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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTGATGGCTGGTCGCATTGTGAAGCATGCAATGGAGATCATTCACTTGCTCACGGACGCCAACCCGATCCAAATTATTGTCGATGCTATCATCAACAGgtatagaggttcaagtgagcaggattccaggacagttttggattttctctctttctctttgcag

Basic information

species Selaginella moellendorffii
transcript EFJ18003
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ18003 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os01g01060.1 (Oryza sativa), 5'ss of exon 2
AGCTGATGGCTGGTCGCATTGTGAAGCATGCAATGGAGATCATTCACTTGCTCACGGACGCCAACCCGATCCAAATTATTGTCGATGCTATCATCAACAGgtatagaggttcaagt--gagcaggattccaggacagttttggattttct--ctctttctctttgcag--------------------------------
|| | |||||||  ||||| || ||||| || ||||||||||| ||| | ||||| ||||||||||| |||||  | || || ||||| ||||||||||||||     || ||| |   |      |||     |    ||  ||| ||    ||  | | ||| ||                                 
AGATCATGGCTGTCCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATCCAGGTCATCGTAGATGCCATCATCAACAGgtaccaccgtccaattcccaattcctttcagttgcgcacttcaattgtccaattcacttttttttcaatcaccctcaccctcttatatgcaaatgcttat

upper sequence: EFJ18003 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os11g29190.4 (Oryza sativa), 5'ss of exon 2
--------------------------AGCTGATGGCTGGTCGCATTGTGAAGCATGCAATGGAGATCATTCACTTGCTCACGGACGCCAACCCGATCCAAATTATTGTCGATGCTATCATCAACAGgta----------tagaggttcaagtgagcaggattccaggacagttttggattttctctctttctctttgcag
                          || | ||||| |  ||||| || ||||| || ||||||||||| ||| | ||||| ||||||||||| || ||  | || ||||| || ||||||||||||||          | | | |||    |  ||   |     ||     |   |||||  |    | | || | | 
GATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGgtcatcgtcgacgccatcatcaacaggtaaccccccctttcgcgcttcgctcgcccaatctctttcgaaccagtaaaattttaccgggatttgttagaac

upper sequence: EFJ18003 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os11g29190.5 (Oryza sativa), 5'ss of exon 2
-----------------------------------------AGCTGATGGCTGGTCGCATTGTGAAGCATGCAATGGAGATCATTCACTTGCTCACGGACGCCAACCCGATCCAAATTATTGTCGATGCTATCATCAACAGgta-tagaggttcaagtgagcaggattccaggacagttttggattttctctctttctctttgcag
                                         || | ||||| |  ||||| || ||||| || ||||||||||| ||| | ||||| ||||||||||| || ||  | || ||||| || ||||||||||||||        |   | |    |    ||    |  ||| | |         |||  |       
GACCAACTCGCTCATGATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACgccaaccccattcaggtcatcgtcgacgccatcatcaacaggtaaccccccctttcgcgcttcgctcgcccaatctctttcgaaccagtaaaattttacc------

upper sequence: EFJ18003 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os11g29190.1 (Oryza sativa), 5'ss of exon 2
AGCTGATGGCTGGTCGCATTGTGAAGCATGCAATGGAGATCATTCACTTGCTCACGGACGCCAACCCGATCCAAATTATTGTCGATGCTATCATCAACAGgta----------tagaggttcaagtgagcaggattccaggacagttttggattttctctctttctctttgcag--------------------------
|| | ||||| |  ||||| || ||||| || ||||||||||| ||| | ||||| ||||||||||| || ||  | || ||||| || ||||||||||||||          | | | |||    |  ||   |     ||     |   |||||  |    | | || | |                           
AGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACGCCAACCCCATTCAGGTCATCGTCGACGCCATCATCAACAGgtaaccccccctttcgcgcttcgctcgcccaatctctttcgaaccagtaaaattttaccgggatttgttagaacaccacacgagaatttatctgagaata

upper sequence: EFJ18003 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: Vv04s0043g00440.t01 (Vitis vinifera), 5'ss of exon 3
AGCTGATGGCTGGTCGCATTGTGAAGCATGCAATGGAGATCATTCACTTGCTCACGGACGCCAACCCGATCCAAATTATTGTCGATGCTATCATCAACAGgtatagag--------gttcaagtgagcaggattccaggacagt-tttggattttctctctttctctttgcag----------------------------------------------------------------------------------------------
|||||||||||| | | ||| |||| ||||| ||||| || ||||||||| | || ||    || || |||||| ||||||| |||||| ||||||||||||||| |         |||  | ||   ||  | | |  |||     || |  ||   | || |  |  ||||                                                                                              
AGCTGATGGCTGTTAGGATTATGAAACATGCCATGGAAATTATTCACTTGTTGACTGATCAGAATCCCATCCAAGTTATTGTTGATGCTGTCATCAACAGgtatacaatctgcagagttacactgtcaagtgtgctataacaccacatgaagatttagttttaccttgagcagtttatattaactccattaatggactttctttttagtatgcctttcacattatcttataatgttttgtttctttgaatatttttggttgctacag

upper sequence: EFJ18003 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S400_33V6.1 (Physcomitrella patens), 5'ss of exon 2
AGCTGATGGCTGGTCGCATTGTGAAGCATGCAATGGAGATCATTCACTTGCTCACGGACGCCAACCCGATCCAAATTATTGTCGATGCTATCATCAACAGgtataga------------------ggttcaagtgagcaggattccaggacagttttggattttctctctttc--tctttgcag--------------------------------------
|| |||||||||  |||||||||||||| || ||||||||||||||| | || || ||    ||||| |||||  | || || ||||||||||||||||||| |  |                  | || | |||   |         |||| | |||       |||  |||  |  | |||                                       
AGTTGATGGCTGTCCGCATTGTGAAGCACGCTATGGAGATCATTCACCTTCTGACTGATCAGAACCCCATCCAGGTCATCGTTGATGCTATCATCAACAGgtttgaatcttatctttctattggtgtttgatgtggaaaatgaaatgcgacactcttgaggcgagtctaattcaattgtagcaatttttagtggcatgaggcatatcttttatctgctgcag

upper sequence: EFJ18003 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S114_143V6.1 (Physcomitrella patens), 5'ss of exon 2
AGCTGATGGCTGGTCGCATTGTGAAGCATGCAATGGAGATCATTCACTTGCTCACGGACGCCAACCCGATCCAAATTATTGTCGATGCTATCATCAACAGgtatagaggttcaagtg-------agcaggat-tccaggacagttttggattttctctctttctctttgcag---------------------------------------------------------------------------------
|| ||||||| |  ||||| |||||||| || ||||||||||| ||| |||| ||||||   ||||| |||||  | || || ||||| ||||||||||||||       || |          ||| | || |   ||  ||    ||    |       |      |  |                                                                                 
AGTTGATGGCGGTGCGCATCGTGAAGCACGCGATGGAGATCATCCACCTGCTGACGGACCAGAACCCCATCCAGGTCATCGTGGATGCCATCATCAACAGgtaggttatctcgaacacttgtttagctgcatattggggggagaggcgggggatgggcgcatgggcgggaggagaggttgcaacaggaatttagggttatgcgggatgatgtggggctcgggagctgagaggtcgcggtgggaatgggtacag

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: 35 (upstream exon), 35 (downstream exon)
Score: 10

AGCTGATGGCTGGTCGCATTGTGAAGCATGCAATGGAGATCATTCACTTGCTCACGGACGCCAACCCGATCCAAATTATTGTCGATGCTATCATCAACAGgtatagaggt ... ctctttgcagTGGTCCTCGCGAAGATGCTACCCGTATTGGTTCCGCTGGTGTTATCAGGCGTCAGGCTGTGGATATCTCCCCTTTGAGGCGTGTCAATCAGGCGATTTAC




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