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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtgaattttatcttgtgaggttcaagaaatactcgtcacttttcatcttgccggccgtggcatgctgtttcacattgctatttttcgtattgcagACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG

Basic information

species Zea mays
transcript GRMZM2G045241_T05
intron # 15
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|76294030|gb|DV033598.1|DV033598
EST:     TTGTGTCCTTGATTTAACTCTCAGTCTGAAGCCAAGTTTTTCTGGAACAG                         ACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG
genomic: TTGTGTCCTTGATTTAACTCTCAGTCTGAAGCCAAGTTTTTCTGGAACAGgtgcgtgaat ... cgtattgcagACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG
EST: gi|78081455|gb|DV509867.1|DV509867
EST:     TTGTGTCCTTGATTTAACTCTCAGTCTGAAGCCAAGNNNNNNNGGAACAG                         ACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG
genomic: TTGTGTCCTTGATTTAACTCTCAGTCTGAAGCCAAGTTTTTCTGGAACAGgtgcgtgaat ... cgtattgcagACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG
EST: gi|211252583|gb|FL430692.1|FL430692
EST:     TTGTGTCCTTGATTTAACTCTCAGTCTGAASCCAAGTTTTTCTGGAACAG                         ACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG
genomic: TTGTGTCCTTGATTTAACTCTCAGTCTGAAGCCAAGTTTTTCTGGAACAGgtgcgtgaat ... cgtattgcagACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG
EST: gi|76908596|gb|DV163020.1|DV163020
EST:     TTGTGTCCTTGATTTAACTCTCAGTCTGAAGCCAAGTTTTTCTGGAACAG                         ACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG
genomic: TTGTGTCCTTGATTTAACTCTCAGTCTGAAGCCAAGTTTTTCTGGAACAGgtgcgtgaat ... cgtattgcagACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG
EST: gi|211489896|gb|FL473954.1|FL473954
EST:     TTGTGTCCTTGATTTAACTCTCAGTCTGAAGCCAAGTTTTTCTGGAACAG                         ACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG
genomic: TTGTGTCCTTGATTTAACTCTCAGTCTGAAGCCAAGTTTTTCTGGAACAGgtgcgtgaat ... cgtattgcagACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG
EST: gi|15080211|gb|BI388982.1|BI388982
EST:     TCTCAGTCTGAAGCCAAGTTTTTCTGGAACAG                         ACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG
genomic: TCTCAGTCTGAAGCCAAGTTTTTCTGGAACAGgtgcgtgaat ... cgtattgcagACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG
EST: gi|211489897|gb|FL473955.1|FL473955
EST:     TTGTGTCCTTGATTTAACTCTCAGTCTGAAGCCAAGTTTTTCTGGAACAG                         ACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG
genomic: TTGTGTCCTTGATTTAACTCTCAGTCTGAAGCCAAGTTTTTCTGGAACAGgtgcgtgaat ... cgtattgcagACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG
EST: gi|78117446|gb|DV535833.1|DV535833
EST:     TTGTGTCCTTGATTTAACTCTCAGTCTGAAGCCAAGTTTTTCTGGAACAG                         ACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG
genomic: TTGTGTCCTTGATTTAACTCTCAGTCTGAAGCCAAGTTTTTCTGGAACAGgtgcgtgaat ... cgtattgcagACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG
EST: gi|211260967|gb|FL474891.1|FL474891
EST:     TTGTGTCCTTGATTTAACTCTCAGTCTGAAGCCAAGTTTTTCTGGAACAG                         ACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG
genomic: TTGTGTCCTTGATTTAACTCTCAGTCTGAAGCCAAGTTTTTCTGGAACAGgtgcgtgaat ... cgtattgcagACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG

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), 35 (downstream exon)
Score: 108

GAACCAAGATTGGAACTGAACCTGTGGGATTTCAGCACAGAACCTGATGATTGTGTCCTTGATTTAACTCTCAGTCTGAAGCCAAGTTTTTCTGGAACAGgtgcgtgaat ... cgtattgcagACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG


Block sizes: 46 (upstream exon), 44 (downstream exon)
Score: 85

GAACCAAGATTGGAACTGAACCTGTGGGATTTCAGCACAGAACCTGATGATTGTGTCCTTGATTTAACTCTCAGTCTGAAGCCAAGTTTTTCTGGAACAGgtgcgtgaat ... cgtattgcagACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 149

GAACCAAGATTGGAACTGAACCTGTGGGATTTCAGCACAGAACCTGATGATTGTGTCCTTGATTTAACTCTCAGTCTGAAGCCAAGTTTTTCTGGAACAGgtgcgtgaat ... cgtattgcagACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 149

GAACCAAGATTGGAACTGAACCTGTGGGATTTCAGCACAGAACCTGATGATTGTGTCCTTGATTTAACTCTCAGTCTGAAGCCAAGTTTTTCTGGAACAGgtgcgtgaat ... cgtattgcagACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcatcttgccggccgtggcatgctgtttcacattgctatttttcgtattgcagACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG
                                     ctatttttc  CT-rich tract
                                      tattttt  TA-rich tract