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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggatttgctcatcatcttttccatttacttgcacaaaataccatgatgtttgaactttttttccttattatgtggcattggcatgttttgtcatgcagcattcaaatgaaaatttttatcaatagcactccattgtcttgattgtgacttccgtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC

Basic information

species Zea mays
transcript GRMZM2G128877_T03
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 15
gtaggatttgctcatcatcttttccatttacttgcacaaaataccatgatgtttgaactttttttccttattatgtggcattggcatgttttgtcatgcagcattcaaatgaaaatttttatcaatagcactccattgtcttgattgtgacttccgtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC
                                              |  |   |    | |||||    |   ||||||||  | | | ||||      ||| ||    ||    | ||| |   |   | |  |||||  ||| |    || ||     ||||||||||||||||||| || |||||||||||||||||||||||||||||||||||||| || |||||||||||||||||||||||||||||||| |||||
----------------------------------------------tagtacgtacgttatttttaaacaagctgtggcataagtaagatttg------agcttt----tgttgttctttgt--gtgatattt-attgt--tgact----ctaccccacattcagCTTGTTGGTAAAGACGCACTGGCAGAATCTGACAAGATTACACTGGAGACAGCAAAACTTCTGAGAGAAGATTATTTGGCACAAAATGCATTCACCCC

upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 12
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 16
gtaggatttgctcatcatcttttccatttacttgcacaaaataccatgatgtttgaactttttttccttattatgtggcattggcatgttttgtc------atgcagcattcaaatgaaaatttttatcaatagcactccattgtcttgattgtgacttccgtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC
                                                                        ||||    ||| | ||  || |       |  |||   |   | |  | | |||   ||  | |||   ||| |       |  |||   ||||| |||||||| || ||||||||||| ||||||   ||||| || ||| |||| ||||| |||||| |||| ||||||||  | || ||||| || ||||| ||
----------------------------------------------------------------------gcatgtaaacttgacttgagttatagaaggaaaacagtgctagcacgttattcttttcgaaaggaacttatttgacccacacattgctttt-tgtgtgcagCTTGTAGGAAAAGATGCGCTAGCAGAAGGGGACAAAATCACATTGGAAACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACC

upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 12
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 16
gtaggatttgctcatcatcttttccatttacttgcacaaaataccatgatgtttgaactttttttccttattatgtggcattggcatgttttgtcatgcagcattcaaatgaaaatttttatcaatagcactccattgtcttgattgtgacttccgtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC
                                |||   |    | |||  |||  | |||  | |   | ||   |   |||       |  |  |  | || ||||||||    |||    | || | | |  ||     ||||| |  |||||     | ||||||||||| || |||||  |||||||| | || || |||||||||||||| ||||||||  |||| || || |||                       
--------------------------------tgctagatgctcaatgg-gttccaccttcctcttaatcttggatttaatttaggaaatcag--actctgc-ttcaaatg---ctttgctgctattgtaattgataagTCTGATTAT--CTTCCAACATTGCAGCTTGTTGGAAAGGATGCTTTGGCAGAAACGGATAAAATTACACTGGAGACTGCAAAGCTCTTGAGGGAGGACTATC----------------------

upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 12
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 16
gtaggatttgctcatcatcttttccatttacttgcacaaaataccatgatgtttgaactttttttccttattatgtggc-attggcatgttttgtcatgcagcattcaaatgaaaatttt--tatcaatagcactccattgtcttgattgtgacttccgtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC
                                                                   | | |      | ||| |      || | | || ||||    ||||    |||  | |   |    | | |  |   |  || ||| ||   |   | |||||||| || ||||||||  | || ||| | || || ||||| || ||||| ||||||||  |||| ||||| ||| | ||||||||||||||||||||
------------------------------------------------------------------ttcactggaaaactattagggaaaattatta-gctgcatgtccatgatccctttatttttcctctttcacaaaaggtctatttctgatttgattac-tgcagCTTGTCGGAAAAGATGCTTTAGCTGAAACAGATAAAATTACTCTAGAGACTGCAAAGCTTTTGAGGGAAGACTATCTTGCACAAAATGCATTTACCCC

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|32929207|gb|CF034019.1|CF034019
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAGgtaggatttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
EST: gi|60338201|gb|DN205174.1|DN205174
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAGgtaggatttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
EST: gi|13149764|gb|BG320086.1|BG320086
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAG                         CTTGTCGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAGgtaggatttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
EST: gi|32831320|gb|CD970998.1|CD970998
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAGgtaggatttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
EST: gi|32928400|gb|CF033212.1|CF033212
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAGgtaggatttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
EST: gi|32837774|gb|CD977452.1|CD977452
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAGgtaggatttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
EST: gi|74035379|gb|DT535868.1|DT535868
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAAGAC
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAGgtaggatttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGA-GAC
EST: gi|5296280|gb|AI783050.1|AI783050
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAG                         CTTGTCGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAGgtaggatttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
EST: gi|5846764|gb|AI999847.1|AI999847
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAG                         CTTGTCGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAGgtaggatttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
EST: gi|32939925|gb|CF044744.1|CF044744
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAGgtaggatttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
EST: gi|211532168|gb|FL123442.1|FL123442
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAGgtaggatttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
EST: gi|211152801|gb|FL123511.1|FL123511
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAG                         CTTGTTGGTNAAGAWGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAGgtaggatttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
EST: gi|211154401|gb|FL123520.1|FL123520
EST:     AGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATNGAA-TTGTGCAG                         CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
genomic: AGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAAT-GAAATTGTGCAGgtaggatttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
EST: gi|5847131|gb|AW000210.1|AW000210
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAG                         CTTGTCGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAGgtaggatttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
EST: gi|33092495|gb|CF052489.1|CF052489
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAGgtaggatttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
EST: gi|5846817|gb|AI999900.1|AI999900
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAG                         CTTGTCGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAGgtaggatttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
EST: gi|5846863|gb|AI999946.1|AI999946
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAG                         CTTGTCGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAGgtaggatttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
EST: gi|67040096|gb|CO466351.1|CO466351
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAGgtaggatttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
EST: gi|149076737|gb|EE165383.2|EE165383
EST:     AGGTGTTGCAGAGGGGAGGAGGATCTAAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCGCTGGCAGAATTTGACAAGATTACACTGGAGACA
genomic: AGGTGTTGCAGA-GGGAGGACGATCT-AAATGAAATTGTGCAGgtaggatttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
EST: gi|32836684|gb|CD976362.1|CD976362
EST:     AAGCACGTGAGGTGCTGCAGAGGAAGTACGATCTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAGgtaggatttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
EST: gi|83278503|gb|DV942511.1|DV942511
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAGgtaggatttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
EST: gi|5343199|gb|AI795384.1|AI795384
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAG                         CTTGTCGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAGgtaggatttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
EST: gi|5296225|gb|AI782905.1|AI782905
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAG                         CTTGTCGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAGgtaggatttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
EST: gi|5325051|gb|AI783242.1|AI783242
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAG                         CTTGTCGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAGgtaggatttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
EST: gi|211156008|gb|FL123543.1|FL123543
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAGgtaggatttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
EST: gi|32910829|gb|CF015641.1|CF015641
EST:     CGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
genomic: CGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAGgtaggatttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
EST: gi|67025855|gb|CO454604.1|CO454604
EST:     AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA
genomic: AAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAGgtaggatttg ... gtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaatttttatcaatagcactccattgtcttgattgtgacttccgtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC
                            tcttgat  putative branch site (score: 4)
                                        cttccgt  putative PPT
     tttttatcaata  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggatttgctcatcatcttttccatttacttgcacaaaataccatgatgtttgaactttttttccttattatgtggcattggcatgttttgtcatgcagcattcaaatgaaaatttttatcaatagcactccattgtcttgattgtgacttccgtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC

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