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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAGgttaaaagtctaaacttgtgtaactctgttttcctatctagaatttttcaatttgcagacccgttattgtttttaacttggtaacttttaacag

Basic information

species Zea mays
transcript GRMZM2G053531_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G053531_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os08g26870.5 (Oryza sativa), 5'ss of exon 9
-----------------------------------------CATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAGgttaaaagtctaaacttgtgtaactctgttttcctatctagaatttttcaatttgcagacccgttattgtttttaacttggtaacttttaacag
                                         || | |||| |||||||||||| | ||| |||||||||||| | |||||||||||| |||||   ||   |  |     | | |||||     |||    | ||| |  | ||     |   ||||| |  | | | ||  |           
AAAAAGCTAGTGGTTTTGAAAAATTGACATTGTTTTTACAGCAACGTGGAGGGACAAACTGATGCTGCTGAGGTCTAAGCGGAAAAACTGGGCCTGAAAGgtttggagctcatgccc---tgaatctgtccaattattctaattttatggaatt-----ctgattatt-tactcaccgtgacag----------

upper sequence: GRMZM2G053531_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os08g26870.3 (Oryza sativa), 5'ss of exon 10
CATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAGgttaaaagtctaaacttgtgtaactctgttttcctatctagaatttttcaatttgcagacccgttattgtttttaacttggtaacttttaacag--------------
|| | |||| |||||||||||| | ||| |||||||||||| | |||||||||||| |||||   ||   |  |     | | |||||     |||    | ||| |  | || | ||    ||| |     | ||   ||  ||  |  ||               
CAACGTGGAGGGACAAACTGATGCTGCTGAGGTCTAAGCGGAAAAACTGGGCCTGAAAGgtttggagctcatgccc---tgaatctgtccaattattctaattttatggaatt-ctgattatttactcaccgtgacagcgtggctcgtctcaatggtgtaaataaag

upper sequence: GRMZM2G053531_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os08g26870.2 (Oryza sativa), 5'ss of exon 10
CATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAGgttaaaagtctaaacttgtgtaactctgttttcctatctagaatttttcaatttgcagacccgttattgtttttaacttggtaacttttaacag
|| | |||| |||||||||||| | ||| |||||||||||| | |||||||||||| |||||   ||   |  |     | | |||||     |||    | ||| |  | ||     |   ||||| |  | | | ||  |           
CAACGTGGAGGGACAAACTGATGCTGCTGAGGTCTAAGCGGAAAAACTGGGCCTGAAAGgtttggagctcatgccc---tgaatctgtccaattattctaattttatggaatt-----ctgattatt-tactcaccgtgacag----------

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|74035418|gb|DT535906.1|DT535906
EST:     AGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAG                         CGTCGCATGTCTGGATGGTGTAAATAAAGATGACGCTCGGCTGAATTCCAG
genomic: AGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAGgttaaaagtc ... cttttaacagCGTCGCATGTCTGGATGGTGTAAATAAAGATGACGCTCAGCTGAATTCCAG
EST: gi|6695554|gb|AW288662.1|AW288662
EST:     AGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAG                         CGTCGCATGTCTGGATGGTGTAAATAAAGATGACGCTCAGCTGAATTCCAG
genomic: AGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAGgttaaaagtc ... cttttaacagCGTCGCATGTCTGGATGGTGTAAATAAAGATGACGCTCAGCTGAATTCCAG
EST: gi|84969850|gb|DW468264.1|DW468264
EST:     AGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAG                         CGTCGCATGTCTGGATGGTGTAAATAAAGATGACGCTCAGCTGAATTCCAG
genomic: AGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAGgttaaaagtc ... cttttaacagCGTCGCATGTCTGGATGGTGTAAATAAAGATGACGCTCAGCTGAATTCCAG
EST: gi|60358119|gb|DN225092.1|DN225092
EST:     AGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAG                         CGTCGCATGTCTGGATGGTGTAAATAAAGATGACGCTCAGCTGAATTCCAG
genomic: AGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAGgttaaaagtc ... cttttaacagCGTCGCATGTCTGGATGGTGTAAATAAAGATGACGCTCAGCTGAATTCCAG
EST: gi|78109883|gb|DV528299.1|DV528299
EST:     AGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAG                         CGTCGCATGTCTGGATGGTGTAAATAAAGATGACGCTCAGCTGAATTCCAG
genomic: AGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAGgttaaaagtc ... cttttaacagCGTCGCATGTCTGGATGGTGTAAATAAAGATGACGCTCAGCTGAATTCCAG
EST: gi|60341680|gb|DN208653.1|DN208653
EST:     AGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAG                         CGTCGCATGTCTGGATGGTGTAAATAAAGATGACGCTCAGCTGAATTCCAG
genomic: AGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAGgttaaaagtc ... cttttaacagCGTCGCATGTCTGGATGGTGTAAATAAAGATGACGCTCAGCTGAATTCCAG
EST: gi|88754483|gb|DY538624.1|DY538624
EST:     AGGACAAACTGATTCGGCTCAGGTTTAAGCGGGAGAACTGGGCCTGAGAG                         CGTCGCATGTCTGGATGGTGTAAATAAAGATGACGCTCAGCTGAATTCCAG
genomic: AGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAGgttaaaagtc ... cttttaacagCGTCGCATGTCTGGATGGTGTAAATAAAGATGACGCTCAGCTGAATTCCAG
EST: gi|113702906|gb|EE680410.1|EE680410
EST:     AGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAG                         CGTCGCATGTCTGGATGGTGTAAATAAAGATGACGCTCAGCTGAATTCCAG
genomic: AGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAGgttaaaagtc ... cttttaacagCGTCGCATGTCTGGATGGTGTAAATAAAGATGACGCTCAGCTGAATTCCAG
EST: gi|60394174|gb|DN227044.1|DN227044
EST:     AGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAG                         CGTCGCATGTCTGGATGGTGTAAATAAAGATGACGCTCAGCTGAATTCCAG
genomic: AGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAGgttaaaagtc ... cttttaacagCGTCGCATGTCTGGATGGTGTAAATAAAGATGACGCTCAGCTGAATTCCAG
EST: gi|116822203|gb|EC865582.1|EC865582
EST:     AGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAG                         CGTCGCATGTCTGGATGGTGTAAATAAAGATGACGCTCGGCTGAATTCCAG
genomic: AGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAGgttaaaagtc ... cttttaacagCGTCGCATGTCTGGATGGTGTAAATAAAGATGACGCTCAGCTGAATTCCAG
EST: gi|32846823|gb|CD986504.1|CD986504
EST:     AGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAG                         CGTCGCATGTCTGGATGGTGTAAATAAAGATGACGCTCGGCTGAATTCCAG
genomic: AGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAGgttaaaagtc ... cttttaacagCGTCGCATGTCTGGATGGTGTAAATAAAGATGACGCTCAGCTGAATTCCAG
EST: gi|6828185|gb|AW331828.1|AW331828
EST:     AGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAG                         CGTCGCATGTCTGGATGGTGTAAATAAAGATGACGCTCAGCTGAATTCCAG
genomic: AGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAGgttaaaagtc ... cttttaacagCGTCGCATGTCTGGATGGTGTAAATAAAGATGACGCTCAGCTGAATTCCAG
EST: gi|60359057|gb|DN226030.1|DN226030
EST:     AGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAG                         CGTCGCATGTCTGGATGGTGTAAATAAAGATGACGCTCAGCTGAATTCCAG
genomic: AGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAGgttaaaagtc ... cttttaacagCGTCGCATGTCTGGATGGTGTAAATAAAGATGACGCTCAGCTGAATTCCAG
EST: gi|78021679|gb|DV490066.1|DV490066
EST:     AGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAG                         CGTCGCATGTCTGGATGGTGTAAATAAAGATGACGCTCAGCTGAATTCCAG
genomic: AGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAGgttaaaagtc ... cttttaacagCGTCGCATGTCTGGATGGTGTAAATAAAGATGACGCTCAGCTGAATTCCAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 44

CATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAGgttaaaagtc ... cttttaacagCGTCGCATGTCTGGATGGTGTAAATAAAGATGACGCTCAGCTGAATTCCAGTATGCACTCCAGACAATTGATACTGTTTATGGCTCTATGTAACTAGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 116

CATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAGgttaaaagtc ... cttttaacagCGTCGCATGTCTGGATGGTGTAAATAAAGATGACGCTCAGCTGAATTCCAGTATGCACTCCAGACAATTGATACTGTTTATGGCTCTATGTAACTAGCTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 97

CATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAGgttaaaagtc ... cttttaacagCGTCGCATGTCTGGATGGTGTAAATAAAGATGACGCTCAGCTGAATTCCAGTATGCACTCCAGACAATTGATACTGTTTATGGCTCTATGTAACTAGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 77

CATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAGgttaaaagtc ... cttttaacagCGTCGCATGTCTGGATGGTGTAAATAAAGATGACGCTCAGCTGAATTCCAGTATGCACTCCAGACAATTGATACTGTTTATGGCTCTATGTAACTAGCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGGCCTGAGAGgttaaaagtctaaacttgtgtaactctgttttcctatctagaatttttcaatttgcagacccgttattgtttttaacttggtaacttttaacag

- - - - - - - - - - - - - - - - - - - - GGAGAA