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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGATCTGCGTGCCGCATCGCGCCGGGACACGGGAGACAATGGCGTTCACGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacggcgatgcttttccacactagagtaggtagagttgtgtcgttgaacccgcggctgggagcgggccagtcgagggtagatttgccccgcccg...

Basic information

species Zea mays
transcript GRMZM2G038848_T02
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|78093374|gb|DV521748.1|DV521748
EST:     CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAG                         AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
genomic: CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
EST: gi|211345290|gb|FL126063.1|FL126063
EST:     CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAG                         AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
genomic: CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
EST: gi|211345286|gb|FL126059.1|FL126059
EST:     CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAG                         AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
genomic: CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
EST: gi|211345287|gb|FL126060.1|FL126060
EST:     CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAG                         AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
genomic: CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
EST: gi|148943028|gb|EC888078.2|EC888078
EST:     CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAG                         AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
genomic: CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
EST: gi|148946776|gb|EC892045.2|EC892045
EST:     CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAG                         AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
genomic: CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
EST: gi|211345285|gb|FL126058.1|FL126058
EST:     CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAG                         AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
genomic: CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
EST: gi|89757643|gb|DY687157.1|DY687157
EST:     CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAG                         AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
genomic: CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
EST: gi|148942779|gb|EC887806.2|EC887806
EST:     CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAG                         AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
genomic: CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
EST: gi|71429367|gb|DR810417.1|DR810417
EST:     CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAG                         AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
genomic: CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
EST: gi|30705270|gb|CD058727.1|CD058727
EST:     CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAG                         AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
genomic: CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
EST: gi|101390742|gb|EB817305.1|EB817305
EST:     CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAG                         AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
genomic: CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
EST: gi|91878697|gb|EB408654.1|EB408654
EST:     GACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGCGCTGGCTCCCCAG                         AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
genomic: GACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCG-GTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
EST: gi|148946555|gb|EC884293.2|EC884293
EST:     CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAG                         AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
genomic: CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
EST: gi|211345293|gb|FL126066.1|FL126066
EST:     CGACGCTCGGCGGCTGTGGGGCGCAGGCTTSGGTGCGGTTGGCTCCCCAG                         AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
genomic: CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
EST: gi|211345288|gb|FL126061.1|FL126061
EST:     CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAG                         AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
genomic: CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
EST: gi|78080160|gb|DV508572.1|DV508572
EST:     CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAG                         AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
genomic: CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
EST: gi|78079274|gb|DV507686.1|DV507686
EST:     CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAG                         AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
genomic: CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
EST: gi|74234671|gb|DT642585.1|DT642585
EST:     CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAG                         AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
genomic: CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
EST: gi|149074521|gb|EE162917.2|EE162917
EST:     CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAG                         AATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG
genomic: CGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAG

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: 176

GGTGATCTGCGTGCCGCATCGCGCCGGGACACGGGAGACAATGGCGTTCACGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAG


Block sizes: 42 (upstream exon), 46 (downstream exon)
Score: 144

GGTGATCTGCGTGCCGCATCGCGCCGGGACACGGGAGACAATGGCGTTCACGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAG


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 60

GGTGATCTGCGTGCCGCATCGCGCCGGGACACGGGAGACAATGGCGTTCACGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 122

GGTGATCTGCGTGCCGCATCGCGCCGGGACACGGGAGACAATGGCGTTCACGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacg ... ccctgtgcagAATGGAATCCTTGGATCTAATTCGAAGCCATTCGCGGGCATCATACTCAAGAAACCTCAGCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGATCTGCGTGCCGCATCGCGCCGGGACACGGGAGACAATGGCGTTCACGACGCTCGGCGGCTGTGGGGCGCAGGCTTCAGTGCGGTTGGCTCCCCAGgtcagtgacggcgatgcttttccacactagagtaggtagagttgtgtcgttgaacccgcggctgggagcgggccagtcgagggtagatttgccccgcccg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccgccc