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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGGGAACAGCGACCTCCCCGTGTGGTTCGAAGCAGGCGCGGCGAAATTCGACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGGgtaaacctcaacctaaacaactgtgacctgtgatttgatttcatggaaattcaactccaatatatcatgacag

Basic information

species Zea mays
transcript GRMZM2G103101_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G103101_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g52650.1 (Oryza sativa), 5'ss of exon 3
CAGGGAACAGCGACCTCCCCGTGTGGTTCGAAGCAGGCGCGGCGAAATTCGACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGGgtaaacctcaacctaaacaactgtgacctgtgatttgatttcatggaaattcaactccaatatatcatgacag---------------------------------------------------------------------------
|||| | || | |||| || |||||||| |||||||| ||  | |||||||||||||| ||||||||||| |||||||| ||||||||  ||||||||||||||   ||| | |   ||||||  || | |  |  |   | |  ||||   | || |||||  |||| ||                                                                             
CAGGAATCAACAACCTGCCAGTGTGGTTTGAAGCAGGTGCAACAAAATTCGACTTCGCTAACACCACGGCACTCTTCTTTGTCCAGCTTCTCTTGATGGGgtaa--ttcagcatc--caactgaaacattttgtcagtggtaaaagaaa---agcttcaataactcataactcaaattgtatgatgaattgatgactttacacatcataagactgacatgttcccatgataactccaattcccaacag
















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|149100655|gb|EE186743.2|EE186743
EST:     GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGG                         GTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
genomic: GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGGgtaaacctca ... atcatgacagGTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
EST: gi|78022949|gb|DV491336.1|DV491336
EST:     GACTTCGCGAACACAACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGG                         GTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
genomic: GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGGgtaaacctca ... atcatgacagGTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
EST: gi|211329945|gb|FL040612.1|FL040612
EST:     GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGG                         GTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
genomic: GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGGgtaaacctca ... atcatgacagGTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
EST: gi|149111433|gb|EE294936.2|EE294936
EST:     GACTTCGCGAACACAACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGG                         GTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
genomic: GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGGgtaaacctca ... atcatgacagGTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
EST: gi|211329944|gb|FL040611.1|FL040611
EST:     GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGG                         GTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
genomic: GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGGgtaaacctca ... atcatgacagGTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
EST: gi|149077487|gb|EE166183.2|EE166183
EST:     GACTTCGCGAACACAACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGG                         GTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
genomic: GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGGgtaaacctca ... atcatgacagGTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
EST: gi|94472956|gb|EB701914.1|EB701914
EST:     GACTTCGCGAACACAACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGG                         GTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
genomic: GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGGgtaaacctca ... atcatgacagGTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
EST: gi|211329942|gb|FL040609.1|FL040609
EST:     GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGG                         GTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
genomic: GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGGgtaaacctca ... atcatgacagGTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
EST: gi|488226|gb|T18807.1|T18807
EST:     GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGG                         GTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
genomic: GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGGgtaaacctca ... atcatgacagGTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
EST: gi|211327787|gb|FL040601.1|FL040601
EST:     GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGG                         GTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
genomic: GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGGgtaaacctca ... atcatgacagGTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
EST: gi|211327788|gb|FL040602.1|FL040602
EST:     GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGG                         GTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
genomic: GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGGgtaaacctca ... atcatgacagGTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
EST: gi|211327789|gb|FL040603.1|FL040603
EST:     GACTTCGCGAACACCACGGGGCTCTTCTTCGTCCAGCTCTTCTTGATGGG                         GTTCGCTGACACCAAGAGGTACATGGACTTCAGAAATCCAGGATCGCAAGC
genomic: GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGGgtaaacctca ... atcatgacagGTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
EST: gi|149100656|gb|EE186744.2|EE186744
EST:     GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGG                         GTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
genomic: GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGGgtaaacctca ... atcatgacagGTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
EST: gi|211329943|gb|FL040610.1|FL040610
EST:     GACTTCGCGAACACCACGGGGCTCTTCTTCGTCCAGCTCTTCTTGATGGG                         GTTCGCTGAAACCAAGAAGTACATGGACTTCAAAAATCCAGGATCGCAAGC
genomic: GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGGgtaaacctca ... atcatgacagGTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
EST: gi|211329938|gb|FL040605.1|FL040605
EST:     GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGG                         GTTCGCTGAAACCAAGAAGTACATGGACTTCAAAAATCCAGGATCGCAAGC
genomic: GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGGgtaaacctca ... atcatgacagGTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
EST: gi|211329939|gb|FL040606.1|FL040606
EST:     GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGG                         GTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
genomic: GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGGgtaaacctca ... atcatgacagGTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
EST: gi|148994267|gb|EE034026.2|EE034026
EST:     GACTTCGCGAACACAACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGG                         GTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
genomic: GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGGgtaaacctca ... atcatgacagGTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
EST: gi|148995804|gb|EE035035.2|EE035035
EST:     GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGG                         GTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
genomic: GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGGgtaaacctca ... atcatgacagGTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
EST: gi|148967697|gb|EE018962.2|EE018962
EST:     GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGG                         GTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
genomic: GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGGgtaaacctca ... atcatgacagGTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
EST: gi|148987230|gb|EE031063.2|EE031063
EST:     GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGG                         GTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC
genomic: GACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGGgtaaacctca ... atcatgacagGTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGC

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 3 RNA-Seq libraries.


Block sizes: 31 (upstream exon), 19 (downstream exon)
Score: 3

CAGGGAACAGCGACCTCCCCGTGTGGTTCGAAGCAGGCGCGGCGAAATTCGACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGGgtaaacctca ... atcatgacagGTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGCAGAGGAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 101

CAGGGAACAGCGACCTCCCCGTGTGGTTCGAAGCAGGCGCGGCGAAATTCGACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGGgtaaacctca ... atcatgacagGTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGCAGAGGAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAG


Block sizes: 43 (upstream exon), 45 (downstream exon)
Score: 11

CAGGGAACAGCGACCTCCCCGTGTGGTTCGAAGCAGGCGCGGCGAAATTCGACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGGgtaaacctca ... atcatgacagGTTCGCTGAAACCAAGAGGTACATGGACTTCAAAAATCCAGGATCGCAAGCAGAGGAAGGGACATTCATAGGGTTAGAGGCTGCACTCGCAGGTCAACAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGGGAACAGCGACCTCCCCGTGTGGTTCGAAGCAGGCGCGGCGAAATTCGACTTCGCGAACACCACGGCGCTCTTCTTCGTCCAGCTCTTCTTGATGGGgtaaacctcaacctaaacaactgtgacctgtgatttgatttcatggaaattcaactccaatatatcatgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC