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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCATAAACTCTGTCTTGCCCTTAGCTACATCCCTCGGATTTGAGCTCGCTACACCGTTCCCTCAGTGGCACCGCCGTGGCCTTCCAGTTTTCCAAGGATgtatgcccctacagtctacacccaaacagttgaacgcaactcccagtgaacgtctctgaacctatagcctccctcaccatggcttcccttgtttgctttgcag

Basic information

species Zea mays
transcript GRMZM2G163713_T01
intron # 12
splice site 5'
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|78118871|gb|DV537255.1|DV537255
EST:     TACACCGTTCCCTCAGTGGCACCGCCGTGGCCTTCCAGTTTTCCAAGGAT                         CTGAACATTTGCTTCGGACGGATCCTGAAGATGGCCTGGAGGGCTTCTTCA
genomic: TACACCGTTCCCTCAGTGGCACCGCCGTGGCCTTCCAGTTTTCCAAGGATgtatgcccct ... tgctttgcagCTGAACATTTGCTTCGGACGGATCCTGAAGATGGCCTGGAGGGCTTCTTCA
EST: gi|24768558|gb|CA403687.1|CA403687
EST:     TACACCGTTCCCTCAGTGGCACCGCCGTGGCCTTCCAGTTTTCCAAGGAT                         CTGAACATTTGCTTCGGACGGATCCTGAAGATGGCCTGGAGGGCTTCTTCA
genomic: TACACCGTTCCCTCAGTGGCACCGCCGTGGCCTTCCAGTTTTCCAAGGATgtatgcccct ... tgctttgcagCTGAACATTTGCTTCGGACGGATCCTGAAGATGGCCTGGAGGGCTTCTTCA
EST: gi|31352925|gb|CD437282.1|CD437282
EST:     TACACCGTTCCCTCAGTGGCACCGCCGTGGCCTTCCAGTTTTCCAAGGAT                         CTGAACATTTGCTTCGGACGGATCCTGAAGATGGCCTGGAGGGCTTCTTCA
genomic: TACACCGTTCCCTCAGTGGCACCGCCGTGGCCTTCCAGTTTTCCAAGGATgtatgcccct ... tgctttgcagCTGAACATTTGCTTCGGACGGATCCTGAAGATGGCCTGGAGGGCTTCTTCA
EST: gi|89251520|gb|DY623306.1|DY623306
EST:     TACACCGTTCCCTCAGTGGCACCGCCGTGGCCTTCCAGTTTTCCAAGGAT                         CTGAACATTTGCTTCGGACGGATCCTGAAGATGGCCTGGAGGGCTTCTTCA
genomic: TACACCGTTCCCTCAGTGGCACCGCCGTGGCCTTCCAGTTTTCCAAGGATgtatgcccct ... tgctttgcagCTGAACATTTGCTTCGGACGGATCCTGAAGATGGCCTGGAGGGCTTCTTCA

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: 43

GTCATAAACTCTGTCTTGCCCTTAGCTACATCCCTCGGATTTGAGCTCGCTACACCGTTCCCTCAGTGGCACCGCCGTGGCCTTCCAGTTTTCCAAGGATgtatgcccct ... tgctttgcagCTGAACATTTGCTTCGGACGGATCCTGAAGATGGCCTGGAGGGCTTCTTCATTGCATTGTTTGTCAGGAAAGCAGGCCCTACTTCAGAAGAGCCTAGCGA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 15

GTCATAAACTCTGTCTTGCCCTTAGCTACATCCCTCGGATTTGAGCTCGCTACACCGTTCCCTCAGTGGCACCGCCGTGGCCTTCCAGTTTTCCAAGGATgtatgcccct ... tgctttgcagCTGAACATTTGCTTCGGACGGATCCTGAAGATGGCCTGGAGGGCTTCTTCATTGCATTGTTTGTCAGGAAAGCAGGCCCTACTTCAGAAGAGCCTAGCGA


Block sizes: 48 (upstream exon), 40 (downstream exon)
Score: 21

GTCATAAACTCTGTCTTGCCCTTAGCTACATCCCTCGGATTTGAGCTCGCTACACCGTTCCCTCAGTGGCACCGCCGTGGCCTTCCAGTTTTCCAAGGATgtatgcccct ... tgctttgcagCTGAACATTTGCTTCGGACGGATCCTGAAGATGGCCTGGAGGGCTTCTTCATTGCATTGTTTGTCAGGAAAGCAGGCCCTACTTCAGAAGAGCCTAGCGA


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 21

GTCATAAACTCTGTCTTGCCCTTAGCTACATCCCTCGGATTTGAGCTCGCTACACCGTTCCCTCAGTGGCACCGCCGTGGCCTTCCAGTTTTCCAAGGATgtatgcccct ... tgctttgcagCTGAACATTTGCTTCGGACGGATCCTGAAGATGGCCTGGAGGGCTTCTTCATTGCATTGTTTGTCAGGAAAGCAGGCCCTACTTCAGAAGAGCCTAGCGA