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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAGgtgaattaactttgcgttttctttcccaatagtaagattctgtgttgtatatgaactatgaagtgctcatgaaattcagaaaatggtaccctgctttag

Basic information

species Zea mays
transcript GRMZM2G038848_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|78093374|gb|DV521748.1|DV521748
EST:     GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAG                         GTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
genomic: GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAGgtgaattaac ... cctgctttagGTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
EST: gi|211345290|gb|FL126063.1|FL126063
EST:     GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAG                         GTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
genomic: GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAGgtgaattaac ... cctgctttagGTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
EST: gi|211345286|gb|FL126059.1|FL126059
EST:     GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAG                         GTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
genomic: GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAGgtgaattaac ... cctgctttagGTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
EST: gi|211345287|gb|FL126060.1|FL126060
EST:     GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAG                         GTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
genomic: GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAGgtgaattaac ... cctgctttagGTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
EST: gi|148943028|gb|EC888078.2|EC888078
EST:     GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAG                         GTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
genomic: GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAGgtgaattaac ... cctgctttagGTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
EST: gi|148946776|gb|EC892045.2|EC892045
EST:     GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAG                         GTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
genomic: GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAGgtgaattaac ... cctgctttagGTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
EST: gi|211345285|gb|FL126058.1|FL126058
EST:     GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAG                         GTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
genomic: GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAGgtgaattaac ... cctgctttagGTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
EST: gi|89757643|gb|DY687157.1|DY687157
EST:     GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAG                         GTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
genomic: GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAGgtgaattaac ... cctgctttagGTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
EST: gi|148942779|gb|EC887806.2|EC887806
EST:     GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAG                         GTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
genomic: GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAGgtgaattaac ... cctgctttagGTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
EST: gi|71429367|gb|DR810417.1|DR810417
EST:     GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAG                         GTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
genomic: GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAGgtgaattaac ... cctgctttagGTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
EST: gi|30705270|gb|CD058727.1|CD058727
EST:     GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAG                         GTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
genomic: GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAGgtgaattaac ... cctgctttagGTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
EST: gi|101390742|gb|EB817305.1|EB817305
EST:     GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAG                         GTTGGATCCCTGCCCCTCCGTGCGAGGGGATCCATTTTTTCTTCACCACGC
genomic: GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAGgtgaattaac ... cctgctttagGTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
EST: gi|91878697|gb|EB408654.1|EB408654
EST:     GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAG                         GTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
genomic: GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAGgtgaattaac ... cctgctttagGTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
EST: gi|148946555|gb|EC884293.2|EC884293
EST:     GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAG                         GTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
genomic: GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAGgtgaattaac ... cctgctttagGTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
EST: gi|211345293|gb|FL126066.1|FL126066
EST:     GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAANCCTCAGCAG                         GTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
genomic: GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAGgtgaattaac ... cctgctttagGTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
EST: gi|211345288|gb|FL126061.1|FL126061
EST:     GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAG                         GTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
genomic: GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAGgtgaattaac ... cctgctttagGTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
EST: gi|78080160|gb|DV508572.1|DV508572
EST:     GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAG                         GTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
genomic: GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAGgtgaattaac ... cctgctttagGTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
EST: gi|78079274|gb|DV507686.1|DV507686
EST:     GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAG                         GTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
genomic: GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAGgtgaattaac ... cctgctttagGTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
EST: gi|74234671|gb|DT642585.1|DT642585
EST:     GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAG                         GTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
genomic: GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAGgtgaattaac ... cctgctttagGTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
EST: gi|149074521|gb|EE162917.2|EE162917
EST:     GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAG                         GTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC
genomic: GATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAGgtgaattaac ... cctgctttagGTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGC

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: 148

AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAGgtgaattaac ... cctgctttagGTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGCAGGCTTTTCTCCCCTAAGGCAGCAGCCCCTAAATCAGGGGATTCCATAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 122

AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAGgtgaattaac ... cctgctttagGTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGCAGGCTTTTCTCCCCTAAGGCAGCAGCCCCTAAATCAGGGGATTCCATAC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 74

AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAGgtgaattaac ... cctgctttagGTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGCAGGCTTTTCTCCCCTAAGGCAGCAGCCCCTAAATCAGGGGATTCCATAC


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 82

AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAGgtgaattaac ... cctgctttagGTTGGATCCCTGCCCCTCCGTGCAAGGGGATCCATTTTTTCTTCACCACGCAGGCTTTTCTCCCCTAAGGCAGCAGCCCCTAAATCAGGGGATTCCATAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAGgtgaattaactttgcgttttctttcccaatagtaagattctgtgttgtatatgaactatgaagtgctcatgaaattcagaaaatggtaccctgctttag

- - - - - - - - - - - - - - - - - - - - - - - - AAGAAA