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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATCAAGAACAACTGCCTGATCGGTGGTGACGACTTCAAGAGTGGGCAGACCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtacaatttatcaatgaaacctgatatccccccttcgaaatgtttttggcagacgacatacttacaataattcgtgtatatgttcatgcag

Basic information

species Zea mays
transcript GRMZM2G004528_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004528_T03 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g09250.3 (Oryza sativa), 5'ss of exon 6
TATCAAGAACAACTGCCTGATCGGTGGTGACGACTTCAAGAGTGGGCAGACCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtacaatttatcaatgaaacctgatatccccccttcgaaatgtttttggcagacgacatacttacaataattcgtgtatatgttcatgcag----------------------------
||| ||||||||||||||||| |||||||| || ||||||||||| ||||| |||||||| || ||| |||||||||| || |||||||||||||||||||||| |   ||  || ||| |   |  |   | ||      |  ||     | ||| || ||| |   || |  | | ||| |  |  | |                            
TATTAAGAACAACTGCCTGATTGGTGGTGATGATTTCAAGAGTGGACAGACAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGTTGGTGCTGGAATAAAGgtaccaaccatatatcaaatcctttggctagctttt----cgcattgaaacgtcgatattcttccggaaacttttttttatatataacctgataagaactttggcttttgttttcgtag

upper sequence: GRMZM2G004528_T03 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA18G02210.3 (Glycine max), 5'ss of exon 6
TATCAAGAACAACTGCCTGATCGGTGGTGACGACTTCAAGAGTGGGCAGACCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtacaatttatcaatgaaacctgatatccccccttcgaaatgtttttggc--agacgacatacttacaataattcgtgtatatg-ttcatgcag-----------------------------------------------------------------------
 |||  ||  |||    |||| ||||| || |||||||||||||| |||||||| |||||||| ||  |||||||||||||||| || ||||| || ||||||||  || |   |  |  || || ||    | | |   |  ||||  |   ||| |  ||        |  |  |||| |   || |||||                                                                        
CATCGCGAGGAACACTTTGATTGGTGGAGATGACTTCAAGAGTGGTCAGACCAAAATGAAATCTGTGTTGGTTGATTTTCTTGTGGGGGCTGGTATCAAGgtaca--ttgttgttata--ctaatgtcatatcatgggtgttatttttactaggacaatctatcctttgcatgttttgtaaacaatttatgcatcgtgctagatttatatgtcaaaaatggagaaatgagttgattttttcaagtgttctgttgatgattgacag

upper sequence: GRMZM2G004528_T03 (Zea mays), 5'ss of exon 6
lower sequence: AT5G10170.1 (Arabidopsis thaliana), 5'ss of exon 6
TATCAAGAACAACTGCCTGATCGGTGGTGACGACTTCAAGAGTGGGCAGACCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtaca-atttatcaatga--aacctgatatccccccttcgaaatgtttttggcagacgacatacttacaataattcgtgtatatgttcatgcag
 || ||||  |||||| ||||||||||||| |||||||||||||| |||||||||||||| || ||||| || ||||| |||||||| || ||||| || ||||  | |  | ||| |  | ||| ||        ||  | ||| |   |  | |  ||  | |||     |||  | |||||||  |     
CATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGTTGGCGCCGGAATCAAAgtacttaatcctaaataagtatcctaattaaatttattttatatggtaacgttacaaaacgaaattaattgcatttatctatatgtatag----

upper sequence: GRMZM2G004528_T03 (Zea mays), 5'ss of exon 6
lower sequence: AT2G22240.1 (Arabidopsis thaliana), 5'ss of exon 4
TATCAAGAACAACTGCCTGATCGGTGGTGACGACTTCAAGAGTGGGCAGACCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtac---aatttatcaatgaa-acctgatatccccccttcgaaatgtttttggcagacgacatacttacaataattcgtgtatatgttcatgcag
|||   ||| || ||  |||| ||||| || || ||||||||||| ||||| ||||||||||| ||  |||||||||| |||||||| ||||| || ||||||    |||| |    ||   | |   || ||   ||| |      || ||  ||   |   ||| | |||   |  |||    |         
TATATCGAAGAATTGTTTGATTGGTGGGGATGATTTCAAGAGTGGTCAGACTAAGATGAAATCCGTTTTGGTTGATTTCCTTGTTGGAGCTGGCATTAAGgtaatagaattaaagcttgtttatcaagtaacctaactt-gcttctcttctgttagtgaaggaactaagaatggattttgtggcag---------

upper sequence: GRMZM2G004528_T03 (Zea mays), 5'ss of exon 6
lower sequence: AT4G39800.1 (Arabidopsis thaliana), 5'ss of exon 6
TATCAAGAACAACTGCCTGATCGGTGGTGACGACTTCAAGAGTGGGCAGACCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtacaatttatcaatgaaacctgatatcccccctt----cgaaatgtttttggcagacgacat-acttacaataatt-cgtgtatatgttcatgcag
 |||| ||||||     |||||||||| || || ||||||||||| || |||||||||||||| ||| |||||||||| || ||||| || ||||| |||||    || |     | | |  | ||  |   |||    |  ||  | |||| || | ||| |   || || | |||  |||| | |||| ||    
GATCAGGAACAATGTTTTGATCGGTGGAGATGATTTCAAGAGTGGTCAAACCAAGATGAAATCTGTCTTGGTTGATTTCCTAGTTGGCGCAGGAATCAAGgtttgtttaacttgcgtatcaagttactctttcttgttactgaaaatatttgtcacaagactttggtttcattgattgtgtgtttttgtttatag--

upper sequence: GRMZM2G004528_T03 (Zea mays), 5'ss of exon 6
lower sequence: PP1S55_204V6.1 (Physcomitrella patens), 5'ss of exon 5
TATCAAGAACAACTGCCTGATCGGTGGTGACGACTTCAAGAGTGGGCAGACCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtacaatttat-caatgaaacctgatatccccccttcgaaatgtttttggcagacgacatacttacaataattcgtgtatatgttc---atgcag------------------------------------------------------------------------------------------
| |  | || ||||   | || |||||||||||||||||||| || || || ||||||||||| || || || || ||||| ||||| || ||||| |||||        | |||||      |  ||          ||    || |  |   ||    |   |   ||    || ||| | ||    || |||                                                                                          
TGTTGAAAAGAACTCATTAATTGGTGGTGACGACTTCAAGAGCGGTCAAACGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAGgtgagccaagtgcaatgtgtagaggaataaatgtaataaagc-cttctaacttgcgctgaatccaacttagaatgtctattttttttggattcaggtgtgtctagaactgaagtttatgctttgcgaagctggaatgattgctatgaaagctttgcactgaacccacaattgttggtgtgcacag

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|32855391|gb|CD995072.1|CD995072
EST:     CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAG                         CCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
genomic: CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtacaattta ... gttcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
EST: gi|32856301|gb|CD995982.1|CD995982
EST:     CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAG                         CCCACCTCGATTGTNNGAGCTACAACCACTTGGGAAACAACGACGGCATGA
genomic: CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtacaattta ... gttcatgcagCCCACCTCGATTGT--GAGCTACAACCACTTGGGAAACAACGACGGCATGA
EST: gi|32855713|gb|CD995394.1|CD995394
EST:     CCTAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAG                         CCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
genomic: CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtacaattta ... gttcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
EST: gi|6637095|gb|AW261367.1|AW261367
EST:     CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAG                         CCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
genomic: CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtacaattta ... gttcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
EST: gi|211037209|gb|FK948218.1|FK948218
EST:     CCAAGATGAAATCGGTCCTGGTTGATTTCCTTGTTGGTGCTGGAATAAAG                         CCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
genomic: CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtacaattta ... gttcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
EST: gi|91871596|gb|EB401553.1|EB401553
EST:     CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAG                         CCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
genomic: CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtacaattta ... gttcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
EST: gi|13516068|gb|BG518344.1|BG518344
EST:     CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAG                         CCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
genomic: CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtacaattta ... gttcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
EST: gi|6527007|gb|AW216231.1|AW216231
EST:     CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGNTGGTGCTGGAATAAAG                         CCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
genomic: CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtacaattta ... gttcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
EST: gi|6637051|gb|AW261323.1|AW261323
EST:     CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAG                         CCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
genomic: CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtacaattta ... gttcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
EST: gi|32831002|gb|CD970680.1|CD970680
EST:     CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAG                         CCCACCTCGATTGTGAGCTACAACCACTTTCGCAAACAACGACGGCATGAA
genomic: CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtacaattta ... gttcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGG-AAACAACGACGGCATGAA
EST: gi|32803449|gb|CD955685.1|CD955685
EST:     CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAG                         CCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGGCGGCATGAAC
genomic: CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtacaattta ... gttcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
EST: gi|32854168|gb|CD993849.1|CD993849
EST:     CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAG                         CCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
genomic: CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtacaattta ... gttcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
EST: gi|211029038|gb|FL245284.1|FL245284
EST:     CCAAGATGAAATCGGTCCTGGTTGATTTCCTTGTTGGTGCTGGAATAAAG                         CCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
genomic: CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtacaattta ... gttcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
EST: gi|33098850|gb|CF058810.1|CF058810
EST:     CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAG                         CCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
genomic: CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtacaattta ... gttcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
EST: gi|6564123|gb|AW231745.1|AW231745
EST:     CCAAGATGAAATCGGTCCTGGT-GATTTTCTTGTTGGTGCTGGAATAAAG                         CCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGG
genomic: CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtacaattta ... gttcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGG
EST: gi|32921535|gb|CF026347.1|CF026347
EST:     CCAAGATGAAATCGGTCCTGGTTGATTTCCTTGTTGGTGCTGGAATAAAG                         CCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
genomic: CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtacaattta ... gttcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
EST: gi|31364344|gb|CD448699.1|CD448699
EST:     CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAG                         CCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
genomic: CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtacaattta ... gttcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
EST: gi|32945128|gb|CF049947.1|CF049947
EST:     CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAG                         CCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
genomic: CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtacaattta ... gttcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
EST: gi|32921566|gb|CF026378.1|CF026378
EST:     CCAAGATGAAATCGGTCCTGGTTGATTTCCTTGTTGGTGCTGGAATAAAG                         CCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
genomic: CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtacaattta ... gttcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
EST: gi|60346856|gb|DN213829.1|DN213829
EST:     CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAG                         CCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
genomic: CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtacaattta ... gttcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
EST: gi|21621348|gb|BQ619354.1|BQ619354
EST:     CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAG                         CCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
genomic: CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtacaattta ... gttcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
EST: gi|32920511|gb|CF025323.1|CF025323
EST:     CCAAGATGAAATCGGTCCTGGCTGATTTCCTTGTTGGTGCTGGAATAAAG                         CCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
genomic: CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtacaattta ... gttcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC
EST: gi|67029746|gb|CO458495.1|CO458495
EST:     CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAG                         CCCACCTCGATTGTGAGCTATAACCACTTGGGAAACAACGACGGCATGAAC
genomic: CCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtacaattta ... gttcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATCAAGAACAACTGCCTGATCGGTGGTGACGACTTCAAGAGTGGGCAGACCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtacaatttatcaatgaaacctgatatccccccttcgaaatgtttttggcagacgacatacttacaataattcgtgtatatgttcatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA