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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCTCTGTTGAATTCGAAGTTGCTGATTGCACCACAAAGGATTACCCAGAAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAAgtatgtttcactctataattcaatccttttccgtgtaagtagttactacttatttccacagttatatcatggaatagaagaaatgcatcttcaggtgaaa...

Basic information

species Zea mays
transcript GRMZM2G170400_T03
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G170400_T03 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os05g47545.1 (Oryza sativa), 5'ss of exon 8
GTGCTCTGTTGAATTCGAAGTTGCTGATTGCACCACAAAGGATTACCCAGAAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAAgtatgtttcactctata-attcaatccttttccgtgtaagtagttactacttatttccacagttatatcatggaatagaagaaatgcatcttcaggtgaaa
||| || ||||| || ||||| ||||||||||||||||||   ||| ||  |||||  ||||| || |||||||||||||||||||| ||||||||||| ||||||||||||  | | | |  |    | |   |  |||||  | |||||||    |||| |||||  | | || ||                       
GTGTTCGGTTGAGTTTGAAGTAGCTGATTGCACCACAAAGACCTACGCACCAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACATgtatgtttcacttcagagaatttacagatgtttctacaagta--tcctacttaa---cacaattatactacg-aacag-----------------------

upper sequence: GRMZM2G170400_T03 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os05g47540.4 (Oryza sativa), 5'ss of exon 6
GTGCTCTGTTGAATTCGAAGTTGCTGATTGCACCACAAAGGATTACCCAGAAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAAgtatgtttcactctata-attcaatccttttccgtgtaagtagttactacttatttccacagttatatcatggaa------tagaagaaatgcatcttcaggtgaaa---------------------------------------------------------------------------
||| || ||||| || ||||| ||||||||||||||||||   ||| ||  |||||  ||||| || |||||||||||||||||||| ||||||||||| ||||||||||||  | | | |  |    | |   |  |||||  | |||||||    |||| |||||  | | |       | |     ||   |  ||| | || |                                                                           
GTGTTCGGTTGAGTTTGAAGTAGCTGATTGCACCACAAAGACCTACGCACCAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACATgtatgtttcacttcagagaatttacagatgtttctacaagta--tcctacttaa---cacaattatactacgaacagctgttcgccagcatagctgatcacgggatacttacctattacaactttgtagttgagttaaccacagaagcaacagtcttacgattgctatacatggttttacag

upper sequence: GRMZM2G170400_T03 (Zea mays), 5'ss of exon 6
lower sequence: AT1G73600.1 (Arabidopsis thaliana), 5'ss of exon 8
GTGCTCTGTTGAATTCGAAGTTGCTGATTGCACCACAAAGGATTACCCAGAAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAAgtat--gtttcactctataattcaatccttttccgtgtaagtagtta-ctacttatt--tccacagttatatcatggaatagaagaaatgcatcttcaggtgaaa
 |||||||| ||||||||||| |||||||||||||  ||||| || || || || |  ||||| || || || ||| | |||||||| || || || |||||||  | |||      |  |||   |||| |   | ||| | | || | | ||  |  |||   ||  ||   |                              
ATGCTCTGTAGAATTCGAAGTAGCTGATTGCACCAAGAAGGAGTATCCTGATAACACCTTTGATGTTATTTATAGCAGAGACACCATTCTACATATCCAAgtataagcttccgctatttcttcttcccttatgactttaatttggtatccattttgtaatccctggtcttactctcag---------------------------

upper sequence: GRMZM2G170400_T03 (Zea mays), 5'ss of exon 6
lower sequence: AT3G18000.1 (Arabidopsis thaliana), 5'ss of exon 8
GTGCTCTGTTGAATTCGAAGTTGCTGATTGCACCACAAAGGATTACCCAGAAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAAgtat---gtttcactctataattcaatccttttccgtgtaagtagttactacttatttccacagttatatcatggaatagaagaaatgcatcttcaggtgaaa
 ||||| ||||| || || ||||||||||||||||||||  | |||||||| |||   ||||| ||||| |||||||||||||| || || ||||| ||||||       | |    ||| |||  || |      |   | | || | | |||| |    |  |  | || |                              
CTGCTCGGTTGAGTTTGAGGTTGCTGATTGCACCACAAAACACTACCCAGATAATTCGTTTGATGTCATTTACAGCCGTGACACTATTCTGCACATCCAAgtactcaacatgatctcatagttctctcttggaagtttataattgtgaatgcttactcattctctcttttcttcag---------------------------

upper sequence: GRMZM2G170400_T03 (Zea mays), 5'ss of exon 6
lower sequence: Vv17s0000g02430.t01 (Vitis vinifera), 5'ss of exon 8
GTGCTCTGTTGAATTCGAAGTTGCTGATTGCACCACAAAGGATTACCCAGAAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAAgta-tgtttcactctataattcaatccttttccgtgtaagtagttactacttatttccacagttatatcatggaatagaagaaatgcatcttcaggtgaaa
|||||| ||||||||||| || ||||| |||||||  ||    || || || || |  ||||| || |||||||||||||||||||| |||||||| |||||| | |  |  ||| |  |         ||  |  |   ||   |    ||| ||  |   || |  | |   ||   ||       |  |  |   |  
GTGCTCAGTTGAATTCGAGGTAGCTGACTGCACCAAGAAATCATATCCTGACAACACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATTCAAgtaatatacctttcttttttctgtgggacttttgaatggttatgcatctgttaattttattattctgcctttatattctagttccatttggttcgaaaag-

upper sequence: GRMZM2G170400_T03 (Zea mays), 5'ss of exon 6
lower sequence: Vv01s0011g05200.t01 (Vitis vinifera), 5'ss of exon 8
GTGCTCTGTTGAATTCGAAGTTGCTGATTGCACCACAAAGGATTACCCAGAAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAAgtatgtttcactctataattcaatccttttccgtgtaagtagttactacttatttccacagttatatcatggaatagaagaaatgcatctt---caggtgaaa-------------------------------------------------------------------------
 |||   || |||||||| ||||||||||||||||  ||    || || || ||||  ||||| || |||||||||||||| ||||| ||||||||||| |||    |      ||  ||     |  || | ||  | |  | |  |   | |   |  | | | |         ||  |    ||||      ||  ||||                                                                         
ATGCCTGGTCGAATTCGAGGTTGCTGATTGCACCAAGAAAACGTATCCTGATAATACATTTGATGTGATCTACAGCCGTGATACCATTCTTCACATACAGgtagtcattttcacatcctttgcagcggtttcatg--aatcatgataaacaactctgaaggatcttttgaatctccgaccatgcacatccaacatagccgaaattttttattattaattatggtttttccttttcttcatataccgccatctgatggtagctgtggaattttttag

upper sequence: GRMZM2G170400_T03 (Zea mays), 5'ss of exon 6
lower sequence: Vv01s0011g05220.t01 (Vitis vinifera), 5'ss of exon 7
GTGCTCTGTTGAATTCGAAGTTGCTGATTGCACCACAAAGGATTACCCAGAAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAAgtatgtttcactctataattcaatccttttccgtgtaagtagttactacttatttccacagttatatcatggaatagaagaaatgcatcttcaggtgaaa---
  |||  |||||||| || ||||| ||||||||||  ||    || || || | ||  ||||| || |||||||| |||||||| || |||||||||||||||    |  || | |  || |  |   || |  |      | |  |   | |   ||    || |   |    |  |     ||||  ||| | |       
TCGCTTGGTTGAATTTGAGGTTGCAGATTGCACCAAGAAAACATATCCTGATAGTACATTTGATGTGATCTACAGTCGTGACACTATTCTTCACATACAAgtaatcattcctat-ttctttatccgaatttcacgattaaggctgtt--ctgtgaacaactataaagggtcttgttaattttgtgcacattctgttcttttct

upper sequence: GRMZM2G170400_T03 (Zea mays), 5'ss of exon 6
lower sequence: EFJ28238 (Selaginella moellendorffii), 5'ss of exon 8
GTGCTCTGTTGAATTCGAAGTTGCTGATTGCACCACAAAGGATTACCCAGAAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAAgtatgtttcactctataattcaatccttttccgtgtaagtagttactacttatttccacagttatatcatggaatagaagaaatgcatcttcaggtgaaa
||||| ||| || || ||||| || |||||||||   ||| | | ||| |   | || || ||||||||||||||||| ||||||||||| || || || |||  | | |||      ||| |||  |  | |  |   |  || |   || ||||     || |     |   |       |||| ||  |||      
GTGCTTTGTCGAGTTTGAAGTCGCGGATTGCACCGAGAAGAACTTCCCCGCCGAGAGCTTCGACGTCATCTACAGCCGAGACACCATCCTCCATATCCAGgtaactcttacttctcgcttccatc--tcgcggctttgct--tttccgtttttttctttgtttctgagtggtgttcttctccatgcttc--cag------

upper sequence: GRMZM2G170400_T03 (Zea mays), 5'ss of exon 6
lower sequence: EFJ29738 (Selaginella moellendorffii), 5'ss of exon 8
GTGCTCTGTTGAATTCGAAGTTGCTGATTGCACCACAAAGGATTACCCAGAAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAAgtatgtttcactctataattcaatccttttccgtgtaagtagttactacttat-ttccacagttatatcatggaatagaagaaatgcatcttcaggtgaaa
||||| ||| || || ||||| || |||||||||   ||| | | ||| |   | || || ||||||||||||||||| ||||||||||| || || || |||  | |  ||      ||| |||      | |     |   |  |   | | || |  ||||    || |   |    |  |||| ||  |||      
GTGCTTTGTCGAGTTTGAAGTCGCGGATTGCACCGAGAAGAACTTCCCCGCCGAGAGCTTCGACGTCATCTACAGCCGAGACACCATCCTCCATATCCAGgtaactctttcttctcgcttccatctcgcggctttgcttttccttttgtctgtgtttctgagtt---ccaggtgttcttcgccatgcttc--cag------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|9952581|gb|BE639269.1|BE639269
EST:     AAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAA                         GACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGGTGGC
genomic: AAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAAgtatgtttca ... tttattatagGACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGGCGGC
EST: gi|211028111|gb|FK976187.1|FK976187
EST:     AAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAA                         GACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGGTGGC
genomic: AAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAAgtatgtttca ... tttattatagGACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGGCGGC
EST: gi|211028113|gb|FK976189.1|FK976189
EST:     AAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAA                         GACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGG
genomic: AAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAAgtatgtttca ... tttattatagGACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGG
EST: gi|32921380|gb|CF026192.1|CF026192
EST:     AAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAA                         GACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGGCGGC
genomic: AAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAAgtatgtttca ... tttattatagGACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGGCGGC
EST: gi|211040369|gb|FK976253.1|FK976253
EST:     AAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAA                         GACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAAT
genomic: AAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAAgtatgtttca ... tttattatagGACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAAT
EST: gi|32849481|gb|CD989162.1|CD989162
EST:     AAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAA                         GACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGGTGGC
genomic: AAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAAgtatgtttca ... tttattatagGACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGGCGGC
EST: gi|26558858|gb|CA831093.1|CA831093
EST:     AAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAA                         GACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGGTGGC
genomic: AAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAAgtatgtttca ... tttattatagGACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGGCGGC
EST: gi|22133812|gb|BQ833918.1|BQ833918
EST:     AAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAA                         GACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGGTGGC
genomic: AAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAAgtatgtttca ... tttattatagGACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGGCGGC
EST: gi|22520840|gb|BU079651.1|BU079651
EST:     AAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAA                         GACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGGTGGC
genomic: AAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAAgtatgtttca ... tttattatagGACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGGCGGC
EST: gi|211467069|gb|FL200605.1|FL200605
EST:     TTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAA                         GACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGGTGGC
genomic: TTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAAgtatgtttca ... tttattatagGACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGGCGGC
EST: gi|211028112|gb|FK976188.1|FK976188
EST:     AAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAA                         GACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGGTGGC
genomic: AAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAAgtatgtttca ... tttattatagGACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGGCGGC
EST: gi|211469585|gb|FL200609.1|FL200609
EST:     TTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAA                         GACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGGTGGC
genomic: TTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAAgtatgtttca ... tttattatagGACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGGCGGC
EST: gi|60357947|gb|DN224920.1|DN224920
EST:     AAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAA                         GACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGGCGGC
genomic: AAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAAgtatgtttca ... tttattatagGACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGGCGGC
EST: gi|4804123|gb|AI665989.1|AI665989
EST:     TAGTTTTGACGTCATCTACAGCCGTGAC-CCATCCTTCACATACAA                         GACAAGCCTGCTCTGTTCAGAAGCTTCTTCNAATGGCTAAAGCCCGGTGGC
genomic: TAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAAgtatgtttca ... tttattatagGACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGGCGGC
EST: gi|113703873|gb|EE681377.1|EE681377
EST:     AAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAA                         GACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGGCGGC
genomic: AAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAAgtatgtttca ... tttattatagGACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGGCGGC
EST: gi|211028109|gb|FK976185.1|FK976185
EST:     AAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAA                         GACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGGTGGC
genomic: AAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAAgtatgtttca ... tttattatagGACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGGCGGC
EST: gi|84979968|gb|DW530317.1|DW530317
EST:     AAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAA                         GACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGGCGGC
genomic: AAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAAgtatgtttca ... tttattatagGACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGGCGGC
EST: gi|87156028|gb|DY400817.1|DY400817
EST:     AAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAA                         GACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGGTGGC
genomic: AAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAAgtatgtttca ... tttattatagGACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGGCGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCTCTGTTGAATTCGAAGTTGCTGATTGCACCACAAAGGATTACCCAGAAAATAGTTTTGACGTCATCTACAGCCGTGACACCATCCTTCACATACAAgtatgtttcactctataattcaatccttttccgtgtaagtagttactacttatttccacagttatatcatggaatagaagaaatgcatcttcaggtgaaa

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