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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatctactccgccaccgttttcctttttcctctaagaaacctacgtgtattctgctactactagtagagtcgagaagaaggtgtgggtacggtctgtgcatgatgaatcatgagtcgagcgcttttccagGGGTTCGAGGCTGCCATCGCAGCCGGCGCGAAGGAAATCGCGGTCTTCGCGTCCGCGTCTGAATCCTTCTCCAGGTCCAACATCAACTGCACCATCGAGG

Basic information

species Zea mays
transcript GRMZM2G095141_T03
intron # 5
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|76016005|gb|DT943175.1|DT943175
EST:     TAAAGCAGGAGCCAGGCGTGCGGTACCCGGTGCTAACACCTAACCTCAGA                         GGGTTCGAGGCTGCCATCGCAGCCGGCGCGAAGGAAATCGCGGTCTTCGCG
genomic: TAAAGCAGGAGCCAGGCGTGCGGTACCCGGTGCTAACACCTAACCTCAGAgtgagatcta ... gcttttccagGGGTTCGAGGCTGCCATCGCAGCCGGCGCGAAGGAAATCGCGGTCTTCGCG
EST: gi|71301051|gb|DR786555.1|DR786555
EST:     TAAAGCAGGAGCCAGGCGTGCGGTACTCGGTGCTAACACCTAACCTCAGA                         GGGTTCGAGGCTGCCATCGCAGCCGGCGCGAAGGAAATCGCGGTCTTCGCG
genomic: TAAAGCAGGAGCCAGGCGTGCGGTACCCGGTGCTAACACCTAACCTCAGAgtgagatcta ... gcttttccagGGGTTCGAGGCTGCCATCGCAGCCGGCGCGAAGGAAATCGCGGTCTTCGCG
EST: gi|78075611|gb|DV504045.1|DV504045
EST:     AAAGCAGGAGCCAGGCGTGCGGTACCCGGTGGCTA-CACCTAACCTCAGA                         GGGGTCGAGGCTGCCATCGCAGC
genomic: AAAGCAGGAGCCAGGCGTGCGGTACCCGGTG-CTAACACCTAACCTCAGAgtgagatcta ... gcttttccagGGGTTCGAGGCTGCCATCGCAGC
EST: gi|149100624|gb|EE186712.2|EE186712
EST:     TAAAGCAGGAGCCAGGCGTGCGGTACCCGGTGCTAACACCTAACCTCAGA                         GGGTTCGAGGCTGCCATCGCAGCCGGCGCGAAAGGAA-TCGCGGTCTTCGC
genomic: TAAAGCAGGAGCCAGGCGTGCGGTACCCGGTGCTAACACCTAACCTCAGAgtgagatcta ... gcttttccagGGGTTCGAGGCTGCCATCGCAGCCGGCGCGAA-GGAAATCGCGGTCTTCGC
EST: gi|71447021|gb|DR828071.1|DR828071
EST:     TAAAGCAGGAGCCAGGCGTGCGGTACCCGGTGCTAACACCTAACCTCAGA                         GGGTTCGAGGCTGCCATCGCAGCCGGC
genomic: TAAAGCAGGAGCCAGGCGTGCGGTACCCGGTGCTAACACCTAACCTCAGAgtgagatcta ... gcttttccagGGGTTCGAGGCTGCCATCGCAGCCGGC
EST: gi|148951347|gb|EC897061.2|EC897061
EST:     TAAAGCAGGAGCCAGGCGTGCGGTACCCGGTGCTAACACCTAACCTCAGA                         GGGTTCGAGGCTGCCATCGCAGCCGGCGCGAAGGAAATCGCGGTCTTCGCG
genomic: TAAAGCAGGAGCCAGGCGTGCGGTACCCGGTGCTAACACCTAACCTCAGAgtgagatcta ... gcttttccagGGGTTCGAGGCTGCCATCGCAGCCGGCGCGAAGGAAATCGCGGTCTTCGCG
EST: gi|91872713|gb|EB402670.1|EB402670
EST:     TAAAGCAGGAGCCAGGCGTGCGGTACCCGGTGCTAACACCTAACCTCAGA                         GGGTTCGAGGCTGCCATCGCAGCCGGCGCGAAGGAAATCGCGGTCTTCGCG
genomic: TAAAGCAGGAGCCAGGCGTGCGGTACCCGGTGCTAACACCTAACCTCAGAgtgagatcta ... gcttttccagGGGTTCGAGGCTGCCATCGCAGCCGGCGCGAAGGAAATCGCGGTCTTCGCG
EST: gi|148951196|gb|EC896884.2|EC896884
EST:     TAAAGCAGGAGCCAGGCGTGCGGTACCCGGTGCTAACACCTAACCTCAGA                         GGGTTCGAGGCTGCCATCGCAGCCGGCGCGAAGGAAATCGCGGTCTTCGCG
genomic: TAAAGCAGGAGCCAGGCGTGCGGTACCCGGTGCTAACACCTAACCTCAGAgtgagatcta ... gcttttccagGGGTTCGAGGCTGCCATCGCAGCCGGCGCGAAGGAAATCGCGGTCTTCGCG
EST: gi|149076596|gb|EE165231.2|EE165231
EST:     TAAAGCAGGAGCCAGGCGTGCGGTACCCGGTGCTAACACCTAACCTCAGA                         GGGTTCGAGGCTGCCATCGCAGCCGGCGCGAAGGAAATCGCGGTCTTCGCG
genomic: TAAAGCAGGAGCCAGGCGTGCGGTACCCGGTGCTAACACCTAACCTCAGAgtgagatcta ... gcttttccagGGGTTCGAGGCTGCCATCGCAGCCGGCGCGAAGGAAATCGCGGTCTTCGCG

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), 46 (downstream exon)
Score: 61

CTAGCCGACGCAGAGGAGGTGCTGAAGGGTATAAAGCAGGAGCCAGGCGTGCGGTACCCGGTGCTAACACCTAACCTCAGAgtgagatcta ... gcttttccagGGGTTCGAGGCTGCCATCGCAGCCGGCGCGAAGGAAATCGCGGTCTTCGCGTCCGCGTCTGAATCCTTCTCCAGGTCCAACATCAACTGCACCATCGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

CTAGCCGACGCAGAGGAGGTGCTGAAGGGTATAAAGCAGGAGCCAGGCGTGCGGTACCCGGTGCTAACACCTAACCTCAGAgtgagatcta ... gcttttccagGGGTTCGAGGCTGCCATCGCAGCCGGCGCGAAGGAAATCGCGGTCTTCGCGTCCGCGTCTGAATCCTTCTCCAGGTCCAACATCAACTGCACCATCGAGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 130

CTAGCCGACGCAGAGGAGGTGCTGAAGGGTATAAAGCAGGAGCCAGGCGTGCGGTACCCGGTGCTAACACCTAACCTCAGAgtgagatcta ... gcttttccagGGGTTCGAGGCTGCCATCGCAGCCGGCGCGAAGGAAATCGCGGTCTTCGCGTCCGCGTCTGAATCCTTCTCCAGGTCCAACATCAACTGCACCATCGAGG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 282

CTAGCCGACGCAGAGGAGGTGCTGAAGGGTATAAAGCAGGAGCCAGGCGTGCGGTACCCGGTGCTAACACCTAACCTCAGAgtgagatcta ... gcttttccagGGGTTCGAGGCTGCCATCGCAGCCGGCGCGAAGGAAATCGCGGTCTTCGCGTCCGCGTCTGAATCCTTCTCCAGGTCCAACATCAACTGCACCATCGAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaaggtgtgggtacggtctgtgcatgatgaatcatgagtcgagcgcttttccagGGGTTCGAGGCTGCCATCGCAGCCGGCGCGAAGGAAATCGCGGTCTTCGCGTCCGCGTCTGAATCCTTCTCCAGGTCCAACATCAACTGCACCATCGAGG
                                            cgcttttcc  CT-rich tract