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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacccaccaccaccgcccttgtgcctggaaccgagaaagcaatcttgtctccaagctctcccccgctcacaacacaaacacgttcttttctcgcagAGCAGCGAGGAGGGTCGGTGCAGCTGGGCGGCGTTCGGCGGCGGGTCGCCGCCGGCGCGCGCGGGCAACCCGCTGGTGCACGACCCCAGCTTCCTGCTGA

Basic information

species Zea mays
transcript GRMZM2G460566_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|149205300|gb|ES700896.1|ES700896
EST:     CCCGCGGCGCCGACCTCATCCTCGGCCCGCCGCCCTTCCTTCTCAACGAG                         AGCAGCGAGGAGGGTCGGTGCAGCTGGGCGGCGTTCGGCGGCGGGTCGCCG
genomic: CCCGCGGCGCCGACCTCATCCTCGGCCCGCCGCCCTTCCTTCTCAACGAGgtacccacca ... tttctcgcagAGCAGCGAGGAGGGTCGGTGCAGCTGGGCGGCGTTCGGCGGCGGGTCGCCG
EST: gi|211250297|gb|FL313182.1|FL313182
EST:     CCCGCGGCGCCGACCTCATCCTCGGCCCGCCGCCCTTCCTGCTCAACGAG                         AGCAGCGAGGAGGGTCGCTGCAGCTGGGCGGCGTTGGGCGGCGGGTCGCCG
genomic: CCCGCGGCGCCGACCTCATCCTCGGCCCGCCGCCCTTCCTTCTCAACGAGgtacccacca ... tttctcgcagAGCAGCGAGGAGGGTCGGTGCAGCTGGGCGGCGTTCGGCGGCGGGTCGCCG
EST: gi|148945571|gb|EC890825.2|EC890825
EST:     CCCGCGGCGCCGACCTCATCCTCGGCCCGCCGCCCTTCCTTCTCAACGAG                         AGCAGCGAGGAGGGTCGGTGCAGCTGGGCGGCGTTCGGCGGCGGGTCGCCG
genomic: CCCGCGGCGCCGACCTCATCCTCGGCCCGCCGCCCTTCCTTCTCAACGAGgtacccacca ... tttctcgcagAGCAGCGAGGAGGGTCGGTGCAGCTGGGCGGCGTTCGGCGGCGGGTCGCCG
EST: gi|149205925|gb|ES701521.1|ES701521
EST:     CCCGCGGCGCCGACCTCATCCTCGGCCCGCCGCCCTTCCTTCTCAACGAG                         AGCAGCGAGGAGGGTCGGTGCAGCTGGGCGGCGTTCGGCGGCGGGTCGCCG
genomic: CCCGCGGCGCCGACCTCATCCTCGGCCCGCCGCCCTTCCTTCTCAACGAGgtacccacca ... tttctcgcagAGCAGCGAGGAGGGTCGGTGCAGCTGGGCGGCGTTCGGCGGCGGGTCGCCG
EST: gi|89106248|gb|DY576465.1|DY576465
EST:     CCCGCGGCGCCGACCTCATCCTCGGCCCGCCGCCCTTCCTTCTCAACGAG                         AGCAGCGAGGATGGG-CGGTGCAGCTGGGCGGCGTTCGGCGGCGGGTCGCC
genomic: CCCGCGGCGCCGACCTCATCCTCGGCCCGCCGCCCTTCCTTCTCAACGAGgtacccacca ... tttctcgcagAGCAGCGAGGA-GGGTCGGTGCAGCTGGGCGGCGTTCGGCGGCGGGTCGCC
EST: gi|211522865|gb|FL340805.1|FL340805
EST:     CCCGCGGCGCCGACCTCATCCTCGGCCCGCCGCCCTTCCTGCTCAACGAG                         AGCGGCGAGGAGGGTCGGTGCAGCTGGGCGGCGTTCGGCGGCGGGTCGCCG
genomic: CCCGCGGCGCCGACCTCATCCTCGGCCCGCCGCCCTTCCTTCTCAACGAGgtacccacca ... tttctcgcagAGCAGCGAGGAGGGTCGGTGCAGCTGGGCGGCGTTCGGCGGCGGGTCGCCG

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: 38 (upstream exon), 48 (downstream exon)
Score: 12

CTGCGCGCCTCGGCCGCGCAGGGCCCAGCAGCAGCTGGTCCACGTCCACCCCCGCGGCGCCGACCTCATCCTCGGCCCGCCGCCCTTCCTTCTCAACGAGgtacccacca ... tttctcgcagAGCAGCGAGGAGGGTCGGTGCAGCTGGGCGGCGTTCGGCGGCGGGTCGCCGCCGGCGCGCGCGGGCAACCCGCTGGTGCACGACCCCAGCTTCCTGCTGA


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 20

CTGCGCGCCTCGGCCGCGCAGGGCCCAGCAGCAGCTGGTCCACGTCCACCCCCGCGGCGCCGACCTCATCCTCGGCCCGCCGCCCTTCCTTCTCAACGAGgtacccacca ... tttctcgcagAGCAGCGAGGAGGGTCGGTGCAGCTGGGCGGCGTTCGGCGGCGGGTCGCCGCCGGCGCGCGCGGGCAACCCGCTGGTGCACGACCCCAGCTTCCTGCTGA


Block sizes: 44 (upstream exon), 45 (downstream exon)
Score: 39

CTGCGCGCCTCGGCCGCGCAGGGCCCAGCAGCAGCTGGTCCACGTCCACCCCCGCGGCGCCGACCTCATCCTCGGCCCGCCGCCCTTCCTTCTCAACGAGgtacccacca ... tttctcgcagAGCAGCGAGGAGGGTCGGTGCAGCTGGGCGGCGTTCGGCGGCGGGTCGCCGCCGGCGCGCGCGGGCAACCCGCTGGTGCACGACCCCAGCTTCCTGCTGA


Block sizes: 41 (upstream exon), 48 (downstream exon)
Score: 56

CTGCGCGCCTCGGCCGCGCAGGGCCCAGCAGCAGCTGGTCCACGTCCACCCCCGCGGCGCCGACCTCATCCTCGGCCCGCCGCCCTTCCTTCTCAACGAGgtacccacca ... tttctcgcagAGCAGCGAGGAGGGTCGGTGCAGCTGGGCGGCGTTCGGCGGCGGGTCGCCGCCGGCGCGCGCGGGCAACCCGCTGGTGCACGACCCCAGCTTCCTGCTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttgtctccaagctctcccccgctcacaacacaaacacgttcttttctcgcagAGCAGCGAGGAGGGTCGGTGCAGCTGGGCGGCGTTCGGCGGCGGGTCGCCGCCGGCGCGCGCGGGCAACCCGCTGGTGCACGACCCCAGCTTCCTGCTGA
                      cgctcac  putative branch site (score: 56)
                                     cacgttcttttctc  putative PPT
                                         ttctttt  TA-rich tract