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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtccttattagcctggcgtgcctgttctcatctattccttgatatcctgattgcaacgtctttaatgcaaccttcatttgtcagGGAGTTTTCGATTACAAGCATGAAAGGTGGTTACCGCCGAGTGTTCCAGCGGCCTATTGGTTTTGAGTG

Basic information

species Zea mays
transcript GRMZM2G096553_T03
intron # 16
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|67025158|gb|CO453907.1|CO453907
EST:     ATGCTCATGGTGTCAA                         GGAGTTTTCGATTACAAGCATGAAAGGTGGTTACCGTCGAGTGTTCCAGCG
genomic: ATGCTCATGGTGTCAAgtgagtcctt ... catttgtcagGGAGTTTTCGATTACAAGCATGAAAGGTGGTTACCGCCGAGTGTTCCAGCG
EST: gi|60347237|gb|DN214210.1|DN214210
EST:     GATGGCATTAGCTTGACGGAGAATGCTCATGGTGTCAA                         GGAGTTTTCGATTACAAGCATGAAAGGTGGTTACCGCCGAGTGTTCCAGCG
genomic: GATGGCATTAGCTTGACGGAGAATGCTCATGGTGTCAAgtgagtcctt ... catttgtcagGGAGTTTTCGATTACAAGCATGAAAGGTGGTTACCGCCGAGTGTTCCAGCG
EST: gi|86465812|gb|DY232185.1|DY232185
EST:     GATGGCATTAGCTTGACGGAGAATGCTCATGGTGTCAA                         GGAGTTTTCGATTACAAGCATGAAAGGTGGTTACCGCCGAGTGTTCCAGCG
genomic: GATGGCATTAGCTTGACGGAGAATGCTCATGGTGTCAAgtgagtcctt ... catttgtcagGGAGTTTTCGATTACAAGCATGAAAGGTGGTTACCGCCGAGTGTTCCAGCG
EST: gi|166619936|gb|EG146972.1|EG146972
EST:     GATGGCATTAGCTTGACGGAGAATGCTCATGGTGTCAA                         A
genomic: GATGGCATTAGCTTGACGGAGAATGCTCATGGTGTCAAgtgagtcctt ... catttgtcag-
EST: gi|166619936|gb|EG146972.1|EG146972
EST:     GATGGCATTAGCTTGACGGAGAATGCTCATGGTGTCAA                         A
genomic: GATGGCATTAGCTTGACGGAGAATGCTCATGGTGTCAAgtgagtcctt ... catttgtcag-
EST: gi|13149317|gb|BG319639.1|BG319639
EST:     GATGGCATTAGCTTGACGGAGAATGCTCATGGTGTCAA                         GGAGTTTTCGATTACAAGCATGAAAGGTGGTTACCGCCGAGTGTTCCAGCG
genomic: GATGGCATTAGCTTGACGGAGAATGCTCATGGTGTCAAgtgagtcctt ... catttgtcagGGAGTTTTCGATTACAAGCATGAAAGGTGGTTACCGCCGAGTGTTCCAGCG
EST: gi|60397731|gb|DN230547.1|DN230547
EST:     ATGGCATTAGCTTGACGGAGAATGCTCATGGTGTCAA                         GGAGTTTTCGATTACAAGCATGAAAGGTGGTTACCGCCGAGTGTTCCAGCG
genomic: ATGGCATTAGCTTGACGGAGAATGCTCATGGTGTCAAgtgagtcctt ... catttgtcagGGAGTTTTCGATTACAAGCATGAAAGGTGGTTACCGCCGAGTGTTCCAGCG
EST: gi|60349430|gb|DN216403.1|DN216403
EST:     GATGGCATTAGCTTGACGGAGAATGCTCATGGTGTCAA                         GGAGTTTTCGATTACAAGCATGAAAGGTGGTTACCGCCGAGTGTTCCAGCG
genomic: GATGGCATTAGCTTGACGGAGAATGCTCATGGTGTCAAgtgagtcctt ... catttgtcagGGAGTTTTCGATTACAAGCATGAAAGGTGGTTACCGCCGAGTGTTCCAGCG
EST: gi|211061095|gb|FL320235.1|FL320235
EST:     GATGGCATTAGCTTGACGGAGAATGCTCATGGTGTCAA                         GGAGTTTTCGATTACAAGCATGAAAGGTGGTTACCGCCGAGTGTTCCAGCG
genomic: GATGGCATTAGCTTGACGGAGAATGCTCATGGTGTCAAgtgagtcctt ... catttgtcagGGAGTTTTCGATTACAAGCATGAAAGGTGGTTACCGCCGAGTGTTCCAGCG
EST: gi|71773678|gb|DR971575.1|DR971575
EST:     GATGGCATTAGCTTGACGGAGAATGCTCATGGTGTCAA                         GGAGTTTTCGATTACAAGCATGAAAGGTGGTTACCGCCGAGTGTTCCAGCG
genomic: GATGGCATTAGCTTGACGGAGAATGCTCATGGTGTCAAgtgagtcctt ... catttgtcagGGAGTTTTCGATTACAAGCATGAAAGGTGGTTACCGCCGAGTGTTCCAGCG
EST: gi|6031366|gb|AW076223.1|AW076223
EST:     GATGGCATTAGCTTGACGGAGAATGCTCATGGTGTCAA                         GGAGTTTTCGATTACAAGCATGAAAGGTGGTTACCGCCGAGTGTTCCAGCG
genomic: GATGGCATTAGCTTGACGGAGAATGCTCATGGTGTCAAgtgagtcctt ... catttgtcagGGAGTTTTCGATTACAAGCATGAAAGGTGGTTACCGCCGAGTGTTCCAGCG

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: 47 (upstream exon), 47 (downstream exon)
Score: 137

GATGGCATTAGCTTGACGGAGAATGCTCATGGTGTCAAgtgagtcctt ... catttgtcagGGAGTTTTCGATTACAAGCATGAAAGGTGGTTACCGCCGAGTGTTCCAGCGGCCTATTGGTTTTGAGTG


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

GATGGCATTAGCTTGACGGAGAATGCTCATGGTGTCAAgtgagtcctt ... catttgtcagGGAGTTTTCGATTACAAGCATGAAAGGTGGTTACCGCCGAGTGTTCCAGCGGCCTATTGGTTTTGAGTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 38

GATGGCATTAGCTTGACGGAGAATGCTCATGGTGTCAAgtgagtcctt ... catttgtcagGGAGTTTTCGATTACAAGCATGAAAGGTGGTTACCGCCGAGTGTTCCAGCGGCCTATTGGTTTTGAGTG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 40

GATGGCATTAGCTTGACGGAGAATGCTCATGGTGTCAAgtgagtcctt ... catttgtcagGGAGTTTTCGATTACAAGCATGAAAGGTGGTTACCGCCGAGTGTTCCAGCGGCCTATTGGTTTTGAGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctattccttgatatcctgattgcaacgtctttaatgcaaccttcatttgtcagGGAGTTTTCGATTACAAGCATGAAAGGTGGTTACCGCCGAGTGTTCCAGCGGCCTATTGGTTTTGAGTG
                                         ccttcattt  CT-rich tract
                             tctttaat  TA-rich tract