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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatctccagttggaatttaagtaggtgtactcagttttaagaaatatcgtatgatgctgacaagtttgcatcctgtgcagGATGTGATGCGCTTGCGTGTGCT

Basic information

species Zea mays
transcript GRMZM2G466281_T02
intron # 5
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|101388019|gb|EB816024.1|EB816024
EST:     AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACG                         GATGTGATGCGCTTGCGTGTGCT
genomic: AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACGgtaatctcca ... tcctgtgcagGATGTGATGCGCTTGCGTGTGCT
EST: gi|76933447|gb|DV173462.1|DV173462
EST:     AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACG                         GATGTGATGCGCTTGCGTGTGCT
genomic: AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACGgtaatctcca ... tcctgtgcagGATGTGATGCGCTTGCGTGTGCT
EST: gi|78108358|gb|DV526776.1|DV526776
EST:     AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACG                         GATGTGATGCGCTTGCGTGTGCT
genomic: AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACGgtaatctcca ... tcctgtgcagGATGTGATGCGCTTGCGTGTGCT
EST: gi|76284393|gb|DV023961.1|DV023961
EST:     AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACG                         GATGTGATGCGCTTGCGTGTGCT
genomic: AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACGgtaatctcca ... tcctgtgcagGATGTGATGCGCTTGCGTGTGCT
EST: gi|148930548|gb|EE285169.2|EE285169
EST:     AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACG                         GATGTGATGCGCTTGCGTGTGCT
genomic: AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACGgtaatctcca ... tcctgtgcagGATGTGATGCGCTTGCGTGTGCT
EST: gi|148948015|gb|EC893516.2|EC893516
EST:     AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACG                         GATGTGATGCGCTTGCGTGTGCT
genomic: AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACGgtaatctcca ... tcctgtgcagGATGTGATGCGCTTGCGTGTGCT
EST: gi|149085392|gb|EE174899.2|EE174899
EST:     AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACG                         GATGTGATGCGCTTGCGTGTGCT
genomic: AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACGgtaatctcca ... tcctgtgcagGATGTGATGCGCTTGCGTGTGCT
EST: gi|88756189|gb|DY540330.1|DY540330
EST:     AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACG                         GATGTGATGCGCTTGCGTGTGCT
genomic: AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACGgtaatctcca ... tcctgtgcagGATGTGATGCGCTTGCGTGTGCT
EST: gi|88756155|gb|DY540296.1|DY540296
EST:     AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACG                         GATGTGATGCGCTTGCGTGTGCT
genomic: AGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACGgtaatctcca ... tcctgtgcagGATGTGATGCGCTTGCGTGTGCT

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), 48 (downstream exon)
Score: 159

ACTTTTGATGCTGTGGATGGAAAACAAGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACGgtaatctcca ... tcctgtgcagGATGTGATGCGCTTGCGTGTGCT


Block sizes: 49 (upstream exon), 23 (downstream exon)
Score: 142

ACTTTTGATGCTGTGGATGGAAAACAAGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACGgtaatctcca ... tcctgtgcagGATGTGATGCGCTTGCGTGTGCT


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 122

ACTTTTGATGCTGTGGATGGAAAACAAGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACGgtaatctcca ... tcctgtgcagGATGTGATGCGCTTGCGTGTGCT


Block sizes: 49 (upstream exon), 28 (downstream exon)
Score: 162

ACTTTTGATGCTGTGGATGGAAAACAAGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACGgtaatctcca ... tcctgtgcagGATGTGATGCGCTTGCGTGTGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtactcagttttaagaaatatcgtatgatgctgacaagtttgcatcctgtgcagGATGTGATGCGCTTGCGTGTGCT
                             tgctgac  putative branch site (score: 162)
       agttttaagaaatat  TA-rich tract