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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTTACTACAGGCTTCAACATACAGAGTTGGCATTAAGgtaaagttgctcttttaagtagtgtactctattaacttctgaggtcag

Basic information

species Selaginella moellendorffii
transcript EFJ24726
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ24726 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: GRMZM2G318635_T01 (Zea mays), 5'ss of exon 18
ATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTTACTACAGGCTTCAACATACAGAGTTGGCATTAAGgtaaagttg--ctcttttaagtagtgtactctattaacttctgaggtcag-------------------------------------------------------------------------------------------------
|||||||||| |||||||||||||| || |||||||||||||||||||| ||  | ||||| || |||||  | || |||||||||||  | ||||||| ||||  |     || | ||  ||   |    |  |||     || | ||                                                                                                  
ATGAGAGGGAACTTGGACTTGACCACCCAGATACAATGAAAAGCTATGGAGATCTTGCTGTTTTCTACTATCGCCTGCAACATACAGAACTAGCATTAAAgtaagttcagagtcatctacttaagctgacatggtaaaaatggacgacactatagttttatttcttcccacttacctgtggagcttgtttcatttaccgttttcatgtttgaactactttatttatgttctgactgttatatttcag

upper sequence: EFJ24726 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: GLYMA06G30000.1 (Glycine max), 5'ss of exon 16
ATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTTACTACAGGCTTCAACATACAGAGTTGGCATTAAGgtaaagttgc-tcttttaa-gtagtgtactctattaacttctgaggtcag--------------------------------------------------
|||| || ||||||||||| |||||||| ||||| |||||||| ||||| ||  | ||||| || || ||  | || ||||||||||||||||| |||| |||   || | | | ||||  ||   |  |  | |    |     | |||                                                  
ATGAAAGAGAGCTTGGACTGGACCATCCTGATACGATGAAAAGTTATGGAGATCTTGCTGTTTTCTATTATCGACTCCAACATACAGAGTTGGCTTTAAAgtatgcttccatatcttaatataaattggttgactgttatacctcggcagtggctttaaagtatgcttccatatatcatattccttagataaattgtttg

upper sequence: EFJ24726 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: GLYMA04G24430.1 (Glycine max), 5'ss of exon 15
ATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTTACTACAGGCTTCAACATACAGAGTTGGCATTAAGgtaaagttgc-tctttta-agtagtgtactctattaacttctgaggtcag--------------------------------------------------
|||| || ||||||||||| |||||||| ||||| |||||||| ||||| ||  | ||||| || || ||  | || ||||||||||||||||| |||| |||   || | | |   | | |  |    |  |||   || |    | |                                                   
ATGAAAGAGAGCTTGGACTGGACCATCCTGATACGATGAAAAGTTATGGGGATCTTGCTGTTTTCTATTATCGACTCCAACATACAGAGTTGGCTTTAAAgtatgcttccatataccatattcttaagataaattgttttttataatgacaatgggtttcatggttcttcgtgtgagaatccactgtcccagtggaccct

upper sequence: EFJ24726 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: GLYMA07G03250.1 (Glycine max), 5'ss of exon 19
ATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTTACTACAGGCTTCAACATACAGAGTTGGCATTAAGgtaaagttg-ctcttttaag-tagtgtactctattaacttctgaggtcag-------------------------------------------------------
||||||||||||| || |||||||| || || || |||||||||||||| ||  |  | |||||||| ||  | || ||||| |  ||||||||  | | ||||  | | || | || |  | || ||     |||| || |||  |                                                          
ATGAGAGGGAGCTAGGGCTTGACCACCCTGACACTATGAAAAGCTATGGGGATCTTTCCGTCTTTTATTATCGTCTGCAACACATTGAGTTGGCTCTGAAgtaagttcgactatattgaactggtttagatgtttaagttatgactttctgcttgttattttgaaattactatttcctcattgatctaaatgtatcttttcacag

upper sequence: EFJ24726 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: GLYMA08G22850.1 (Glycine max), 5'ss of exon 17
ATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTTACTACAGGCTTCAACATACAGAGTTGGCATTAAGgtaaagttgctctttt--aagtagtgtactctattaacttctgaggtcag-------------------------------------------------------
||||||| |||||||| |||||||| || || || |||||||||||||| ||  |  |||||||||| ||  | || ||||| |  ||||||||  | | ||||  |     || |  || | || ||     |||| || |||  |                                                          
ATGAGAGAGAGCTTGGGCTTGACCACCCTGACACTATGAAAAGCTATGGGGATCTTTCTGTCTTTTATTATCGTCTGCAACACATTGAGTTGGCTCTGAAgtaagttcaactttatggaattggtttagatgtttaagttatgaatttctgcttgttattctgaaattactattttctcattgatctaaatctatcttttgacag

upper sequence: EFJ24726 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: AT1G01320.1 (Arabidopsis thaliana), 5'ss of exon 19
ATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTTACTACAGGCTTCAACATACAGAGTTGGCATTAAGgtaaagtt-gctcttttaagtagtgtactctattaacttctga-ggtcag------------------------------------------------------
|||||||||| ||||||||||| ||||| ||||||||||| || ||||||||  | |||||||| || || |||||||| ||||||||| ||||  | | ||||  || || || || | |     |   |    |  |  || |||                                                         
ATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCTATTATAGGCTTCAGCATACAGAGCTGGCTCTCAAgtaagtttagcactcttgattttaaaagaatcgcgaggttagatggtttaaatgtttgatgtctctttccatcatctaaacctggatatgattgtttttgttag

upper sequence: EFJ24726 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: AT4G28080.1 (Arabidopsis thaliana), 5'ss of exon 18
ATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTTACTACAGGCTTCAACATACAGAGTTGGCATTAAGgtaaagttgct----cttttaagtagtgtact-cta-----ttaacttctgaggtcag------------------------
|||| ||||| ||||||||||| || || || |||||||||||||| || ||| |||||||||| || ||  | ||||| || |||||||| || || | |||   ||  |     |   ||   |   ||| |||     |||| | ||  |||  |                        
ATGAAAGGGAACTTGGACTTGATCACCCAGACACAATGAAAAGCTACGGCGACCTGGCTGTCTTCTATTATCGTCTTCAGCACACAGAGTTAGCCTTGAAgtatgctttttgcatttcccaaagcgccaactactacaaatttaattgcttcggtttgctaacatgttattccttttcgtag

upper sequence: EFJ24726 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: Vv11s0037g00840.t01 (Vitis vinifera), 5'ss of exon 18
ATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTTACTACAGGCTTCAACATACAGAGTTGGCATTAAGgtaaagttgctcttttaagtagtgtactctattaacttctgaggtcag-------------------------------------------------------
||||||| |||||||||||||| ||||| |||||||||||||| ||||| ||  | ||||| || || ||  ||||||| ||||||||||| ||||| | |||   ||    | |||     | | |||  ||| ||| |    |                                                          
ATGAGAGAGAGCTTGGACTTGATCATCCTGATACAATGAAAAGTTATGGGGATCTTGCTGTTTTCTATTATCGGCTTCAGCATACAGAGTTAGCATTGAAgtacgctt---ttattatacttttttctcccttagctttttgtcttttttgatactatggtggttatccttgtggttttgttcttgttttctggaatgctgtt

upper sequence: EFJ24726 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: Vv09s0002g07530.t01 (Vitis vinifera), 5'ss of exon 18
ATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTTACTACAGGCTTCAACATACAGAGTTGGCATTAAGgtaaagttgctcttttaagtagtgtactctattaacttctgaggtcag-------------------------------------------------------
|||||||||| ||||| ||||||||||| |||||||||||||||||||| ||  |  | || ||||||||  | || ||||| |  || |||||  | | ||||  | |   |      | |  | || |  || |||   |                                                             
ATGAGAGGGAACTTGGGCTTGACCATCCTGATACAATGAAAAGCTATGGAGATCTTTCAGTTTTTTACTATCGTCTCCAACACATTGAATTGGCTCTGAAgtaagctagaagt---ggctggccttctgttctagctttcaaaacttaacattttaaagtttctcgtaaatagttacttaaaaagagtgaagttcaatttcaa

upper sequence: EFJ24726 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: PP1S73_28V6.1 (Physcomitrella patens), 5'ss of exon 13
ATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTTACTACAGGCTTCAACATACAGAGTTGGCATTAAGgtaaagttgctcttttaagtagtgtactctatt------aacttctgaggtcag-------------------------------------------------------------------------------------------------
||||| | || |||||||||||||| || ||||| |||||||| ||||||||  |||| || ||||||||  | |||||||| || ||||||||| | | ||||  |         ||| |  |   ||| ||      |   ||| || ||||                                                                                                 
ATGAGCGAGAACTTGGACTTGACCACCCAGATACCATGAAAAGTTATGGTGATCTGGCAGTATTTTACTATCGTCTTCAACACACCGAGTTGGCACTTAAgtaagttctaatacccaagcacaggtttctttttggagaatggtctaagatcagagtgtctttgagatcgttaatgattagttgttccgatttttgaactggaattatacgggaaggactgccgctcaatttttattttgttggaatgcag

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), 26 (downstream exon)
Score: 7

ATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTTACTACAGGCTTCAACATACAGAGTTGGCATTAAGgtaaagttgc ... ctgaggtcagATACGTTAATCGGGCACTTTACTTGCTGCACTTGATCTGTGGACCCTCACATCCGAATACAGCTGCTACTTATATAAATGTAGCTATGATGGAGGAGGCT




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