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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgctgaacatatatgtacataagtggcagtaatccacactctacagtctttgctttccctagcaagaatcaagcatgcaatgtgacatctatcttgtaaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGGTGAGAACAGGATTGGGTTTGCCAAATCTGCATGAGGACTGGAGTTCTGC

Basic information

species Zea mays
transcript GRMZM2G077233_T05
intron # 11
splice site 3'
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|78179647|gb|DV550020.1|DV550020
EST:     ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG                         GATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
genomic: ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaa ... aaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
EST: gi|32840610|gb|CD980291.1|CD980291
EST:     ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG                         GATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
genomic: ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaa ... aaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
EST: gi|76289739|gb|DV029307.1|DV029307
EST:     ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG                         GATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
genomic: ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaa ... aaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
EST: gi|116822883|gb|EC866344.1|EC866344
EST:     ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG                         GATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
genomic: ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaa ... aaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
EST: gi|76291014|gb|DV030582.1|DV030582
EST:     ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG                         GATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
genomic: ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaa ... aaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
EST: gi|32839672|gb|CD979353.1|CD979353
EST:     ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG                         GATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
genomic: ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaa ... aaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
EST: gi|60348336|gb|DN215309.1|DN215309
EST:     ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG                         GATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
genomic: ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaa ... aaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
EST: gi|60396697|gb|DN229564.1|DN229564
EST:     ATCAGTGGGTTTATGGCATTTGACATACCGCCTCCTCGTGGTCCTCTCTG                         GATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
genomic: ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaa ... aaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
EST: gi|8577168|gb|BE129805.1|BE129805
EST:     ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG                         GATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
genomic: ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaa ... aaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
EST: gi|211384116|gb|FL248479.1|FL248479
EST:     ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG                         GATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
genomic: ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaa ... aaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
EST: gi|113633153|gb|DW791221.1|DW791221
EST:     TTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG                         GATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
genomic: TTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaa ... aaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
EST: gi|60346328|gb|DN213301.1|DN213301
EST:     ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG                         GATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
genomic: ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaa ... aaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
EST: gi|91876412|gb|EB406369.1|EB406369
EST:     ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG                         GATACTTGGTGATGTTTTTATGGGTGCCTACCCCCCTGTTTTTGACTTCGG
genomic: ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaa ... aaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
EST: gi|83278626|gb|DV942634.1|DV942634
EST:     ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG                         GATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
genomic: ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaa ... aaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
EST: gi|5915565|gb|AW053206.1|AW053206
EST:     ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG                         GATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
genomic: ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaa ... aaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
EST: gi|32858947|gb|CD998628.1|CD998628
EST:     ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG                         GATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
genomic: ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaa ... aaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG

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: 48 (upstream exon), 49 (downstream exon)
Score: 260

TGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaa ... aaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGGTGAGAACAGGATTGGGTTTGCCAAATCTGCATGAGGACTGGAGTTCTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 291

TGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaa ... aaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGGTGAGAACAGGATTGGGTTTGCCAAATCTGCATGAGGACTGGAGTTCTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 531

TGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaa ... aaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGGTGAGAACAGGATTGGGTTTGCCAAATCTGCATGAGGACTGGAGTTCTGC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 353

TGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaa ... aaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGGTGAGAACAGGATTGGGTTTGCCAAATCTGCATGAGGACTGGAGTTCTGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttccctagcaagaatcaagcatgcaatgtgacatctatcttgtaaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGGTGAGAACAGGATTGGGTTTGCCAAATCTGCATGAGGACTGGAGTTCTGC
                                            taaacatt  TA-rich tract