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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTTCTGACATACAACCACTGATCCGATCAGTTCTGGATGGATTCAACGTTTGTATTTTTGCATATGGCCAGACTGGTTCTGGCAAAACTTACACTATGgtactataaaataaatcataataaaaaattgtcatcactacaatagtaatattactgattatgatatctgttttgttgttattatttaatctttag

Basic information

species Zea mays
transcript GRMZM2G173700_T03
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G173700_T03 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os05g44560.1 (Oryza sativa), 5'ss of exon 14
TTTTTCTGACATACAACCACTGATCCGATCAGTTCTGGATGGATTCAACGTTTGTATTTTTGCATATGGCCAGACTGGTTCTGGCAAAACTTACACTATGgtacta----taaaataaatcataataa---aaaattgtcatca--ctacaatagtaatattactgattatgatatctgttttgt-tgtt--attatt--taatctttag-----------------------------------
||| || ||||| ||||| ||||| ||||||||||| ||||||||||| |||||||||||||| ||||| || |||||||| || ||||||||||| |||||||||    | |   | ||  || |     |  |||||  | |   || | |  |  | ||  |   |||  ||   |||  |  || |  | |  |  |||  |||                                     
TTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTACACAATGgtactaacttttaccgatattttactggctcagcattgttgttaacttatattgatcttttttattggtattgtactggttcagcatgatgcactgctactaacttttgatcacttatgttctattccaataattttgttcttag

upper sequence: GRMZM2G173700_T03 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA13G33390.1 (Glycine max), 5'ss of exon 10
TTTTTCTGACATACAACCACTGATCCGATCAGTTCTGGATGGATTCAACGTTTGTATTTTTGCATATGGCCAGACTGGTTCTGGCAAAACTTACACTATGgtactataaaataaatcataataaaaaattgtcatcactaca-atagtaatattactgattatgatatctgttttgttgttattatttaatctttag
 | | ||||||||||| |  | || |||||||| || ||||| || || || ||||| ||||| ||||||||||||||||| || ||||||||||| ||||||    |   || ||    ||| | |    |||||| |  | |||     |||||| ||| |      |    |||  |||||  |||        
GTATGCTGACATACAAGCCTTTATACGATCAGTACTTGATGGGTTTAATGTATGTATATTTGCTTATGGCCAGACTGGTTCAGGGAAAACTTACACAATGgtaagcaactttatat----atatatatcattcatcattttagataaaggaattactcattcta-----taagatgtcattatttcttag-------

upper sequence: GRMZM2G173700_T03 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA07G10190.1 (Glycine max), 5'ss of exon 13
--TTTTTCTGACATACAACCACTGATCCGATCAGTTCTGGATGGATTCAACGTTTGTATTTTTGCATATGGCCAGACTGGTTCTGGCAAAACTTACACTATGgtactataaaataaatcataataaaaaattgtcatcactacaatagtaatattactgattatgatatctgttttgttgttattatttaatctttag
   | |  ||| ||||||    | || |||||||| || ||||| || || || ||||| ||||| ||||||||||||||||  || ||||||||||| ||||||    |   || ||    | | | | |  |  | | |  | | |   | |||                                          
GTGTATGTTGAAATACAAGATTTTATACGATCAGTGCTTGATGGCTTTAATGTATGTATATTTGCTTATGGCCAGACTGgtttaggaaaaacttacacaatggtaagcaactttatattcacacatatattgattttaatttaattcgccgtcttag-----------------------------------------

upper sequence: GRMZM2G173700_T03 (Zea mays), 5'ss of exon 11
lower sequence: AT1G18410.1 (Arabidopsis thaliana), 5'ss of exon 13
TTTTTCTGACATACAACCACTGATCCGATCAGTTCTGGATGGATTCAACGTTTGTATTTTTGCATATGGCCAGACTGGTTCTGGCAAAACTTACACTATGgtact-ataaaataaatcataataaaaaattgtcatcactacaatagtaatattactgattatgatatctgttttgttgttattatttaatctttag
 ||||| || ||| |||| || || ||||||||||| || || | ||| || ||||| ||||||||||| ||||| || || || ||||||||||| |||||||| ||  | ||    || |  |  || ||      | | |  | | ||   ||| |   | ||| |  | |  ||||| || |  |        
ATTTTCAGATATAAAACCTCTTATTCGATCAGTTCTTGACGGGTACAATGTATGTATCTTTGCATATGGTCAGACAGGATCAGGGAAAACTTACACAATGgtactcattcactagtatatcacgattaagtg-----gccagacaaatgatgccact-acattcataccattatcattgtttttgtccag-------

upper sequence: GRMZM2G173700_T03 (Zea mays), 5'ss of exon 11
lower sequence: AT1G73860.1 (Arabidopsis thaliana), 5'ss of exon 13
TTTTTCTGACATACAACCACTGATCCGATCAGTTCTGGATGGATTCAACGTTTGTATTTTTGCATATGGCCAGACTGGTTCTGGCAAAACTTACACTATGgtactataaaataaatcataataaaaaattgtcatcactacaatagtaatattactgattatgatatctgttttgttgttattatttaatctttag
 ||||| ||||||  ||| ||| |  | ||||| || ||||| | ||| |||||||| ||||||||||||||||| || || || |||||||| || |||||| | ||       |  |     | | |    |  | | || ||| ||||   |||||   | | |    || |||    || ||| |       
CTTTTCAGACATAAGACCGCTGGTTAGGTCAGTACTTGATGGGTACAATGTTTGTATATTTGCATATGGCCAGACAGGATCAGGGAAAACTTATACAATGgta-tgtattcactgttgtttctgagagt----aagatttca-taggaataacgctgat-gcgcttttaccttcgttccctttctttcag------

upper sequence: GRMZM2G173700_T03 (Zea mays), 5'ss of exon 11
lower sequence: AT1G63640.1 (Arabidopsis thaliana), 5'ss of exon 14
TTTTTCTGACATACAACCACTGATCCGATCAGTTCTGGATGGATTCAACGTTTGTATTTTTGCATATGGCCAGACTGGTTCTGGCAAAACTTACACTATGgta--ctataaaataaatcataataaaaaattgtcatcactacaatagtaatat-tactgattatgatatctgttttgttgttattatttaatctttag
||| |  || |  | |||| | || |||||  |||| ||||| |  || |||||||| ||||| ||||| |||||||||||||| |||||||| || ||||||   || ||  |  ||  |  |||  |  ||   | ||  ||||  | |||  |  |  | |   | ||| |||||     |               
TTTCTTAGATACTCGACCATTAATTCGATCCATTCTTGATGGCTATAATGTTTGTATATTTGCCTATGGTCAGACTGGTTCTGGAAAAACTTATACAATGgtaaattacaagcttgattttgttaacgatatgctttaac--caatgattataagtttttctaacagtttctattttgcaaacacag------------

upper sequence: GRMZM2G173700_T03 (Zea mays), 5'ss of exon 11
lower sequence: EFJ28715 (Selaginella moellendorffii), 5'ss of exon 10
TTTTTCTGACATACAACCACTGATCCGATCAGTTCTGGATGGATTCAACGTTTGTATTTTTGCATATGGCCAGACTGGTTCTGGCAAAACTTACACTATGgta--ctataaaataaatcataataaaaa-attgtcatc-actacaatagtaatattactgattatgatatctgttttgttgttattatttaatctttag
||||   ||    || ||  |||| ||||| || || ||||| |||||||| ||||||||||| ||||| |||||||||||||| ||||| || |||||||||  || | |  |   | |  ||      |||  | || | |     ||                                                  
TTTTCTGGATGCGCAGCCTTTGATTCGATCGGTGCTTGATGGTTTCAACGTCTGTATTTTTGCGTATGGACAGACTGGTTCTGGAAAAACATATACTATGgtaagctgtgagctccgttaggatttgtgtattaacgtctattgatgcag--------------------------------------------------

upper sequence: GRMZM2G173700_T03 (Zea mays), 5'ss of exon 11
lower sequence: EFJ30678 (Selaginella moellendorffii), 5'ss of exon 10
TTTTTCTGACATACAACCACTGATCCGATCAGTTCTGGATGGATTCAACGTTTGTATTTTTGCATATGGCCAGACTGGTTCTGGCAAAACTTACACTATGgtactataaaataaatcataataaaaaattgtcatcactacaatagtaatattactgattatgatatctgttttgttgttattatttaatctttag
||||   ||    || ||  |||| ||||| || || ||||| |||||||| ||||||||||| ||||| |||||||||||||| ||||| || |||||||||   |    | |       ||| |  |    || |      || | ||                                              
TTTTCTGGATGCGCAGCCTTTGATTCGATCGGTGCTTGATGGTTTCAACGTCTGTATTTTTGCGTATGGACAGACTGGTTCTGGAAAAACATATACTATGgtaaggt---gtgagctccgttaagatttgtgtattaacgtc-tattgatgcag------------------------------------------

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 151

TTTTTCTGACATACAACCACTGATCCGATCAGTTCTGGATGGATTCAACGTTTGTATTTTTGCATATGGCCAGACTGGTTCTGGCAAAACTTACACTATGgtactataaa ... taatctttagAGTGGGCCTACCACATCAAAACAAGATTGGGGTGTCAATTATCGAGCTTTAAATGATTTGTTTGATATTTCACTAAGTAGGAGAAATGCCTTCTCATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 21

TTTTTCTGACATACAACCACTGATCCGATCAGTTCTGGATGGATTCAACGTTTGTATTTTTGCATATGGCCAGACTGGTTCTGGCAAAACTTACACTATGgtactataaa ... taatctttagAGTGGGCCTACCACATCAAAACAAGATTGGGGTGTCAATTATCGAGCTTTAAATGATTTGTTTGATATTTCACTAAGTAGGAGAAATGCCTTCTCATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 45

TTTTTCTGACATACAACCACTGATCCGATCAGTTCTGGATGGATTCAACGTTTGTATTTTTGCATATGGCCAGACTGGTTCTGGCAAAACTTACACTATGgtactataaa ... taatctttagAGTGGGCCTACCACATCAAAACAAGATTGGGGTGTCAATTATCGAGCTTTAAATGATTTGTTTGATATTTCACTAAGTAGGAGAAATGCCTTCTCATATG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 62

TTTTTCTGACATACAACCACTGATCCGATCAGTTCTGGATGGATTCAACGTTTGTATTTTTGCATATGGCCAGACTGGTTCTGGCAAAACTTACACTATGgtactataaa ... taatctttagAGTGGGCCTACCACATCAAAACAAGATTGGGGTGTCAATTATCGAGCTTTAAATGATTTGTTTGATATTTCACTAAGTAGGAGAAATGCCTTCTCATATG