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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCCTCTCGTCCTCCCGGCGTCATCGTCGCCGCCCTGATCTCCGCAGGCCGGCGTGTGGCGGAGATCCATCCGTGCTTGAACTGACTCCTTCCTTAGCTAgtaaggaaaccctagctcatctgcatgcatcttttggttcgttctgtggaatgatcctttgtttgatgtgagttgtcaaatccttcgacctggtgtgata...

Basic information

species Zea mays
transcript GRMZM2G118731_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|76909048|gb|DV163196.1|DV163196
EST:     GGCGTGTGGCGGAGATCCATCCGTGCTTGAACTGACTCCTTCCTTAGCTA                         CAAGTACCTATTATCAACCATGTTTGGACGCATGCCAAGGAAGAGTAGTAA
genomic: GGCGTGTGGCGGAGATCCATCCGTGCTTGAACTGACTCCTTCCTTAGCTAgtaaggaaac ... ccgttcatagCAAGTACCTATTATCAACCATGTTTGGACGCATGCCAAGGAAGAGTAGTAA
EST: gi|76293182|gb|DV032750.1|DV032750
EST:     GGCGTGTGGCGGAGATCCATCCGTGCTTGAACTGACTCCTTCCTTAGCTA                         CAAGTACCTATTATCAACCATGTTTGGACGCATGCCAAGGAAGAGTAGTAA
genomic: GGCGTGTGGCGGAGATCCATCCGTGCTTGAACTGACTCCTTCCTTAGCTAgtaaggaaac ... ccgttcatagCAAGTACCTATTATCAACCATGTTTGGACGCATGCCAAGGAAGAGTAGTAA
EST: gi|211439726|gb|FL188864.1|FL188864
EST:     GGCGTGTGGCGGAGATCCATCCGTGCTTGAACTGACTCCTTCCTTAGCTA                         CAAGTACCTATTATCAACCATGTTTGGACGCATGCCAAGGAAGAGTAGTAA
genomic: GGCGTGTGGCGGAGATCCATCCGTGCTTGAACTGACTCCTTCCTTAGCTAgtaaggaaac ... ccgttcatagCAAGTACCTATTATCAACCATGTTTGGACGCATGCCAAGGAAGAGTAGTAA
EST: gi|211003695|gb|FL188865.1|FL188865
EST:     GGCGTGTGGCGGAGATCCATCCGTGCTTGAACTGACTCCTTCCTTAGCTA                         CAAGTACCTATTATCAACCATGTTTGGACGCATGCCAAGGAAGAGTAGTAA
genomic: GGCGTGTGGCGGAGATCCATCCGTGCTTGAACTGACTCCTTCCTTAGCTAgtaaggaaac ... ccgttcatagCAAGTACCTATTATCAACCATGTTTGGACGCATGCCAAGGAAGAGTAGTAA
EST: gi|87152878|gb|DY397667.1|DY397667
EST:     GGCGTGTGGCGGAGATCCATCCGTGCTTGAACTGACTCCTTCCTTAGCTA                         CAAGTACCTATTATCAACCATGTTTGGACGCATGCCAAGGAAGAGTAGTAA
genomic: GGCGTGTGGCGGAGATCCATCCGTGCTTGAACTGACTCCTTCCTTAGCTAgtaaggaaac ... ccgttcatagCAAGTACCTATTATCAACCATGTTTGGACGCATGCCAAGGAAGAGTAGTAA
EST: gi|148964320|gb|EC905716.2|EC905716
EST:     GGCGTGTGGCGGAGATCCATCCGTGCTTGAACTGACTCCTTCCTTAGCTA                         CAAGTACCTATTATCAACCATGTTTGGACGCATGCCAAGGAAGAGTAGTAA
genomic: GGCGTGTGGCGGAGATCCATCCGTGCTTGAACTGACTCCTTCCTTAGCTAgtaaggaaac ... ccgttcatagCAAGTACCTATTATCAACCATGTTTGGACGCATGCCAAGGAAGAGTAGTAA
EST: gi|31348685|gb|CD433042.1|CD433042
EST:     GGCGTGTGGCGGAGATCCATCCGTGCTTGAACTGACTCCTTCCTTAGCTA                         CAAGTACCTATTATCAACCATGTTTGGACGCATGCCAAGGAAGAGTAGTAA
genomic: GGCGTGTGGCGGAGATCCATCCGTGCTTGAACTGACTCCTTCCTTAGCTAgtaaggaaac ... ccgttcatagCAAGTACCTATTATCAACCATGTTTGGACGCATGCCAAGGAAGAGTAGTAA
EST: gi|91877653|gb|EB407610.1|EB407610
EST:     GGCGTGTGGCGGAGATCCATCCGTGCTTGAACTGACTCCTTCCTTAGCTA                         CAAGTACCTATTATCAACCATGTTTGGACGCATGCCAAGGAAGAGTAGTAA
genomic: GGCGTGTGGCGGAGATCCATCCGTGCTTGAACTGACTCCTTCCTTAGCTAgtaaggaaac ... ccgttcatagCAAGTACCTATTATCAACCATGTTTGGACGCATGCCAAGGAAGAGTAGTAA
EST: gi|148931484|gb|EC874496.2|EC874496
EST:     GGCGTGTGGCGGAGATCCATCCGTGCTTGAACTGACTCCTTCCTTAGCTA                         CAAGTACCTATTATCAACCATGTTTGGACGCATGCCAAGGAAGAGTAGTAA
genomic: GGCGTGTGGCGGAGATCCATCCGTGCTTGAACTGACTCCTTCCTTAGCTAgtaaggaaac ... ccgttcatagCAAGTACCTATTATCAACCATGTTTGGACGCATGCCAAGGAAGAGTAGTAA
EST: gi|149037356|gb|EE155375.2|EE155375
EST:     GGCGTGTGGCGGAGATCCATCCGTGCTTGAACTGACTCCTTCCTTAGCTA                         CAAGTACCTATTATCAACCATGTTTGGACGCATGCCAAGGAAGAGTAGTAA
genomic: GGCGTGTGGCGGAGATCCATCCGTGCTTGAACTGACTCCTTCCTTAGCTAgtaaggaaac ... ccgttcatagCAAGTACCTATTATCAACCATGTTTGGACGCATGCCAAGGAAGAGTAGTAA
EST: gi|148955629|gb|EC901294.2|EC901294
EST:     GGCGTGTGGCGGAGATCCATCCGTGCTTGAACTGACTCCTTCCTTAGCTA                         CAAGTACCTATTATCAACCATGTTTGGACGCATGCCAAGGAAGAGTAGTAA
genomic: GGCGTGTGGCGGAGATCCATCCGTGCTTGAACTGACTCCTTCCTTAGCTAgtaaggaaac ... ccgttcatagCAAGTACCTATTATCAACCATGTTTGGACGCATGCCAAGGAAGAGTAGTAA
EST: gi|18963675|gb|BM660568.1|BM660568
EST:     GGCGTGTGGCGGAGATCCATCCGTGCTTGAACTGACTCCTTCCTTAGCTA                         CAAGTACCTATTATCAACCATGTTTGGACGCATGCCAAGGAAGAGTAGTAA
genomic: GGCGTGTGGCGGAGATCCATCCGTGCTTGAACTGACTCCTTCCTTAGCTAgtaaggaaac ... ccgttcatagCAAGTACCTATTATCAACCATGTTTGGACGCATGCCAAGGAAGAGTAGTAA
EST: gi|18964089|gb|BM660803.1|BM660803
EST:     CTTGAACTGACTCCTTCCTTAGCTA                         CAAGTACCTATTATCAACCATGTTTGGACGCATGCCAAGGAAGAGTAGTAA
genomic: CTTGAACTGACTCCTTCCTTAGCTAgtaaggaaac ... ccgttcatagCAAGTACCTATTATCAACCATGTTTGGACGCATGCCAAGGAAGAGTAGTAA

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), 48 (downstream exon)
Score: 109

CGCCTCTCGTCCTCCCGGCGTCATCGTCGCCGCCCTGATCTCCGCAGGCCGGCGTGTGGCGGAGATCCATCCGTGCTTGAACTGACTCCTTCCTTAGCTAgtaaggaaac ... ccgttcatagCAAGTACCTATTATCAACCATGTTTGGACGCATGCCAAGGAAGAGTAGTAACAATACCAAGTATTACGAGGTTCTTGGTGTGTCTAAGACCGCAAGTCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 53

CGCCTCTCGTCCTCCCGGCGTCATCGTCGCCGCCCTGATCTCCGCAGGCCGGCGTGTGGCGGAGATCCATCCGTGCTTGAACTGACTCCTTCCTTAGCTAgtaaggaaac ... ccgttcatagCAAGTACCTATTATCAACCATGTTTGGACGCATGCCAAGGAAGAGTAGTAACAATACCAAGTATTACGAGGTTCTTGGTGTGTCTAAGACCGCAAGTCAG


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

CGCCTCTCGTCCTCCCGGCGTCATCGTCGCCGCCCTGATCTCCGCAGGCCGGCGTGTGGCGGAGATCCATCCGTGCTTGAACTGACTCCTTCCTTAGCTAgtaaggaaac ... ccgttcatagCAAGTACCTATTATCAACCATGTTTGGACGCATGCCAAGGAAGAGTAGTAACAATACCAAGTATTACGAGGTTCTTGGTGTGTCTAAGACCGCAAGTCAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 112

CGCCTCTCGTCCTCCCGGCGTCATCGTCGCCGCCCTGATCTCCGCAGGCCGGCGTGTGGCGGAGATCCATCCGTGCTTGAACTGACTCCTTCCTTAGCTAgtaaggaaac ... ccgttcatagCAAGTACCTATTATCAACCATGTTTGGACGCATGCCAAGGAAGAGTAGTAACAATACCAAGTATTACGAGGTTCTTGGTGTGTCTAAGACCGCAAGTCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCCTCTCGTCCTCCCGGCGTCATCGTCGCCGCCCTGATCTCCGCAGGCCGGCGTGTGGCGGAGATCCATCCGTGCTTGAACTGACTCCTTCCTTAGCTAgtaaggaaaccctagctcatctgcatgcatcttttggttcgttctgtggaatgatcctttgtttgatgtgagttgtcaaatccttcgacctggtgtgata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC