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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCATCCTAAGATCATCCATCGTGACATTAAGGCGGCGAACATCCTTCTGGATTATAACTACGAGCCAAAGgtagaccccagacagccgaaattctttttattcttgcgtgcctgccctgcatgcttgactgaaagatgcaaatcttttggcacag

Basic information

species Zea mays
transcript GRMZM2G358830_T02
intron # 3
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|149104119|gb|EE289551.2|EE289551
EST:     GTGACATTAAGGCGGCGAACATCCTTCTGGATTATAACTACGAGCCAAAG                         GTTGCAGATTTTGGGTTGGCCAAATACCAAGCAGCTGAAGTAACCTCTGTT
genomic: GTGACATTAAGGCGGCGAACATCCTTCTGGATTATAACTACGAGCCAAAGgtagacccca ... tttggcacagGTTGCAGATTTTGGGTTGGCCAAATACCAAGCAGCTGAAGTAACCTCTGTT
EST: gi|71769046|gb|DR966983.1|DR966983
EST:     GTGACATTAAGGCGGCGAACATCCTTCTGGATTATAACTACGAGCCAAAG                         GTTGCAGATTTTGGGTTGGCCAAATACCAAGCAGCTGAAGTAACCTCTGTT
genomic: GTGACATTAAGGCGGCGAACATCCTTCTGGATTATAACTACGAGCCAAAGgtagacccca ... tttggcacagGTTGCAGATTTTGGGTTGGCCAAATACCAAGCAGCTGAAGTAACCTCTGTT
EST: gi|149084848|gb|EE174353.2|EE174353
EST:     GTGACATTAAGGCGGCGAACATCCTTCTGGATTATAACTACGAGCCAAAG                         GTTGCAGATTTTGGGTTGGCCAAATACCAAGCAGCTGAAGTAACCTCTGTT
genomic: GTGACATTAAGGCGGCGAACATCCTTCTGGATTATAACTACGAGCCAAAGgtagacccca ... tttggcacagGTTGCAGATTTTGGGTTGGCCAAATACCAAGCAGCTGAAGTAACCTCTGTT
EST: gi|76926939|gb|DV171065.1|DV171065
EST:     GTGACATTAAGGCGGCGAACATCCTTCTGGATTATAACTACGAGCCAAAG                         GTTGCAGATTTTGGGTTGGCCAAATACCAAGCAGCTGAAGTAACCTCTGTT
genomic: GTGACATTAAGGCGGCGAACATCCTTCTGGATTATAACTACGAGCCAAAGgtagacccca ... tttggcacagGTTGCAGATTTTGGGTTGGCCAAATACCAAGCAGCTGAAGTAACCTCTGTT
EST: gi|148952361|gb|EC898175.2|EC898175
EST:     GTGACATTAAGGCGGCGAACATCCTTCTGGATTATAACTACGAGCCAAAG                         GTTGCAGATTTTGGGTTGGCCAAATACCAAGCAGCTGAAGTAACCTCTGTT
genomic: GTGACATTAAGGCGGCGAACATCCTTCTGGATTATAACTACGAGCCAAAGgtagacccca ... tttggcacagGTTGCAGATTTTGGGTTGGCCAAATACCAAGCAGCTGAAGTAACCTCTGTT
EST: gi|148929996|gb|EE285849.2|EE285849
EST:     GTGACATTAAGGCGGCGAACATCCTTCTGGATTATAACTACGAGCCAAAG                         GTTGCAGATTTTGGGTTGGCCAAATACCAAGCAGCTGAAGTAACCTCTGTT
genomic: GTGACATTAAGGCGGCGAACATCCTTCTGGATTATAACTACGAGCCAAAGgtagacccca ... tttggcacagGTTGCAGATTTTGGGTTGGCCAAATACCAAGCAGCTGAAGTAACCTCTGTT
EST: gi|76017809|gb|DT944979.1|DT944979
EST:     GTGACATTAAGGCGGCGAACATCCTTCTGGATTATAACTACGAGCCAAAG                         GTTGCAGATTTTGGGTTGGCCAAATACCAAGCAGCTGAAGTAACCTCTGTT
genomic: GTGACATTAAGGCGGCGAACATCCTTCTGGATTATAACTACGAGCCAAAGgtagacccca ... tttggcacagGTTGCAGATTTTGGGTTGGCCAAATACCAAGCAGCTGAAGTAACCTCTGTT
EST: gi|71769047|gb|DR966984.1|DR966984
EST:     GTGACATTAAGGCGGCGAACATCCTTCTGGATTATAACTACGAGCCAAAG                         GTTGCAGATTTTGGGGTGGCCAAATACCAAGCAGCTGAAGTAAACTCTGTT
genomic: GTGACATTAAGGCGGCGAACATCCTTCTGGATTATAACTACGAGCCAAAGgtagacccca ... tttggcacagGTTGCAGATTTTGGGTTGGCCAAATACCAAGCAGCTGAAGTAACCTCTGTT

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: 46 (upstream exon), 41 (downstream exon)
Score: 16

GTCATCCTAAGATCATCCATCGTGACATTAAGGCGGCGAACATCCTTCTGGATTATAACTACGAGCCAAAGgtagacccca ... tttggcacagGTTGCAGATTTTGGGTTGGCCAAATACCAAGCAGCTGAAGTAACCTCTGTTTCTACGCGTGTAATGGGGACTTTCGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 80

GTCATCCTAAGATCATCCATCGTGACATTAAGGCGGCGAACATCCTTCTGGATTATAACTACGAGCCAAAGgtagacccca ... tttggcacagGTTGCAGATTTTGGGTTGGCCAAATACCAAGCAGCTGAAGTAACCTCTGTTTCTACGCGTGTAATGGGGACTTTCGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 253

GTCATCCTAAGATCATCCATCGTGACATTAAGGCGGCGAACATCCTTCTGGATTATAACTACGAGCCAAAGgtagacccca ... tttggcacagGTTGCAGATTTTGGGTTGGCCAAATACCAAGCAGCTGAAGTAACCTCTGTTTCTACGCGTGTAATGGGGACTTTCGG


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 29

GTCATCCTAAGATCATCCATCGTGACATTAAGGCGGCGAACATCCTTCTGGATTATAACTACGAGCCAAAGgtagacccca ... tttggcacagGTTGCAGATTTTGGGTTGGCCAAATACCAAGCAGCTGAAGTAACCTCTGTTTCTACGCGTGTAATGGGGACTTTCGG