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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGCGTCTTTAGCAGTTCGAAGTGGCAATGGTCTTCTCCTGAAAGGTGGAAAAGAAGCCATGAGATCGAACACAGTATTACATAAGgtattttctcatgctgacattacatgtttttagattggtgtctgaaatttttttatag

Basic information

species Zea mays
transcript GRMZM2G375504_T03
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G375504_T03 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os05g38150.1 (Oryza sativa), 5'ss of exon 10
ATTGCGTCTTTAGCAGTTCGAAGTGGCAATGGTCTTCTCCTGAAAGGTGGAAAAGAAGCCATGAGATCGAACACAGTATTACATAAGgtattttc---tcatgctgacattaca--tgtttttagattggtgtctgaaatttttttatag----------------------
||||| ||||| ||| |||||||||| |||||||||||||| ||||||||||||||||| || ||||| |||||  |||| ||||||||||| ||   | ||  ||   ||| |  || |||  | ||  ||  | || | || | | |                       
ATTGCATCTTTGGCAATTCGAAGTGGTAATGGTCTTCTCCTAAAAGGTGGAAAAGAAGCTATCAGATCAAACACGATATTGCATAAGgtattatccttttatcttgtggttaaaattgctttctggttt-tgctttaactgttgtaaaaaacatcgatttattcttttctag

upper sequence: GRMZM2G375504_T03 (Zea mays), 5'ss of exon 10
lower sequence: Vv13s0019g02360.t01 (Vitis vinifera), 5'ss of exon 11
ATTGCGTCTTTAGCAGTTCGAAGTGGCAATGGTCTTCTCCTGAAAGGTGGAAAAGAAGCCATGAGATCGAACACAGTATTACATAAGgtattttct--catgctgacattacatgtttttagattggtgtctgaaatttttttatag--------------------------------------------------------------------------------
|| || || |||||| | |||||||| ||||| |||||| |||||||||||||||| |||| | |||| ||  || | || || ||||| || | |   |  || |   |  |||       ||||  ||   | |||  ||| ||                                                                                 
ATAGCTTCATTAGCAATCCGAAGTGGGAATGGACTTCTCTTGAAAGGTGGAAAAGAGGCCAAGCGATCTAATGCAATCTTGCACAAGgttttctttattaaactaagtatttatggaagataattgaagtgcaacattggtttttatttttcttggtctaaatgagtatttatgaaaggttttctttcattttctgaatcttattactcttttttcttaaattttag
















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|213179639|gb|FM187655.1|FM187655
EST:     TCCTGAAAGGTGGAAAAGAAGCCATGAGATCGAACACAGTATTACATAAG                         GTTATAACTGGCGCAATTCCTGACAACGTGGGTCAAAAACTTATTGGCCTT
genomic: TCCTGAAAGGTGGAAAAGAAGCCATGAGATCGAACACAGTATTACATAAGgtattttctc ... ttttttatagGTTATAACTGGCGCAATTCCTGACAACGTGGGTCAAAAACTTATTGGCCTT
EST: gi|211356647|gb|FL094993.1|FL094993
EST:     TCCTGAAAGGTGGAAAAGAAGCCATGAGATCGAACACAGTATTACATAAG                         GTTATAACTGGCGCAATTCCTGACAACGTGGGTCAAAAACTTATTGGCCTT
genomic: TCCTGAAAGGTGGAAAAGAAGCCATGAGATCGAACACAGTATTACATAAGgtattttctc ... ttttttatagGTTATAACTGGCGCAATTCCTGACAACGTGGGTCAAAAACTTATTGGCCTT
EST: gi|60348148|gb|DN215121.1|DN215121
EST:     TCCTGAAAGGTGGAAAAGAAGCCATGAGATCGAACACAGTATTACATAAG                         GTTATAACTGGCGCAATTCCTGACAACGTGGGTCAAAAACTTATTGGCCTT
genomic: TCCTGAAAGGTGGAAAAGAAGCCATGAGATCGAACACAGTATTACATAAGgtattttctc ... ttttttatagGTTATAACTGGCGCAATTCCTGACAACGTGGGTCAAAAACTTATTGGCCTT
EST: gi|32934077|gb|CF038889.1|CF038889
EST:     TCCTGAAAGGTGGAAAAGAAGCCATGAGATCGAACACAGTATTACATAAG                         GTTATAACTGGCGCAATTCCTGACAACGTGGGTCAAAAACTTATTGGCCTT
genomic: TCCTGAAAGGTGGAAAAGAAGCCATGAGATCGAACACAGTATTACATAAGgtattttctc ... ttttttatagGTTATAACTGGCGCAATTCCTGACAACGTGGGTCAAAAACTTATTGGCCTT
EST: gi|32933434|gb|CF038246.1|CF038246
EST:     AAAAGAAGCCATGAGATCGAACACAGTATTACATAAG                         GTTATAACTGGCGCAATTCCTGACAACGTGGGTCAAAAACTTATTGGCCTT
genomic: AAAAGAAGCCATGAGATCGAACACAGTATTACATAAGgtattttctc ... ttttttatagGTTATAACTGGCGCAATTCCTGACAACGTGGGTCAAAAACTTATTGGCCTT
EST: gi|32934404|gb|CF039216.1|CF039216
EST:     TCCTGAAAGGTGGAAAAGAAGCCATGAGATCGAACACAGTATTACATAAG                         GTTATAACTGGCGCAATTCCTGACAACGTGGGTCAAAAACTTATTGGCCTT
genomic: TCCTGAAAGGTGGAAAAGAAGCCATGAGATCGAACACAGTATTACATAAGgtattttctc ... ttttttatagGTTATAACTGGCGCAATTCCTGACAACGTGGGTCAAAAACTTATTGGCCTT
EST: gi|67032674|gb|CO461423.1|CO461423
EST:     TCCTGAAAGGTGGAAAAGAAGCCATGAGATCGAACACAGTATTACATAAG                         GTTATAACTGGCGCAATTCCTGACAACGTGGGTCAAAAACTTATTGGCCTT
genomic: TCCTGAAAGGTGGAAAAGAAGCCATGAGATCGAACACAGTATTACATAAGgtattttctc ... ttttttatagGTTATAACTGGCGCAATTCCTGACAACGTGGGTCAAAAACTTATTGGCCTT
EST: gi|6564207|gb|AW231829.1|AW231829
EST:     TCCTGAAAGGTGGAAAAGAAGCCATGAGATCGAACACAGTATTACATAAG                         GTTATAACTGGCGCAATTCCTGACAACGT
genomic: TCCTGAAAGGTGGAAAAGAAGCCATGAGATCGAACACAGTATTACATAAGgtattttctc ... ttttttatagGTTATAACTGGCGCAATTCCTGACAACGT
EST: gi|78024065|gb|DV492452.1|DV492452
EST:     TCCTGAAAGGTGGAAAAGAAGCCATGAGATCGAACACAGTATTACATAAG                         GTTATAACTGGCGCAATTCCTGACAACGTGGGTCAAAAACTTATTGGCCTT
genomic: TCCTGAAAGGTGGAAAAGAAGCCATGAGATCGAACACAGTATTACATAAGgtattttctc ... ttttttatagGTTATAACTGGCGCAATTCCTGACAACGTGGGTCAAAAACTTATTGGCCTT
EST: gi|6021994|gb|AW066922.1|AW066922
EST:     TCCTGAAAGGTGGAAAAGAAGCCATGAGATCGAACACAGTATTACATAAG                         GTTATAACTGGCGCAATTCCTGACAACGTGGGTCAAAAACTTATTGGCCTT
genomic: TCCTGAAAGGTGGAAAAGAAGCCATGAGATCGAACACAGTATTACATAAGgtattttctc ... ttttttatagGTTATAACTGGCGCAATTCCTGACAACGTGGGTCAAAAACTTATTGGCCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGCGTCTTTAGCAGTTCGAAGTGGCAATGGTCTTCTCCTGAAAGGTGGAAAAGAAGCCATGAGATCGAACACAGTATTACATAAGgtattttctcatgctgacattacatgtttttagattggtgtctgaaatttttttatag

- - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC