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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcctggctatatatacgaaagtcgcccctcccttaatggttgcgatgtgttttctaattctctacatattatattcattgagttttttttttttttgcagGATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCCTTTGCAG

Basic information

species Zea mays
transcript GRMZM2G368908_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G368908_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g56646.1 (Oryza sativa), 3'ss of exon 7
-tcctggctatatata---cgaaagtcgcccctcccttaatggttgcgatgtgttttctaattctctacatattatattcattgagttttttttttttttgcagGATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCCTTTGCAG
   || || | | | |     ||  |    |     |   | | ||  |    ||| || || |  |  |||   | || |||    ||||       |  |||||||| |||||||| || || ||||| || ||||| ||||| ||||||||||||||||
taacttgccaaacaaaatttaaatataattcaaagttctgttgctgaaacaattttactgatgcagttaataacctgtttatt----ttttaaaaaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCCTTTGCAG
















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|16745925|gb|BM032355.1|BM032355
EST:     TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAG                         GATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAGgttagtccct ... ttttttgcagGATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
EST: gi|18384637|gb|BM417836.1|BM417836
EST:     TTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAG                         GATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
genomic: TTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAGgttagtccct ... ttttttgcagGATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
EST: gi|18384913|gb|BM418112.1|BM418112
EST:     TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAG                         GATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAGgttagtccct ... ttttttgcagGATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
EST: gi|60340869|gb|DN207842.1|DN207842
EST:     TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAG                         GATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAGgttagtccct ... ttttttgcagGATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
EST: gi|60355241|gb|DN222214.1|DN222214
EST:     TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAG                         GATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAGgttagtccct ... ttttttgcagGATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
EST: gi|60399723|gb|DN232533.1|DN232533
EST:     TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAG                         GATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAGgttagtccct ... ttttttgcagGATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
EST: gi|16746047|gb|BM032477.1|BM032477
EST:     TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAG                         GATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAGgttagtccct ... ttttttgcagGATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
EST: gi|211028541|gb|FL445307.1|FL445307
EST:     TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAG                         GATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAGgttagtccct ... ttttttgcagGATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
EST: gi|18383928|gb|BM417128.1|BM417128
EST:     TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAG                         GATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAGgttagtccct ... ttttttgcagGATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
EST: gi|108824177|gb|EC278185.1|EC278185
EST:     TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAG                         GATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAGgttagtccct ... ttttttgcagGATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
EST: gi|18384504|gb|BM417703.1|BM417703
EST:     TAATTGAAGGGAAGCTCCCACTGAATCATGAGA-TTTGTATCATTTGCAG                         GATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAGgttagtccct ... ttttttgcagGATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
EST: gi|32857775|gb|CD997456.1|CD997456
EST:     TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAG                         GATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAGgttagtccct ... ttttttgcagGATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
EST: gi|211046828|gb|FL451687.1|FL451687
EST:     ATCATGAGATTTTGTATCATTTGCAG                         GATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
genomic: ATCATGAGATTTTGTATCATTTGCAGgttagtccct ... ttttttgcagGATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
EST: gi|87153027|gb|DY397816.1|DY397816
EST:     TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAG                         GATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAGgttagtccct ... ttttttgcagGATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
EST: gi|32934297|gb|CF039109.1|CF039109
EST:     TCCCACTGAATCATGAGATTTTGTATCATTTGCAG                         GATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
genomic: TCCCACTGAATCATGAGATTTTGTATCATTTGCAGgttagtccct ... ttttttgcagGATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
EST: gi|18384506|gb|BM417705.1|BM417705
EST:     TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAG                         GATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAGgttagtccct ... ttttttgcagGATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
EST: gi|16925720|gb|BM078788.1|BM078788
EST:     TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAG                         GATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAGgttagtccct ... ttttttgcagGATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
EST: gi|110520623|gb|EE024807.1|EE024807
EST:     TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAG                         GATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAGgttagtccct ... ttttttgcagGATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgttttctaattctctacatattatattcattgagttttttttttttttgcagGATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCCTTTGCAG
      ttctaat  putative branch site (score: 2)
                                     ttttttttttttttgc  putative PPT
               tctacatattatattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcctggctatatatacgaaagtcgcccctcccttaatggttgcgatgtgttttctaattctctacatattatattcattgagttttttttttttttgcagGATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCCTTTGCAG

tcctggc
- - - - - - - - - - - - - - - - - - tggttgc