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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAGAACTTGGAAAATCTTGATCTTTACCATTATGCTCTTTTCTCAGACAATGTTTTGTCAGCATCAGTTGTGGTCAACTCAACCATCATGAATGCAAAGgttagtgtaatccccatcttgaaactggaagtgtaatatcttcattatgtctaccatggaatggcccattatatagcacttttgatttttttttctataa...

Basic information

species Zea mays
transcript GRMZM2G565856_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G565856_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA07G08910.1 (Glycine max), 5'ss of exon 5
CGAGAACTTGGAAAATCTTGATCTTTACCATTATGCTCTTTTCTCAGACAATGTTTTGTCAGCATCAGTTGTGGTCAACTCAACCATCATGAATGCAAAGgttagtgtaatccccatcttga----aactggaagtgta-atatcttcattatgtc-taccatggaatggcccattatatagcacttttgatttttttttctataa
 ||||| ||||| ||||    |||||| || || || || |||||||||||||| ||| | ||||| ||||| ||||||||||| || |||||||||||||| | |   |    | | || |    | | | | ||||    |  | |||| | || |   || || ||  | | || || |  | ||  |           |   
TGAGAATTTGGAGAATCCCAGTCTTTATCACTACGCACTGTTCTCAGACAATGTCTTGGCTGCATCTGTTGTTGTCAACTCAACTATTATGAATGCAAAGgtgacttggactgtctttttaaccataccagtatgtgtgtgcaagtgcattgtttccttttatagattg--caaata-atggtgccttgaaggagcaccaaaa---

upper sequence: GRMZM2G565856_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA09G40260.1 (Glycine max), 5'ss of exon 8
CGAGAACTTGGAAAATCTTGATCTTTACCATTATGCTCTTTTCTCAGACAATGTTTTGTCAGCATCAGTTGTGGTCAACTCAACCATCATGAATGCAAAGgttagtgtaatccccatcttgaaactggaagtgtaatatcttcattatgtctaccatggaatggcccattatatagcacttttgatttttttttctataa--------------------------------------------------------------------------------------------------------
 ||||| ||||| |||| |  ||| || |||||||| || ||||| |||||||| ||| | ||||| ||||| ||||||||||| ||  ||||||||||||| | | ||| |    | ||   | |   |||||  ||| | |   |||||||    |  ||       |||| |  |    | |||| |  ||  |                                                                                                           
TGAGAATTTGGAGAATCCTAGTCTCTATCATTATGCCCTGTTCTCGGACAATGTCTTGGCTGCATCTGTTGTTGTCAACTCAACTATTGTGAATGCAAAGgtgact-taaacagtcttttacca-taccagtgtg-tatgtgc---atgtctatatagatattcttttatatagatgatgaataatttgtgcttgcactgtacaacccggacatattttgtttgtgcagtgcatccctgactcagtaaataatataattaaactttgccttcattatcttatgtttgtgtcttcaacattgcag

upper sequence: GRMZM2G565856_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA03G02250.1 (Glycine max), 5'ss of exon 13
CGAGAACTTGGAAAATCTTGATCTTTACCATTATGCTCTTTTCTCAGACAATGTTTTGTCAGCATCAGTTGTGGTCAACTCAACCATCATGAATGCAAAGgttagtgtaatccccatcttgaaactggaagtgta-----atatcttcattatgtctaccatggaatggcccattatatagcacttttgatttttttttctataa---------------------------------------------------------------------------------------
 ||||| ||||| ||||    |||||| || || || || |||||||| ||||| ||| | ||||| ||||| ||||||||||| || |||||||| ||||| | |        | | || |   |   ||| |        |  |||||| | ||         || ||  || |    ||    ||||   |  |    |||                                                                                        
TGAGAATTTGGAGAATCCCAGTCTTTATCACTACGCACTGTTCTCAGATAATGTCTTGGCTGCATCTGTTGTTGTCAACTCAACTATTATGAATGCTAAGgtgacttgggctgtctttttaaccataccagtatttgtgtgcaagttcattgtttccttttatagattgcaaataagggtgc---cttgaccatggtcaacatatcgtgcatgtgaaagtgtatctatgatttagtaaattatattattaaaaccaggcctcataacttagtttctgtcttcaatgttgcag

upper sequence: GRMZM2G565856_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA18G45750.1 (Glycine max), 5'ss of exon 7
CGAGAACTTGGAAAATCTTGATCTTTACCATTATGCTCTTTTCTCAGACAATGTTTTGTCAGCATCAGTTGTGGTCAACTCAACCATCATGAATGCAAAGgttagtgtaatccccatcttgaaactggaagtgtaatatcttcattatgtctaccatggaatggcccattatatagcacttttgatttttttttctataa--------------------------------------------------------------------------------------------------------
 ||||| ||||| |||| |  ||| || |||||||| || ||||| |||||||| ||| | ||||| ||||| ||||||||||||||  ||||||||||||| | |   |    | | ||  |  |   |||||  | | | |||  | | ||   || |||      ||||| |  |    | |||| |  ||  |                                                                                                           
TGAGAATTTGGAGAATCCTAGTCTCTATCATTATGCCCTGTTCTCGGACAATGTCTTGGCTGCATCTGTTGTTGTCAACTCAACCATTGTGAATGCAAAGgtgacttggactgtctttttcca--taccagtgtg-tgtgtacat-gtctgtatagtg-aatttttttttatagatgatgaataatttgtgcttgcactgtacaacccggacatagtttgtttgcttgtgcatccctgacaaaataaataatataattaaactttgccttcattatcttatgttcgtgtcttccaacgttgtag

upper sequence: GRMZM2G565856_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv15s0048g01300.t01 (Vitis vinifera), 5'ss of exon 8
CGAGAACTTGGAAAATCTTGATCTTTACCATTATGCTCTTTTCTCAGACAATGTTTTGTCAGCATCAGTTGTGGTCAACTCAACCATCATGAATGCAAAGgt----tagtgtaatccccatcttgaaactggaagtgtaatatcttcattatgtctaccatggaatggcccattatatagcacttttgatttttttttctataa
 ||||| ||||||||||   ||||||||||||||||||| ||||| || ||||| ||| | || |||||||| ||||||||||||||| ||||||| |||||    | ||| | |      ||| | ||| | |   | |  |  || |  | ||    |   ||    ||| ||| ||| |      | ||| | | | ||  
TGAGAATTTGGAAAATCCAAATCTTTACCATTATGCTCTCTTCTCTGATAATGTATTGGCTGCTTCAGTTGTTGTCAACTCAACCATCTTGAATGCCAAGgtgaagtggtggatttatttactttatactagcatctttaagtgatcttcttatcctagacttaaaacaccagtat-tagtatcccctaatttatctac-at--

upper sequence: GRMZM2G565856_T01 (Zea mays), 5'ss of exon 9
lower sequence: PP1S251_8V6.1 (Physcomitrella patens), 5'ss of exon 8
CGAGAACTTGGAAAATCTTGATCTTTACCATTATGCTCTTTTCTCAGACAATGTTTTGTCAGCATCAGTTGTGGTCAACTCAACCATCATGAATGCAAAGgttagtgtaatccccatcttgaaactggaagtgtaatatcttcattatgtctaccatggaatggcccattatatagcacttttgatttttttttctataa---
  | || |||||| ||| || | | | ||| |||||||||||||| |||||  ||||| ||||| |||||||||| ||||| || || |  ||||| |||||  |  |  ||   ||     ||    || | |    | | |   |     ||  ||   ||    ||   |   |  || | | |||||      ||    
AAATAAATTGGAAGATCCTGCTTTGTTCCACTATGCTCTTTTCTCTGACAACATTTTGGCAGCAGCAGTTGTGGTGAACTCCACTATTACCAATGCGAAGgtatgccttttctaaatagcagaatcccaattttgcagtttac---aaacgaacgttgtcttgaaaaataggactacttttatcagtttttgccacgtatatc

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAGAACTTGGAAAATCTTGATCTTTACCATTATGCTCTTTTCTCAGACAATGTTTTGTCAGCATCAGTTGTGGTCAACTCAACCATCATGAATGCAAAGgttagtgtaatccccatcttgaaactggaagtgtaatatcttcattatgtctaccatggaatggcccattatatagcacttttgatttttttttctataa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG