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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACACGACTTGAAATGTTGTCCAAGAAGTATGGGTGCACACCTGCTCAACTCGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTGgtaatgtcctgacatcatatattcatatgttaatactgaagatcatgtttatgttctactctgcctatgagcagggtcaaacctttccatcaacaaacca...

Basic information

species Zea mays
transcript GRMZM5G813143_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G813143_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os10g28320.2 (Oryza sativa), 5'ss of exon 5
ACACGACTTGAAATGTTGTCCAAGAAGTATGGGTGCACACCTGCTCAACTCGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTGgtaatgtcctgacatcatatattcatatgttaatactgaagatcatgtttatgttct--actctgcctatgagcagggtcaaacctttccatcaacaaacca
|||||| |||||  | |  |||  |||||||| ||| | ||||||||||| |||||||||||||||||||||||||| || ||||| || || ||||||||||||||  | |    || || |    ||| | |     |  | || ||  |||  |  |  || | ||    |||| | ||     ||  | | |    | 
ACACGAATTGAAGAGCTTGCCACCAAGTATGGCTGCTCCCCTGCTCAACTTGCTCTCTCCTGGGTTCTTCATCAAGGGGATGATGTTGTTCCAATCCCTGgtaatgtgttaaacatatttagtacgctgtcagtgtcagaagt-attttcctgtcttggatactccatactgtcaggcttaacatggtcttttacctgttc-

upper sequence: GRMZM5G813143_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os10g28320.3 (Oryza sativa), 5'ss of exon 5
--------------------------------------------------------------------------ACACGACTTGAAATGTTGTCCAAGAAGTATGGGTGCACACCTGCTCAACTCGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTGgtaatgtcctgacatcatatattcatatgttaatactgaagatcatgtttatgttctactctgcctatgagcagggtcaaacctttccatcaacaaacca
                                                                          |||||| |||||  | |  |||  |||||||| ||| | ||||||||||| |||||||||||||||||||||||||| || ||||| || || ||||||||||||||  | |   ||||| ||  || |                                                                       
TCTTCTTTGCTACTTCACAGACTAGACATCCAAGGTACAATGGGGAAAACTTGGAGAAGAATAAAGTTTTCTACACACGAATTGAAGAGCTTGCCACCAAgtatggctgctcccctgctcaacttgctctctcctgggttcttcatcaaggggatgatgttgttccaatccctggtaatgtgttaaa--catat-ttagtacg-----------------------------------------------------------------------

upper sequence: GRMZM5G813143_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA03G40680.1 (Glycine max), 5'ss of exon 6
ACACGACTTGAAATGTTGTCCAAGAAGTATGGGTGCACACCTGCTCAACTCGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTGgtaatgtcctgacatcatatattcatatgttaatactgaagatcatgtttatgttctactctgcctatgagcagggtcaaacctttccatcaacaaacca------
 |  |  | ||||  ||| |  |||||||||| || ||| || | ||||| |||||  | ||| |||||||||||||||| |||||||| |||||||||||| |     |     |  |  ||  || |  || | |  |  | ||  ||    | |  | ||  | | ||     |  | |  |  ||  | | | | |      
TCTAGGATAGAAAAATTGGCAGAGAAGTATGGATGTACATCTTCGCAACTTGCTCTTGCATGGATTCTTCATCAAGGAGACGATGTGGTACCCATCCCTGgtgagtgatt--ttcctgactttggtacgc-aacatttgatctaattcttg-actttgttgtg--tgtcagtcaatttgatctctaacactagcgatcaaatcaat

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|91877298|gb|EB407255.1|EB407255
EST:     CGCTCTCTCCTGGGTTTTTCATCAAGGAGAAGATGTGGTCCCCATCCCTG                         GAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGTTGTAAAGGTAA
genomic: CGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTGgtaatgtcct ... ctgaatccagGAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA
EST: gi|76292810|gb|DV032378.1|DV032378
EST:     CGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTG                         GAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA
genomic: CGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTGgtaatgtcct ... ctgaatccagGAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA
EST: gi|88747188|gb|DY531329.1|DY531329
EST:     CGCTCTCTCCTGGGTTTTTCATCAAGGAGAAGATGTGGTCCCCATCCCTG                         GAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA
genomic: CGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTGgtaatgtcct ... ctgaatccagGAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA
EST: gi|211464993|gb|FL442786.1|FL442786
EST:     CGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTG                         GAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA
genomic: CGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTGgtaatgtcct ... ctgaatccagGAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA
EST: gi|76021183|gb|DT948353.1|DT948353
EST:     CGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTG                         GAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA
genomic: CGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTGgtaatgtcct ... ctgaatccagGAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA
EST: gi|91875442|gb|EB405399.1|EB405399
EST:     CGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTG                         GAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA
genomic: CGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTGgtaatgtcct ... ctgaatccagGAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA
EST: gi|78114482|gb|DV532871.1|DV532871
EST:     CGCTCTCTCCTGGGTTTTTCATCAAGGAGAAGATGTGGTCCCCATCCCTG                         GAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA
genomic: CGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTGgtaatgtcct ... ctgaatccagGAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA
EST: gi|89250463|gb|DY622249.1|DY622249
EST:     CGCTCTCTCCTGGGTTCTTCATCAGGGAGAAGATGTGGTCCCCATCCCTG                         GAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA
genomic: CGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTGgtaatgtcct ... ctgaatccagGAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA
EST: gi|89761100|gb|DY689250.1|DY689250
EST:     CGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTG                         GAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA
genomic: CGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTGgtaatgtcct ... ctgaatccagGAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA
EST: gi|76288051|gb|DV027619.1|DV027619
EST:     CGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTG                         GAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA
genomic: CGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTGgtaatgtcct ... ctgaatccagGAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA
EST: gi|101392432|gb|EB818145.1|EB818145
EST:     CGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTG                         GAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA
genomic: CGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTGgtaatgtcct ... ctgaatccagGAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA
EST: gi|89755224|gb|DY685733.1|DY685733
EST:     CGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTG                         GAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA
genomic: CGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTGgtaatgtcct ... ctgaatccagGAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA
EST: gi|76011255|gb|DT938425.1|DT938425
EST:     CGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTG                         GAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA
genomic: CGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTGgtaatgtcct ... ctgaatccagGAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA
EST: gi|60355056|gb|DN222029.1|DN222029
EST:     CGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTG                         GAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA
genomic: CGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTGgtaatgtcct ... ctgaatccagGAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA
EST: gi|91873436|gb|EB403393.1|EB403393
EST:     CGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTG                         GAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA
genomic: CGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTGgtaatgtcct ... ctgaatccagGAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA
EST: gi|78112031|gb|DV530427.1|DV530427
EST:     CGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTG                         GAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA
genomic: CGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTGgtaatgtcct ... ctgaatccagGAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA
EST: gi|60341512|gb|DN208485.1|DN208485
EST:     CGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTG                         GAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA
genomic: CGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTGgtaatgtcct ... ctgaatccagGAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAA

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: 48 (upstream exon), 47 (downstream exon)
Score: 87

ACACGACTTGAAATGTTGTCCAAGAAGTATGGGTGCACACCTGCTCAACTCGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTGgtaatgtcct ... ctgaatccagGAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAAGGCTGAGCAAGGAAGACCTCGAAGAAATCTCAGGCGCATTCCCTGCTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 38

ACACGACTTGAAATGTTGTCCAAGAAGTATGGGTGCACACCTGCTCAACTCGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTGgtaatgtcct ... ctgaatccagGAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAAGGCTGAGCAAGGAAGACCTCGAAGAAATCTCAGGCGCATTCCCTGCTGG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 85

ACACGACTTGAAATGTTGTCCAAGAAGTATGGGTGCACACCTGCTCAACTCGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTGgtaatgtcct ... ctgaatccagGAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAAGGCTGAGCAAGGAAGACCTCGAAGAAATCTCAGGCGCATTCCCTGCTGG


Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 12

ACACGACTTGAAATGTTGTCCAAGAAGTATGGGTGCACACCTGCTCAACTCGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTGgtaatgtcct ... ctgaatccagGAACAACAAAAGCCAAGAACCTTGACGAAAATATCGGTGCTGTAAAGGTAAGGCTGAGCAAGGAAGACCTCGAAGAAATCTCAGGCGCATTCCCTGCTGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACACGACTTGAAATGTTGTCCAAGAAGTATGGGTGCACACCTGCTCAACTCGCTCTCTCCTGGGTTCTTCATCAAGGAGAAGATGTGGTCCCCATCCCTGgtaatgtcctgacatcatatattcatatgttaatactgaagatcatgtttatgttctactctgcctatgagcagggtcaaacctttccatcaacaaacca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caacaaac