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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaagccgacaccaccaaggccgagcgacttgctgagacggacaaggtactctagtccacgacgaacgaaattgagcttatggattccctgttcttctcagGAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGTTGAGTATTAACAGACTCGGGCGGTTCGTGTCGCTGGGCGCTCGGAGGCC

Basic information

species Zea mays
transcript GRMZM2G095141_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095141_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g04210.1 (Oryza sativa), 3'ss of exon 1
gaagccgacaccaccaaggccgagcgacttgctgagacggacaaggtactctagtccacgacgaacgaaattgagcttatggattccctgttcttctcagGAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGTTGAGTATTAACAGACTCGGGCGGTTCGTGTCGCTGGGCGCTCGGAGGCC-------
    |           | |      ||  |  | |  |     ||  ||     || |      |    |     ||| |  |     |    |        || ||||||||||||||||||||||| ||||| || ||||| || |||||||||||||||||||| |   |||||   || |     ||| | ||  |       
----ctcctgttcttcatgtgttttgagattataactcaattcagtgacatatatcaagtgttcatatcaacagtcttcttcacattgtaacatctgattccagAATGTCGAGCCTCGAGGAGCCGCTCGGTCTTGGGGACCTTCCAAAGTTGAGTATTAACAGACTTGAAAGGTTC---TCTCCAAATGCTTGCAGAGCAAGTGCT

upper sequence: GRMZM2G095141_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g04020.1 (Oryza sativa), 3'ss of exon 1
gaagccgacaccaccaaggccgagcgacttgctgagacggacaaggtactctagtccacgacgaacgaa--attgagcttatggattccctgttcttctcagGAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGTTGAGTATTAACAGACTCGGGCGGTTCGTGTCGCTGGGCGCTCGGAGGCC-------
|   |  |   | || |  ||| |||  |   | | |     ||  ||      | ||   | |   |    || |  || |  |  ||   | |||| ||| |    |||| |||||||||||||| || ||||| || |||||||| |||||||||||||||||||| |   |||||   || |   | ||  | ||  |       
gttcctcaactcccccaccccgggcgtgtcctttatatat-taacatatcaagattcatctcaacatagttgttaaaattgta-acgcctcctgcttcacagAA----TGTCAAGCCTCGAGGAGCCACTTGGTCTTGGGGACCTGCCAAAGTTGAGTATTAACAGACTTGAAAGGTTC---TCTCCAAGTGCCTGCAGAGCAAGTGTT
















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|211335900|gb|FL358434.1|FL358434
EST:     GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAG                         GAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGT
genomic: GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAGgtactgcgca ... ttcttctcagGAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGT
EST: gi|211386581|gb|FL357085.1|FL357085
EST:     GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAG                         GAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCCAAGT
genomic: GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAGgtactgcgca ... ttcttctcagGAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGT
EST: gi|71301051|gb|DR786555.1|DR786555
EST:     GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAG                         GAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGT
genomic: GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAGgtactgcgca ... ttcttctcagGAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGT
EST: gi|211512679|gb|FL346133.1|FL346133
EST:     GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAG                         GAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCCAAGT
genomic: GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAGgtactgcgca ... ttcttctcagGAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGT
EST: gi|78075611|gb|DV504045.1|DV504045
EST:     GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAG                         GAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGT
genomic: GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAGgtactgcgca ... ttcttctcagGAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGT
EST: gi|149081591|gb|EE170732.2|EE170732
EST:     GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAG                         GAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGT
genomic: GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAGgtactgcgca ... ttcttctcagGAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGT
EST: gi|148941574|gb|EC886510.2|EC886510
EST:     GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAG                         GAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGT
genomic: GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAGgtactgcgca ... ttcttctcagGAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGT
EST: gi|149100624|gb|EE186712.2|EE186712
EST:     GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCC--                         --AGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGT
genomic: GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAGgtactgcgca ... ttcttctcagGAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGT
EST: gi|78078033|gb|DV506448.1|DV506448
EST:     GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAG                         GAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGT
genomic: GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAGgtactgcgca ... ttcttctcagGAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGT
EST: gi|71447021|gb|DR828071.1|DR828071
EST:     GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAG                         GAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGT
genomic: GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAGgtactgcgca ... ttcttctcagGAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGT
EST: gi|211347508|gb|FL349165.1|FL349165
EST:     GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAG                         GAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCCAAGT
genomic: GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAGgtactgcgca ... ttcttctcagGAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGT
EST: gi|148951347|gb|EC897061.2|EC897061
EST:     GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAG                         GAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGT
genomic: GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAGgtactgcgca ... ttcttctcagGAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGT
EST: gi|211310888|gb|FL144806.1|FL144806
EST:     GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAG                         GAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCCAAGT
genomic: GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAGgtactgcgca ... ttcttctcagGAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGT
EST: gi|148959199|gb|EE010648.2|EE010648
EST:     GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAG                         GAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGT
genomic: GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAGgtactgcgca ... ttcttctcagGAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGT
EST: gi|91872713|gb|EB402670.1|EB402670
EST:     GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAG                         GAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGT
genomic: GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAGgtactgcgca ... ttcttctcagGAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGT
EST: gi|148951196|gb|EC896884.2|EC896884
EST:     GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAG                         GAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGT
genomic: GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAGgtactgcgca ... ttcttctcagGAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGT
EST: gi|149076596|gb|EE165231.2|EE165231
EST:     GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAG                         GAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGT
genomic: GCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAGgtactgcgca ... ttcttctcagGAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGT

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: 46 (upstream exon), 39 (downstream exon)
Score: 12

CCTTTTCCCTCCCTCGACCGACGACCGTCCGTCCACCACCGGATCCAGGAGCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAGgtactgcgca ... ttcttctcagGAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGTTGAGTATTAACAGACTCGGGCGGTTCGTGTCGCTGGGCGCTCGGAGGCC


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 27

CCTTTTCCCTCCCTCGACCGACGACCGTCCGTCCACCACCGGATCCAGGAGCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAGgtactgcgca ... ttcttctcagGAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGTTGAGTATTAACAGACTCGGGCGGTTCGTGTCGCTGGGCGCTCGGAGGCC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 22

CCTTTTCCCTCCCTCGACCGACGACCGTCCGTCCACCACCGGATCCAGGAGCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAGgtactgcgca ... ttcttctcagGAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGTTGAGTATTAACAGACTCGGGCGGTTCGTGTCGCTGGGCGCTCGGAGGCC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 46

CCTTTTCCCTCCCTCGACCGACGACCGTCCGTCCACCACCGGATCCAGGAGCGACCCTCCCTCGTGCTCGTCGACGATCGACCGGCCGCCGATCGTCCAGgtactgcgca ... ttcttctcagGAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGTTGAGTATTAACAGACTCGGGCGGTTCGTGTCGCTGGGCGCTCGGAGGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtactctagtccacgacgaacgaaattgagcttatggattccctgttcttctcagGAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGTTGAGTATTAACAGACTCGGGCGGTTCGTGTCGCTGGGCGCTCGGAGGCC
                                      ttccctgttcttctc  CT-rich tract
                      aaattga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaagccgacaccaccaaggccgagcgacttgctgagacggacaaggtactctagtccacgacgaacgaaattgagcttatggattccctgttcttctcagGAAGGATGTCGAGCCTCGAGGAGCCGCTGGGTCTCGGAGACCTGCCTAAGTTGAGTATTAACAGACTCGGGCGGTTCGTGTCGCTGGGCGCTCGGAGGCC

- - - - caccacc
- - - - - - - - - - - - - -cttgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ccacgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttatg