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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGGAGATGATGCAGCAGGAGATCATCCCACCGCTGAAGGATGCCTTGGAGGCGGAGGACGACGTGTCCCAGGTGCAGCTCGCCTTCCAAAACAACACGgtaagtagtcagtacttaatcactcaaatacagaatgcttggagctagtgaacgtactagttcctgagttactaaaaactggtggcattggtactgtgca...

Basic information

species Zea mays
transcript GRMZM2G009320_T02
intron # 2
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|211165892|gb|FL257810.1|FL257810
EST:     AAGCCGAAGACGACCTGTTCCAAGTGCAACTCGGCTTCCAAAACAACACG                         CTGGAAGGATCCTTCATAAAGAACGACGTCCCTTATTATTTTTGGGCCTTC
genomic: AGGCGGAGGACGACGTGTCCCAGGTGCAGCTCGCCTTCCAAAACAACACGgtaagtagtc ... tggattgcagCTGGAGGGATCCTTCATAAAGAACGACGTCCCTTATTATTTTTGGGCCTTC
EST: gi|4688541|gb|AI637211.1|AI637211
EST:     AGGCGGAGGACGACGTGTCCCAGGTGCAGCTCGCCTTCCAAAACAACACG                         CTGGAGGGATCCTTCATAAAGAACGACGTCCCTTATTATTTTTGGGCCTTC
genomic: AGGCGGAGGACGACGTGTCCCAGGTGCAGCTCGCCTTCCAAAACAACACGgtaagtagtc ... tggattgcagCTGGAGGGATCCTTCATAAAGAACGACGTCCCTTATTATTTTTGGGCCTTC
EST: gi|211533145|gb|FL165883.1|FL165883
EST:     AGGCGGAGGACGACGTGTCCCAGGTGCAGCTCGCCTTCCAAAACAACACG                         CTGGAGGGATCCTTCATAAAGAACGACGTCCCTTATTATTTTTGGGCCTTC
genomic: AGGCGGAGGACGACGTGTCCCAGGTGCAGCTCGCCTTCCAAAACAACACGgtaagtagtc ... tggattgcagCTGGAGGGATCCTTCATAAAGAACGACGTCCCTTATTATTTTTGGGCCTTC
EST: gi|211533148|gb|FL165886.1|FL165886
EST:     GGCGGAGGACGACGTGTCCCCAG-TGCAGCTCGCCTTCCAAAACCACACG                         CTTGAAGGATCCTTCATTAAGGACGACGTCCCTTAATATTTTTGGGCCTT
genomic: GGCGGAGGACGACGTGTCCC-AGGTGCAGCTCGCCTTCCAAAACAACACGgtaagtagtc ... tggattgcagCTGGAGGGATCCTTCATAAAGAACGACGTCCCTTATTATTTTTGGGCCTT
EST: gi|37394767|gb|CF634660.1|CF634660
EST:     AGGCGGAGGACGACGTGTCCCAGGTGCAGCTCGCCTTCCAAAACAACACG                         CTGGAGGGATCCTTCATAAAGAACGACGTCCCTTATTATTTTTGGGCCTTC
genomic: AGGCGGAGGACGACGTGTCCCAGGTGCAGCTCGCCTTCCAAAACAACACGgtaagtagtc ... tggattgcagCTGGAGGGATCCTTCATAAAGAACGACGTCCCTTATTATTTTTGGGCCTTC
EST: gi|5740068|gb|AI947758.1|AI947758
EST:     AGGCGGAGGACGACGTGTCCCAGGNGCAGCTCGCCTTCCAAAACAACACG                         CTGGAGGGATCCTTTCATAAAGA
genomic: AGGCGGAGGACGACGTGTCCCAGGTGCAGCTCGCCTTCCAAAACAACACGgtaagtagtc ... tggattgcagCTGGAGGGATCCTT-CATAAAGA
EST: gi|13126459|gb|BG317029.1|BG317029
EST:     AGGCGGAGGACGACGTGTCCCAGGTGCAGCTCGCCTTCCAAAACAACACG                         CTGGAGGGATCCTTCATAAAGAACGACGTCCCTTATTATTTTTGGGCCTTC
genomic: AGGCGGAGGACGACGTGTCCCAGGTGCAGCTCGCCTTCCAAAACAACACGgtaagtagtc ... tggattgcagCTGGAGGGATCCTTCATAAAGAACGACGTCCCTTATTATTTTTGGGCCTTC

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: 31 (upstream exon), 19 (downstream exon)
Score: 1

GCCGGAGATGATGCAGCAGGAGATCATCCCACCGCTGAAGGATGCCTTGGAGGCGGAGGACGACGTGTCCCAGGTGCAGCTCGCCTTCCAAAACAACACGgtaagtagtc ... tggattgcagCTGGAGGGATCCTTCATAAAGAACGACGTCCCTTATTATTTTTGGGCCTTCTTTCCAAAAGGAGACCTCACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 173

GCCGGAGATGATGCAGCAGGAGATCATCCCACCGCTGAAGGATGCCTTGGAGGCGGAGGACGACGTGTCCCAGGTGCAGCTCGCCTTCCAAAACAACACGgtaagtagtc ... tggattgcagCTGGAGGGATCCTTCATAAAGAACGACGTCCCTTATTATTTTTGGGCCTTCTTTCCAAAAGGAGACCTCACAG


Block sizes: 47 (upstream exon), 41 (downstream exon)
Score: 19

GCCGGAGATGATGCAGCAGGAGATCATCCCACCGCTGAAGGATGCCTTGGAGGCGGAGGACGACGTGTCCCAGGTGCAGCTCGCCTTCCAAAACAACACGgtaagtagtc ... tggattgcagCTGGAGGGATCCTTCATAAAGAACGACGTCCCTTATTATTTTTGGGCCTTCTTTCCAAAAGGAGACCTCACAG


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

GCCGGAGATGATGCAGCAGGAGATCATCCCACCGCTGAAGGATGCCTTGGAGGCGGAGGACGACGTGTCCCAGGTGCAGCTCGCCTTCCAAAACAACACGgtaagtagtc ... tggattgcagCTGGAGGGATCCTTCATAAAGAACGACGTCCCTTATTATTTTTGGGCCTTCTTTCCAAAAGGAGACCTCACAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCGGAGATGATGCAGCAGGAGATCATCCCACCGCTGAAGGATGCCTTGGAGGCGGAGGACGACGTGTCCCAGGTGCAGCTCGCCTTCCAAAACAACACGgtaagtagtcagtacttaatcactcaaatacagaatgcttggagctagtgaacgtactagttcctgagttactaaaaactggtggcattggtactgtgca

- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actaaaaa