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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagtattagatgtcgctcttgcgaaagcacaacatgcttccctcctacaatgttacaagtgctattttaacttaacagttgtttttttactgatgtcaagGAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAATTGAAGCTTAGTGAAATTGAGCAGCTTGCTAAAGGGCGAGGCCTGACAG

Basic information

species Zea mays
transcript GRMZM2G047509_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047509_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g14020.1 (Oryza sativa), 3'ss of exon 3
cagtattagatgtcgctcttgcgaaa-gcacaacatgcttccctcctacaatgttacaagtgctat--tttaacttaacagttgtttttttactgatgtcaagGAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAATTGAAGCTTAGTGAAATTGAGCAGCTTGCTAAAGGGCGAGGCCTGACAG
 || | ||   || | |   | || | |       |  || ||   | |  | ||   | ||| |   | || |||||| |||||||||  | |||| ||||||||||||||| | ||||||||||| || ||||||| ||||| ||||||||| ||| ||||  |||||||||||| || |||||||| ||||||||  |||
-agcaatatgcgtaggttcagagagatgtttgttttcatttccaggttccttattgataatgccaaaatatagcttaacggttgttttt--attgatctcaagGAATTGAAACAACGGGAAGAGAGTTTATCTAAAGATTTGGAGGATCTTAAACTGAGGCTTGCTGAAATTGAGCACCTCGCTAAAGGACGAGGCCTTTCAG
















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|211206703|gb|FL036107.1|FL036107
EST:     ACGCAAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAG                         GAATTGAMACGAAGGGAAGAGAGTATAGC
genomic: ACGCAAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAGgtacgccctg ... tgatgtcaagGAATTGAAACGAAGGGAAGAGAGTATAGC
EST: gi|94478836|gb|EB707794.1|EB707794
EST:     ACGCAAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAG                         GAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA
genomic: ACGCAAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAGgtacgccctg ... tgatgtcaagGAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA
EST: gi|40335360|gb|CK369430.1|CK369430
EST:     ACGCAAGGTCCGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAG                         GAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA
genomic: ACGCAAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAGgtacgccctg ... tgatgtcaagGAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA
EST: gi|17932144|gb|BM269104.1|BM269104
EST:     ACGCAAGGTCTGAGGCTAGGAAGGAGAAAGCTCGTAGACAGGAACTTGAG                         GAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA
genomic: ACGCAAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAGgtacgccctg ... tgatgtcaagGAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA
EST: gi|44900751|gb|CK827296.1|CK827296
EST:     ACGCAAGGTCCGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAG                         GAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA
genomic: ACGCAAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAGgtacgccctg ... tgatgtcaagGAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA
EST: gi|211206710|gb|FL036114.1|FL036114
EST:     ACGCAAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAG                         GAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA
genomic: ACGCAAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAGgtacgccctg ... tgatgtcaagGAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA
EST: gi|32866858|gb|CF006540.1|CF006540
EST:     ACGCAAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAG                         GAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA
genomic: ACGCAAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAGgtacgccctg ... tgatgtcaagGAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA
EST: gi|16377746|gb|BI992098.1|BI992098
EST:     ACGCAAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAG                         GAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA
genomic: ACGCAAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAGgtacgccctg ... tgatgtcaagGAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA
EST: gi|211009994|gb|FL448808.1|FL448808
EST:     ACGCAAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAG                         GAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA
genomic: ACGCAAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAGgtacgccctg ... tgatgtcaagGAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA
EST: gi|16927681|gb|BM080750.1|BM080750
EST:     ACGCAAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAG                         GAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA
genomic: ACGCAAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAGgtacgccctg ... tgatgtcaagGAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA
EST: gi|148965768|gb|EE016647.2|EE016647
EST:     ACGCAAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAG                         GAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA
genomic: ACGCAAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAGgtacgccctg ... tgatgtcaagGAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA
EST: gi|18178346|gb|BM379556.1|BM379556
EST:     ACGCAAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAG                         GAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA
genomic: ACGCAAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAGgtacgccctg ... tgatgtcaagGAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA
EST: gi|211009995|gb|FL448809.1|FL448809
EST:     AAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAAACTTGAG                         GAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAA
genomic: AAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGG-AACTTGAGgtacgccctg ... tgatgtcaagGAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAA
EST: gi|13126108|gb|BG316558.1|BG316558
EST:     ACGCAAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAG                         GAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA
genomic: ACGCAAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAGgtacgccctg ... tgatgtcaagGAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA
EST: gi|14243915|gb|BG841647.2|BG841647
EST:     ACGCAAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAG                         GAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA
genomic: ACGCAAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAGgtacgccctg ... tgatgtcaagGAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA
EST: gi|211206704|gb|FL036108.1|FL036108
EST:     ACGCAAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAG                         GAATTGAAACGAAGGGAAGAGAGTATAGCT
genomic: ACGCAAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAGgtacgccctg ... tgatgtcaagGAATTGAAACGAAGGGAAGAGAGTATAGCT
EST: gi|18169109|gb|BM338949.1|BM338949
EST:     TAGACAGGAACTTGAG                         GAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA
genomic: TAGACAGGAACTTGAGgtacgccctg ... tgatgtcaagGAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA
EST: gi|211206709|gb|FL036113.1|FL036113
EST:     CGCAAGGTCCGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACCTTGAG                         GAATTGAAACGAAGG
genomic: CGCAAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAAC-TTGAGgtacgccctg ... tgatgtcaagGAATTGAAACGAAGG
EST: gi|211117534|gb|FL480257.1|FL480257
EST:     AGCTCGTAGACAGGAACTTGAG                         GAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGHTCTTAAA
genomic: AGCTCGTAGACAGGAACTTGAGgtacgccctg ... tgatgtcaagGAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA
EST: gi|16925125|gb|BM078193.1|BM078193
EST:     ACGCAAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAG                         GAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA
genomic: ACGCAAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAGgtacgccctg ... tgatgtcaagGAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA
EST: gi|16918056|gb|BM073556.1|BM073556
EST:     ACGCAAGGTTTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAG                         GAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA
genomic: ACGCAAGGTCTGAGGCTAGGAAGGAGGAAGCTCGTAGACAGGAACTTGAGgtacgccctg ... tgatgtcaagGAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacaatgttacaagtgctattttaacttaacagttgtttttttactgatgtcaagGAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAATTGAAGCTTAGTGAAATTGAGCAGCTTGCTAAAGGGCGAGGCCTGACAG
                                          tactgat  putative branch site (score: 2)
                                    tttttttact  CT-rich tract
                 tattttaacttaacag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagtattagatgtcgctcttgcgaaagcacaacatgcttccctcctacaatgttacaagtgctattttaacttaacagttgtttttttactgatgtcaagGAATTGAAACGAAGGGAAGAGAGTATAGCTAAAGAATTGGAAGATCTTAAATTGAAGCTTAGTGAAATTGAGCAGCTTGCTAAAGGGCGAGGCCTGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - gctcttg
- - - - - - - - - - - - - -cacaaca
- - - - - - - - - - - - - - - - - tgcttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -caagtgc