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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGAACAAGTCCGTCACTGAGGCTGATGCCCAGGACGCTGACGGGGGAGCTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctactttccgcgccgcatcctccgtctccatttgcaagtcggccacgcacgggcacggggccgaagatctagggtttctgaacgtgatgtatttggatttgctccag

Basic information

species Zea mays
transcript GRMZM2G132060_T01
intron # 1
splice site 5'
intron type U2

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|211162505|gb|FL243924.1|FL243924
EST:     CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAG                         GTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
genomic: CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
EST: gi|211162502|gb|FL243921.1|FL243921
EST:     CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAG                         GTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
genomic: CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
EST: gi|211160898|gb|FL243904.1|FL243904
EST:     CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAG                         GTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
genomic: CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
EST: gi|211164093|gb|FL243928.1|FL243928
EST:     CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAG                         GTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
genomic: CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
EST: gi|23357746|gb|BU645395.1|BU645395
EST:     CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAG                         GTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
genomic: CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
EST: gi|20811117|gb|BQ295595.1|BQ295595
EST:     CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAG                         GTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
genomic: CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
EST: gi|211159306|gb|FL243892.1|FL243892
EST:     CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAG                         GTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
genomic: CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
EST: gi|211160905|gb|FL243911.1|FL243911
EST:     CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAG                         GTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
genomic: CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
EST: gi|211160903|gb|FL243909.1|FL243909
EST:     CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAG                         GTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
genomic: CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
EST: gi|148930320|gb|EE284721.2|EE284721
EST:     CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAG                         GTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
genomic: CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
EST: gi|148936928|gb|EC881083.2|EC881083
EST:     CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAG                         GTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
genomic: CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
EST: gi|148974670|gb|EE025472.2|EE025472
EST:     CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAG                         GTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
genomic: CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
EST: gi|211164092|gb|FL243927.1|FL243927
EST:     CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAG                         GTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
genomic: CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
EST: gi|211162500|gb|FL243919.1|FL243919
EST:     CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAG                         GTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
genomic: CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
EST: gi|211159299|gb|FL243885.1|FL243885
EST:     CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAG                         GTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
genomic: CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
EST: gi|148944299|gb|EC889396.2|EC889396
EST:     CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAG                         GTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
genomic: CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
EST: gi|211160895|gb|FL243901.1|FL243901
EST:     CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAG                         GTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
genomic: CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
EST: gi|5566945|gb|AI881856.1|AI881856
EST:     CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAG                         GTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
genomic: CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
EST: gi|148931686|gb|EC874876.2|EC874876
EST:     CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAG                         GTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
genomic: CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
EST: gi|211159308|gb|FL243894.1|FL243894
EST:     CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAG                         GTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
genomic: CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
EST: gi|5555529|gb|AI881480.1|AI881480
EST:     CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAG                         GTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
genomic: CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
EST: gi|50336536|gb|CO531662.1|CO531662
EST:     CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAG                         GTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
genomic: CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
EST: gi|91050200|gb|EB160618.1|EB160618
EST:     CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAG                         GTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
genomic: CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
EST: gi|211162494|gb|FL243913.1|FL243913
EST:     CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAG                         GTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
genomic: CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
EST: gi|211162496|gb|FL243915.1|FL243915
EST:     CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAG                         GTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
genomic: CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
EST: gi|87155460|gb|DY400249.1|DY400249
EST:     CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAG                         GTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
genomic: CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
EST: gi|211159303|gb|FL243889.1|FL243889
EST:     CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAG                         GTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
genomic: CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
EST: gi|211159301|gb|FL243887.1|FL243887
EST:     CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAG                         GTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
genomic: CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
EST: gi|148931684|gb|EC874873.2|EC874873
EST:     CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAG                         GTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
genomic: CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
EST: gi|148966452|gb|EE017460.2|EE017460
EST:     CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAG                         GTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
genomic: CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
EST: gi|89761601|gb|DY689546.1|DY689546
EST:     CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAG                         GTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
genomic: CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
EST: gi|211160900|gb|FL243906.1|FL243906
EST:     CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAG                         GTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT
genomic: CTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCT

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), 49 (downstream exon)
Score: 686

GAAGAACAAGTCCGTCACTGAGGCTGATGCCCAGGACGCTGACGGGGGAGCTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCTCTCCTGGATGATTTCAAGGCCATCTTCGAGAAGTTCACCTTCAAGGACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 421

GAAGAACAAGTCCGTCACTGAGGCTGATGCCCAGGACGCTGACGGGGGAGCTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCTCTCCTGGATGATTTCAAGGCCATCTTCGAGAAGTTCACCTTCAAGGACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 597

GAAGAACAAGTCCGTCACTGAGGCTGATGCCCAGGACGCTGACGGGGGAGCTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCTCTCCTGGATGATTTCAAGGCCATCTTCGAGAAGTTCACCTTCAAGGACG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 353

GAAGAACAAGTCCGTCACTGAGGCTGATGCCCAGGACGCTGACGGGGGAGCTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctact ... tttgctccagGTTGAGGTGGAGATAGAGTACGTGCCGGAGAAGGCCGAGCTTGACGACCCTCTCCTGGATGATTTCAAGGCCATCTTCGAGAAGTTCACCTTCAAGGACG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGAACAAGTCCGTCACTGAGGCTGATGCCCAGGACGCTGACGGGGGAGCTTCCAGCTCCGACGCCAAGGAGAACGCCGATCCCAACCCCGAGCCACAGgtgagctactttccgcgccgcatcctccgtctccatttgcaagtcggccacgcacgggcacggggccgaagatctagggtttctgaacgtgatgtatttggatttgctccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA