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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgctgcttccccactctgccgcgtcaccgccaacgcaaccaatccgcacgggccggagcatgagacggggtcgggcacggcgcagGCTGCAGGTTCTCCTATGGCACGGCGGGCTTCCGCGCCGACGGCGCCACCATGGCGCCTGCCGTCTGCCGCGCCGGCATCCTCGCCGCGCTCCGCTCCGT

Basic information

species Zea mays
transcript GRMZM2G166597_T01
intron # 1
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|94473760|gb|EB702718.1|EB702718
EST:     GCAGCGCCGCCGCCTTATCGCCGCCGCGACCCGCTTCCCTCTCCCAAGCG                         GCTGCAGGTTCTCCTATGGCACGGCGGGCTTCCGCGCCGACGGCGCCACCA
genomic: GCAGCGCCGCCGCCTTATCGCCGCCGCGACCCGCTTCCCTCTCCCAAGCGgtacgtgctg ... cacggcgcagGCTGCAGGTTCTCCTATGGCACGGCGGGCTTCCGCGCCGACGGCGCCACCA
EST: gi|78111494|gb|DV529891.1|DV529891
EST:     GCAGCGCCGCCGCCTTATCGCCGCCGCGACCCGCTTCCCTCTCCCAAGCG                         GCTGCAGGTTCTCCTATGGCACGGCGGGCTTCCGCGCCGACGGCGCCACCA
genomic: GCAGCGCCGCCGCCTTATCGCCGCCGCGACCCGCTTCCCTCTCCCAAGCGgtacgtgctg ... cacggcgcagGCTGCAGGTTCTCCTATGGCACGGCGGGCTTCCGCGCCGACGGCGCCACCA
EST: gi|149005495|gb|EE040053.2|EE040053
EST:     GCAGCGCCGCCGCCTTATCGCCGCCGCGACCCGCTTCCCTCTCCCAAGCG                         GCTGCAGGTTCTCCTATGGCACGGCGGGCTTCCGCGCCGACGGCGCCACCA
genomic: GCAGCGCCGCCGCCTTATCGCCGCCGCGACCCGCTTCCCTCTCCCAAGCGgtacgtgctg ... cacggcgcagGCTGCAGGTTCTCCTATGGCACGGCGGGCTTCCGCGCCGACGGCGCCACCA
EST: gi|71319129|gb|DR796327.1|DR796327
EST:     GCAGCGCCGCCGCCTTATCGCCGCCGCGACCCGCTTCCCTCTCCCAAGCG                         GCTGCAGGTTCTCCTATGGCACGGCGGGCTTCCGCGCCGACGGCGCCACCA
genomic: GCAGCGCCGCCGCCTTATCGCCGCCGCGACCCGCTTCCCTCTCCCAAGCGgtacgtgctg ... cacggcgcagGCTGCAGGTTCTCCTATGGCACGGCGGGCTTCCGCGCCGACGGCGCCACCA
EST: gi|211452223|gb|FL399794.1|FL399794
EST:     GCAGCGCCGCCGCCTTATCGCCGCCGCGACCCGCTTCCCTCTCCCAAGCG                         GCTGCAGGTTCTCCTATGGCACGGCGGGCTTCCGCGCCGACGGCGCCACCA
genomic: GCAGCGCCGCCGCCTTATCGCCGCCGCGACCCGCTTCCCTCTCCCAAGCGgtacgtgctg ... cacggcgcagGCTGCAGGTTCTCCTATGGCACGGCGGGCTTCCGCGCCGACGGCGCCACCA
EST: gi|76917160|gb|DV166705.1|DV166705
EST:     GCAGCGCCGCCGCCTTATCGCCGCCGCGACCCGCTTCCCTCTCCCAAGCG                         GCTGCAGGTTCTCCTATGGCACGGCGGGCTTCCGCGCCGACGGCGCCACCA
genomic: GCAGCGCCGCCGCCTTATCGCCGCCGCGACCCGCTTCCCTCTCCCAAGCGgtacgtgctg ... cacggcgcagGCTGCAGGTTCTCCTATGGCACGGCGGGCTTCCGCGCCGACGGCGCCACCA

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), 42 (downstream exon)
Score: 31

TCCGATCAGGACGACGCCATGGCCGCCAACCAGGAGGAGCAGGAGCAGGAGCAGCGCCGCCGCCTTATCGCCGCCGCGACCCGCTTCCCTCTCCCAAGCGgtacgtgctg ... cacggcgcagGCTGCAGGTTCTCCTATGGCACGGCGGGCTTCCGCGCCGACGGCGCCACCATGGCGCCTGCCGTCTGCCGCGCCGGCATCCTCGCCGCGCTCCGCTCCGT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 26

TCCGATCAGGACGACGCCATGGCCGCCAACCAGGAGGAGCAGGAGCAGGAGCAGCGCCGCCGCCTTATCGCCGCCGCGACCCGCTTCCCTCTCCCAAGCGgtacgtgctg ... cacggcgcagGCTGCAGGTTCTCCTATGGCACGGCGGGCTTCCGCGCCGACGGCGCCACCATGGCGCCTGCCGTCTGCCGCGCCGGCATCCTCGCCGCGCTCCGCTCCGT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 12

TCCGATCAGGACGACGCCATGGCCGCCAACCAGGAGGAGCAGGAGCAGGAGCAGCGCCGCCGCCTTATCGCCGCCGCGACCCGCTTCCCTCTCCCAAGCGgtacgtgctg ... cacggcgcagGCTGCAGGTTCTCCTATGGCACGGCGGGCTTCCGCGCCGACGGCGCCACCATGGCGCCTGCCGTCTGCCGCGCCGGCATCCTCGCCGCGCTCCGCTCCGT


Block sizes: 47 (upstream exon), 40 (downstream exon)
Score: 19

TCCGATCAGGACGACGCCATGGCCGCCAACCAGGAGGAGCAGGAGCAGGAGCAGCGCCGCCGCCTTATCGCCGCCGCGACCCGCTTCCCTCTCCCAAGCGgtacgtgctg ... cacggcgcagGCTGCAGGTTCTCCTATGGCACGGCGGGCTTCCGCGCCGACGGCGCCACCATGGCGCCTGCCGTCTGCCGCGCCGGCATCCTCGCCGCGCTCCGCTCCGT