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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAGgtattattttgctccattattttgatgtccaaccaattattttacaccaaattttagtgatcagcacctactttttttcgttcctctcctgttccag

Basic information

species Zea mays
transcript GRMZM2G091563_T01
intron # 7
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|211309278|gb|FL056037.1|FL056037
EST:     AACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAG                         CTGCTGACCTATGGACGAAGAATTCCTACCCCAGAGCTTTTTGCAAGAATA
genomic: AACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAGgtattatttt ... cctgttccagCTGCTGACCTATGGACGAAGAATTCCTACCCCAGAGCTTTTTGCAAGAATA
EST: gi|30306632|gb|CD001305.1|CD001305
EST:     AACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAG                         CTGCTGACCTATGGACGAAGAATTCCTACCCCAGAGCTTTTTGCAAGAATA
genomic: AACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAGgtattatttt ... cctgttccagCTGCTGACCTATGGACGAAGAATTCCTACCCCAGAGCTTTTTGCAAGAATA
EST: gi|32164812|gb|CD670451.1|CD670451
EST:     AACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAG                         CTGCTGACCTATGGACGAAGAATTCCTACCCCAGAGCTTTTTGCAAGAATA
genomic: AACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAGgtattatttt ... cctgttccagCTGCTGACCTATGGACGAAGAATTCCTACCCCAGAGCTTTTTGCAAGAATA
EST: gi|60337054|gb|DN204027.1|DN204027
EST:     AACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAG                         CTGCTGACCTATGGACGAAGAATTCCTACCCCAGAGCTTTTTGCAAGAATA
genomic: AACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAGgtattatttt ... cctgttccagCTGCTGACCTATGGACGAAGAATTCCTACCCCAGAGCTTTTTGCAAGAATA
EST: gi|60339171|gb|DN206144.1|DN206144
EST:     AACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAG                         CTGCTGACCTATGGACGAAGAATTCCTACCCCAGAGCTTTTTGCAAGAATA
genomic: AACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAGgtattatttt ... cctgttccagCTGCTGACCTATGGACGAAGAATTCCTACCCCAGAGCTTTTTGCAAGAATA
EST: gi|4730783|gb|AI649949.1|AI649949
EST:     AACTCCNCCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAG                         CTGCTGACCTATGGACGAAGAATTCCTACCCCAGAGCTTTTTGCAAGAATA
genomic: AACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAGgtattatttt ... cctgttccagCTGCTGACCTATGGACGAAGAATTCCTACCCCAGAGCTTTTTGCAAGAATA
EST: gi|31909603|gb|CD651001.1|CD651001
EST:     AACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAG                         CTGCTGACCTATGGACGAAGAATTCCTACCCCAGAGCTTTTTGCAAGAATA
genomic: AACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAGgtattatttt ... cctgttccagCTGCTGACCTATGGACGAAGAATTCCTACCCCAGAGCTTTTTGCAAGAATA
EST: gi|38688415|gb|CK145446.1|CK145446
EST:     GCTGTTGTCGAGGACATTGGCCGCCAG                         CTGCTGACCTATGGACGAAGAATTCCTACCCCAGAGCTTTTTGCAAGAATA
genomic: GCTGTTGTCGAGGACATTGGCCGCCAGgtattatttt ... cctgttccagCTGCTGACCTATGGACGAAGAATTCCTACCCCAGAGCTTTTTGCAAGAATA
EST: gi|83279407|gb|DV943415.1|DV943415
EST:     AACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAG                         CTGCTGACCTATGGACGAAGAATTCCTACCCCAGAGCTTTTTGCAAGAATA
genomic: AACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAGgtattatttt ... cctgttccagCTGCTGACCTATGGACGAAGAATTCCTACCCCAGAGCTTTTTGCAAGAATA
EST: gi|32848125|gb|CD987806.1|CD987806
EST:     AACTCCACCTTGATGGTTCAACTACTGTTGTCGAGAACATTGGCCGCCAC                         CTCCTGACCTATGCACGAAGAATTCCTACCCCAGAGCTTTTTGCAAGAATA
genomic: AACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAGgtattatttt ... cctgttccagCTGCTGACCTATGGACGAAGAATTCCTACCCCAGAGCTTTTTGCAAGAATA
EST: gi|29544108|gb|CB604488.1|CB604488
EST:     AACTCCNCCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAG                         CTGCTGACCTATGGACGAAGAATTCCTACCCCAGAGCTTTTTGCAAGAATA
genomic: AACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAGgtattatttt ... cctgttccagCTGCTGACCTATGGACGAAGAATTCCTACCCCAGAGCTTTTTGCAAGAATA
EST: gi|60355748|gb|DN222721.1|DN222721
EST:     AACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAG                         CTGCTGACCTATGGACGAAGAATTCCTACCCCAGAGCTTTTTGCAAGAATA
genomic: AACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAGgtattatttt ... cctgttccagCTGCTGACCTATGGACGAAGAATTCCTACCCCAGAGCTTTTTGCAAGAATA
EST: gi|87151703|gb|DY396492.1|DY396492
EST:     GGACATTGGCCGCCAG                         CTGCTGACCTATGGACGAAGAATTCCTACCCCAGAGCTTTTTGCAAGAATA
genomic: GGACATTGGCCGCCAGgtattatttt ... cctgttccagCTGCTGACCTATGGACGAAGAATTCCTACCCCAGAGCTTTTTGCAAGAATA
EST: gi|5895629|gb|AW036875.1|AW036875
EST:     AACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAG                         CTGCTGACCTATGGACGAAGAATTCCTACCCCAGAGCTTTTTGCAAGAATA
genomic: AACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAGgtattatttt ... cctgttccagCTGCTGACCTATGGACGAAGAATTCCTACCCCAGAGCTTTTTGCAAGAATA

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), 47 (downstream exon)
Score: 121

CTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAGgtattatttt ... cctgttccagCTGCTGACCTATGGACGAAGAATTCCTACCCCAGAGCTTTTTGCAAGAATAGATGCTGTTGATGCAAGCACTGTGAAGCGTGTTGCAAACCGCTTCATCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 215

CTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAGgtattatttt ... cctgttccagCTGCTGACCTATGGACGAAGAATTCCTACCCCAGAGCTTTTTGCAAGAATAGATGCTGTTGATGCAAGCACTGTGAAGCGTGTTGCAAACCGCTTCATCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 152

CTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAGgtattatttt ... cctgttccagCTGCTGACCTATGGACGAAGAATTCCTACCCCAGAGCTTTTTGCAAGAATAGATGCTGTTGATGCAAGCACTGTGAAGCGTGTTGCAAACCGCTTCATCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 372

CTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAGgtattatttt ... cctgttccagCTGCTGACCTATGGACGAAGAATTCCTACCCCAGAGCTTTTTGCAAGAATAGATGCTGTTGATGCAAGCACTGTGAAGCGTGTTGCAAACCGCTTCATCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGAAGTCCTCAATCCAACTCCACCTTGATGGTTCAACTGCTGTTGTCGAGGACATTGGCCGCCAGgtattattttgctccattattttgatgtccaaccaattattttacaccaaattttagtgatcagcacctactttttttcgttcctctcctgttccag

- - - - - - - - - - - - - - - - - - -  GCTGTT