTGAACTGCGCGACATTATGCAATTTGGTAGCAGCAACACAGCCGTCTTTTTCAAAA

Basic information

species Physcomitrella patens
transcript PP1S364_50V6.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S364_50V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 14
gtatgtgggagcgccttcatctttgtatgctttatcacttccataaacatttttatgaccagctgcgttgtgacgcttttccctcatatgttatttcatgactttgattatcgtggggtatagggtttttgacgttgttgcctgcatttattttgtcacgtttctgtattgcagGTGCATTTTTTCCGACCTGTGCCTAAAGAGTATTTGCATTCAGCTGAACTGCGCGACATTATGCAATTTGGTAGCAGCAACACAGCCGTCTTTTTCAAAA
                                       |   ||||||     || || || |    |            | | ||||   | || |  | |   |||||       |  |  ||  ||    ||||     |  |||  ||  |||  |  || ||     | | ||||||||||| || || ||||| || |||||||| ||||||||  || | ||||| ||||||||||| |||||||| || || |||||||| ||||
------------------------------------gtatgactaaacaaaaaaataactagttaaactaaa---------cattatat---agtttactattacaattattaaaaaatgaactgtgcttttaattgt-----gttttttcttgatcaattggctata-----gATTCATTTTTTCCGTCCAGTTCCTAAGGAATATTTGCACTCAGCTGAGTTGAGAGACATAATGCAATTTGGAAGCAGCAATACTGCAGTCTTTTTTAAAA

upper sequence: PP1S364_50V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 11
gtatgtgggagcgccttcatctttgtatgctttatcacttccataaacatttttatgaccagctgcgttgtgacgcttttccctcatatgttatttcatgactttgattatcgtggggtatagggtttttgacgttgttgcctgcatttattttgtcacgtttctgtattgcagGTGCATTTTTTCCGACCTGTGCCTAAAGAGTATTTGCATTCAGCTGAACTGCGCGACATTATGCAATTTGGTAGCAGCAACACAGCCGTCTTTTTCAAAA
                                                     |||||| |  ||       |           |||    || || || | |   |||||    |  |  |  ||  ||    |  |||  ||| |||  ||  || | ||       |  || | ||||||||||| || || ||||| || |||||||| ||||||||  || | ||||| ||||||||||| ||||| || || || ||||| || ||||
----------------------------------------------------gtatgactaaatgaaaaactagttaaactaaacattatatagtttatcattacaattattaaagaatgaattgtgcttt---taattgtgtgccttttcttgatc-cattg----gctatagATTCATTTTTTCCGTCCAGTTCCTAAGGAATATTTGCACTCAGCTGAGTTGAGAGACATAATGCAATTTGGAAGCAGTAATACTGCAGTCTTCTTTAAAA

upper sequence: PP1S364_50V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: AT5G65930.1 (Arabidopsis thaliana), 3'ss of exon 8
gtatgtgggagcgccttcatctttgtatgctttatcacttccataaacatttttatgaccagctgcgttgtgacgcttttccctcatatgttatttcatgactttgattatcgtggggtatagggtttttgacgttgttgcctgcatttattttgtcacgtttctgtattgcagGTGCATTTTTTCCGACCTGTGCCTAAAGAGTATTTGCATTCAGCTGAACTGCGCGACATTATGCAATTTGGTAGCAGCAACACAGCCGTCTTTTTCAAAA
                                                            ||   |  | | |   || | | | ||   || |   |  ||| | ||| | ||  || ||     | |  | |||||||  |   || | |||||    || || | ||| |||| || ||||| ||||| || |||||||| ||| |||| || |||||||| || ||||| ||||||||||| ||||| ||||| || |||||||||||||
---------------------------------------------------------gttagtctcaatataaatgttatacattatgactt-taaaaaaactgttattgttgtttggaattcaaatct--atgttgttggat---ttgaatttgttgt-ttgctttcttgtagGTTCACTTTTTTCGACCGGTTCCTAAAGAATATCTGCACTCTGCTGAACTACGTGACATCATGCAATTTGGCAGCAGTAACACTGCTGTCTTTTTCAAAA

upper sequence: PP1S364_50V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 10
gtatgtgggagcgccttcatctttgtatgctttatcacttccataaacatttttatgaccagctgcgttgtgacgcttttccctcatatgttatttcatgactttgattatcgtggggtatagggtttttgacgttgttgcctgcatttattttgtcacgtttctgtattgcagGTGCATTTTTTCCGACCTGTGCCTAAAGAGTATTTGCATTCAGCTGAACTGCGCGACATTATGCAATTTGGTAGCAGCAACACAGCCGTCTTTTTCAAAA
                                                       |||    | | ||| |     | |    | || ||| |  |    | ||||||  |  ||   |||||   | ||| |       | || ||||  ||  |||        | |  ||||| ||||||||||| || || || ||||||||||||||||| ||||||||  | || || |||||||||||||||||||| || || || ||||| || |
------------------------------------------------------gtgagt--cagagttatattattataatgt-atctgt-acattgcaaatttgatgtt--tgaattatagatctattg-caacagaacatgaatttgattgttcat-------tctcacagGTTCATTTTTTCCGTCCAGTTCCAAAAGAGTATTTGCATTCTGCTGAACTAAGAGATATAATGCAATTTGGTAGCAGCAATACTGCTGTATTTTTTAAGA

upper sequence: PP1S364_50V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: EFJ30174 (Selaginella moellendorffii), 3'ss of exon 10
gtatgtgggagcgccttcatctttgtatgctttatcacttccataaacatttttatgaccagctgcgttgtgacgcttttccctcatatgttatttcatgactttgattatcgtggggtatagggtttttgacgttgttgcctgcatttattttgtcacgtttctgtattgcagGTGCATTTTTTCCGACCTGTGCCTAAAGAGTATTTGCATTCAGCTGAACTGCGCGACATTATGCAATTTGGTAGCAGCAACACAGCCGTCTTTTTCAAAA
                                                                                                                        || |       |  ||  ||   ||   | ||||| || || | | | |  ||||| ||||||||||| || || |||||||| ||||| ||||| ||||| ||| | ||||| ||||||||||| || ||||| || || || ||||| ||||
-----------------------------------------------------------------------------------------------------------------------gtacgtgcaagtatattcatgttcgc---tgttttgacatgtgtttct-taacagGTTCATTTTTTCCGGCCAGTACCTAAAGAATATTTACATTCGGCTGAGCTGAGAGACATCATGCAATTTGGAAGTAGCAATACCGCAGTGTTTTTTAAAA

upper sequence: PP1S364_50V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: EFJ06058 (Selaginella moellendorffii), 3'ss of exon 10
gtatgtgggagcgccttcatctttgtatgctttatcacttccataaacatttttatgaccagctgcgttgtgacgcttttccctcatatgttatttcatgactttgattatcgtggggtatagggtttttgacgttgttgcctgcatttattttgtcacgtttctgtattgcagGTGCATTTTTTCCGACCTGTGCCTAAAGAGTATTTGCATTCAGCTGAACTGCGCGACATTATGCAATTTGGTAGCAGCAACACAGCCGTCTTTTTCAAAA
                                                                                                                        || |       |  ||  ||   ||     ||||| || || | | | |  ||||| ||||||||||| || || |||||||| ||||| ||||| ||||| ||  | ||||| ||||||||||| || ||||| || || || ||||| ||||
-----------------------------------------------------------------------------------------------------------------------gtacgtgcaagtatattcatgttcgcg---gttttgacatgtgtttct-taacagGTTCATTTTTTCCGGCCAGTACCTAAAGAATATTTACATTCGGCTGAGCTTAGAGACATCATGCAATTTGGAAGTAGCAATACCGCAGTGTTTTTTAAAA

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: 32 (upstream exon), 25 (downstream exon)
Score: 9

ACTCCCTTATGGAAATTCGGTGTTCTTTACTGTTACAAAAATTGAGGACCCTATTGGATTGCTGCCAGGGCGGATTATTCTTGGCATCAACAAGCGTGGGgtatgtggga ... tgtattgcagGTGCATTTTTTCCGACCTGTGCCTAAAGAGTATTTGCATTCAGCTGAACTGCGCGACATTATGCAATTTGGTAGCAGCAACACAGCCGTCTTTTTCAAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagggtttttgacgttgttgcctgcatttattttgtcacgtttctgtattgcagGTGCATTTTTTCCGACCTGTGCCTAAAGAGTATTTGCATTCAGCTGAACTGCGCGACATTATGCAATTTGGTAGCAGCAACACAGCCGTCTTTTTCAAAA
       ttttgac  putative branch site (score: 9)
                                       cgtttct  putative PPT
                          atttattttgt  TA-rich tract