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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGGATTTTCCCAGCAATCAGTTTGATAGGCGACAGCGTGATTGTCGGGgtgagtctgaatccagtaaaatgccacagcatagtatctattttttcccccgcaaagacaaatgaaaatgattacaaacatcgaaaacaaatctatgcctcgcatgacatgtttttttctggacacgacggtaactcgattgcgtgttaataaactattttgacctgcag

Basic information

species Zea mays
transcript GRMZM2G124918_T01
intron # 11
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|16926475|gb|BM079543.1|BM079543
EST:     CGGGATTTTCCCAGCAATCAGTTTGATAGGCGACAGCGTGATTGTCGGG                         ATCTTCTACTTCATTGGCTTTGCACTGTTCTGCCTAGAGTCTTTGCTAAGC
genomic: CGGGATTTTCCCAGCAATCAGTTTGATAGGCGACAGCGTGATTGTCGGGgtgagtctga ... tgacctgcagATCTTCTACTTCATTGGCTTTGCACTGTTCTGCCTAGAGTCTTTGCTAAGC
EST: gi|14243814|gb|BG841530.2|BG841530
EST:     CGGGATTTTCCCAGCAATCAGTTTGATAGGCGACAGCGTGATTGTCGGG                         ATCTTCTACTTCATTGGCTTTGCACTGTTCTGCCTAGAGTCTTTGCTAAGC
genomic: CGGGATTTTCCCAGCAATCAGTTTGATAGGCGACAGCGTGATTGTCGGGgtgagtctga ... tgacctgcagATCTTCTACTTCATTGGCTTTGCACTGTTCTGCCTAGAGTCTTTGCTAAGC
EST: gi|95107983|gb|EB740212.1|EB740212
EST:     CGGGATTTTCCCAGCAATCAGTTTGATAGGCGACAGCGTGATTGTCGGG                         N
genomic: CGGGATTTTCCCAGCAATCAGTTTGATAGGCGACAGCGTGATTGTCGGGgtgagtctga ... tgacctgcag-
EST: gi|95107983|gb|EB740212.1|EB740212
EST:     CGGGATTTTCCCAGCAATCAGTTTGATAGGCGACAGCGTGATTGTCGGG                         N
genomic: CGGGATTTTCCCAGCAATCAGTTTGATAGGCGACAGCGTGATTGTCGGGgtgagtctga ... tgacctgcag-
EST: gi|28984995|gb|BQ539599.2|BQ539599
EST:     CGGGATTTTCCCAGCAATCAGTTTGATAGGCGACAGCGTGATTGTCGGG                         ATCTTCTACTTCATTGGCTTTGCACTGTTCTGCCTAGAGTCTTTGCTAAGC
genomic: CGGGATTTTCCCAGCAATCAGTTTGATAGGCGACAGCGTGATTGTCGGGgtgagtctga ... tgacctgcagATCTTCTACTTCATTGGCTTTGCACTGTTCTGCCTAGAGTCTTTGCTAAGC

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: 43 (upstream exon), 46 (downstream exon)
Score: 4

CGGGATTTTCCCAGCAATCAGTTTGATAGGCGACAGCGTGATTGTCGGGgtgagtctga ... tgacctgcagATCTTCTACTTCATTGGCTTTGCACTGTTCTGCCTAGAGTCTTTGCTAAGCATGTGTGTCATTCAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 83

CGGGATTTTCCCAGCAATCAGTTTGATAGGCGACAGCGTGATTGTCGGGgtgagtctga ... tgacctgcagATCTTCTACTTCATTGGCTTTGCACTGTTCTGCCTAGAGTCTTTGCTAAGCATGTGTGTCATTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 61

CGGGATTTTCCCAGCAATCAGTTTGATAGGCGACAGCGTGATTGTCGGGgtgagtctga ... tgacctgcagATCTTCTACTTCATTGGCTTTGCACTGTTCTGCCTAGAGTCTTTGCTAAGCATGTGTGTCATTCAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 45

CGGGATTTTCCCAGCAATCAGTTTGATAGGCGACAGCGTGATTGTCGGGgtgagtctga ... tgacctgcagATCTTCTACTTCATTGGCTTTGCACTGTTCTGCCTAGAGTCTTTGCTAAGCATGTGTGTCATTCAG