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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttcttgactcttgccctctgttatgttcctcccctctctgtctgtccctggcaaaacgggcttatgcttcttcttcttcttcttcttctttttgttcgctgctgtcagGTTATCCAAAGATCATCCATCGTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAG

Basic information

species Zea mays
transcript GRMZM2G470499_T04
intron # 2
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|78086935|gb|DV515328.1|DV515328
EST:     AGGGATCGCGGTTGGCTCCGCGAAGGGCCTCGCGTACCTGCACGAAGACT                         GTTATCCAAAGATCATCCATCGTGACATCAAAGCGGCGAACATCCTTCTGG
genomic: A-GGATCGCGGTTGGCTCCGCGAAGGGCCTCGCGTACCTGCACGAAGACTgtgagttctt ... ctgctgtcagGTTATCCAAAGATCATCCATCGTGACATCAAAGCGGCGAACATCCTTCTGG
EST: gi|101401541|gb|EB822450.1|EB822450
EST:     GAGGATCGCGGTTGGCTCCGCGAAGGGCCTCGCGTACCTGCACGAAGACT                         GTTATCCAAAGATCATCCATCGTGACATCAAAGCGGCGAACATCCTTCTGG
genomic: GAGGATCGCGGTTGGCTCCGCGAAGGGCCTCGCGTACCTGCACGAAGACTgtgagttctt ... ctgctgtcagGTTATCCAAAGATCATCCATCGTGACATCAAAGCGGCGAACATCCTTCTGG
EST: gi|71315889|gb|DR794631.1|DR794631
EST:     GAGGATCGCGGTTGGCTCCGCGAAGGGCCTCGCGTACCTGCACGAAGACT                         GTTATCCAAAGATCATCCATCGTGACATCAAAGCGGCGAACATCCTTCTGG
genomic: GAGGATCGCGGTTGGCTCCGCGAAGGGCCTCGCGTACCTGCACGAAGACTgtgagttctt ... ctgctgtcagGTTATCCAAAGATCATCCATCGTGACATCAAAGCGGCGAACATCCTTCTGG
EST: gi|149012054|gb|EE042472.2|EE042472
EST:     GAGGATCGCGGTTGGCTCCGCGAAGGGCCTCGCGTACCTGCACGAAGACT                         GTTATCCAAAGATCATCCATCGTGACATCAAAGCGGCGAACATCCTTCTGG
genomic: GAGGATCGCGGTTGGCTCCGCGAAGGGCCTCGCGTACCTGCACGAAGACTgtgagttctt ... ctgctgtcagGTTATCCAAAGATCATCCATCGTGACATCAAAGCGGCGAACATCCTTCTGG
EST: gi|148972877|gb|EE023879.2|EE023879
EST:     GAGGATCGCGGTTGGCTCCGCGAAGGGCCTCGCGTACCTGCACGAAGACT                         GTTATCCAAAGATCATCCATCGTGACATCAAAGCGGCGAACATCCTTCTGG
genomic: GAGGATCGCGGTTGGCTCCGCGAAGGGCCTCGCGTACCTGCACGAAGACTgtgagttctt ... ctgctgtcagGTTATCCAAAGATCATCCATCGTGACATCAAAGCGGCGAACATCCTTCTGG
EST: gi|71303565|gb|DR787892.1|DR787892
EST:     GAGGATCGCGGTTGGCTCCGCGAAGGGCCTCGCGTACCTGCACGAAGACT                         GTTATCCAAAGATCATCCATCGTGACATCAAAGCGGCGAACATCCTTCTGG
genomic: GAGGATCGCGGTTGGCTCCGCGAAGGGCCTCGCGTACCTGCACGAAGACTgtgagttctt ... ctgctgtcagGTTATCCAAAGATCATCCATCGTGACATCAAAGCGGCGAACATCCTTCTGG

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), 48 (downstream exon)
Score: 185

GGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCGCGGTTGGCTCCGCGAAGGGCCTCGCGTACCTGCACGAAGACTgtgagttctt ... ctgctgtcagGTTATCCAAAGATCATCCATCGTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 55

GGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCGCGGTTGGCTCCGCGAAGGGCCTCGCGTACCTGCACGAAGACTgtgagttctt ... ctgctgtcagGTTATCCAAAGATCATCCATCGTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAG


Block sizes: 46 (upstream exon), 41 (downstream exon)
Score: 32

GGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCGCGGTTGGCTCCGCGAAGGGCCTCGCGTACCTGCACGAAGACTgtgagttctt ... ctgctgtcagGTTATCCAAAGATCATCCATCGTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAG


Block sizes: 46 (upstream exon), 38 (downstream exon)
Score: 8

GGACAGGGAGTGGCAGGCCGACGCTGGACTGGCCGAGGCGGTGGAGGATCGCGGTTGGCTCCGCGAAGGGCCTCGCGTACCTGCACGAAGACTgtgagttctt ... ctgctgtcagGTTATCCAAAGATCATCCATCGTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacgggcttatgcttcttcttcttcttcttcttctttttgttcgctgctgtcagGTTATCCAAAGATCATCCATCGTGACATCAAAGCGGCGAACATCCTTCTGGATTACCATTACGAGCCAAAG
       cttatgcttcttcttc  CT-rich tract
                                ttcttttt  TA-rich tract