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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTCTTCCATGTTAAAGgtgagctcacagctattccctgttttttatgttgtcaaatggtatgtatccccatcaagcgcatggttactcttaataatttccctatggctgtctgttg...

Basic information

species Zea mays
transcript GRMZM2G353213_T02
intron # 4
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|148945681|gb|EC890953.2|EC890953
EST:     TACCACGGTCTCTTCCATGTTAAAG                         AGATATGCCATGCAACAAGCATTTAAGTCAATGATGACCCAGTCAGCACCA
genomic: TACCACGGTCTCTTCCATGTTAAAGgtgagctcac ... tctgttgcagAGATATGCCATGCAACAAGCATTTAAGTCAATGATGACCCAGTCAGCACCA
EST: gi|31348764|gb|CD433121.1|CD433121
EST:     TACCACGGTCTCTTCCATGTTAAAG                         AGATATGCCATGCAACAAGCATTTAAGTCAATGATGACCCAGTCAGCACCA
genomic: TACCACGGTCTCTTCCATGTTAAAGgtgagctcac ... tctgttgcagAGATATGCCATGCAACAAGCATTTAAGTCAATGATGACCCAGTCAGCACCA
EST: gi|211025069|gb|FL063417.1|FL063417
EST:     TACCACGGTCTCTTCCATGTTAAAG                         AGATATGCCATGGCA-CAAGCATTTAAGTCCATGATGACCCAGTCAGCACC
genomic: TACCACGGTCTCTTCCATGTTAAAGgtgagctcac ... tctgttgcagAGATATGCCATG-CAACAAGCATTTAAGTCAATGATGACCCAGTCAGCACC
EST: gi|71448507|gb|DR829557.1|DR829557
EST:     TACCACGGTCTCTTCCATGTTAAAG                         AGATATGCCATGCAACAAGCATTTAAGTCAATGATGACCCAGTCAGCACCA
genomic: TACCACGGTCTCTTCCATGTTAAAGgtgagctcac ... tctgttgcagAGATATGCCATGCAACAAGCATTTAAGTCAATGATGACCCAGTCAGCACCA
EST: gi|91055447|gb|EB165865.1|EB165865
EST:     TACCACGGTCTCTTCCATGTTAAAG                         AGATATGCCATGCAACAAGCATTTAAGTCAATGATGACCCAGTCAGCACCA
genomic: TACCACGGTCTCTTCCATGTTAAAGgtgagctcac ... tctgttgcagAGATATGCCATGCAACAAGCATTTAAGTCAATGATGACCCAGTCAGCACCA
EST: gi|211025064|gb|FL063412.1|FL063412
EST:     TACCACGGTCTCTTCCATGGTAAAG                         AGATATGCCATGCA
genomic: TACCACGGTCTCTTCCATGTTAAAGgtgagctcac ... tctgttgcagAGATATGCCATGCA
EST: gi|149109665|gb|EE293452.2|EE293452
EST:     TACCACGGTCTCTTCCATGTTAAAG                         AGATATGCCATGCAACAAGCATTTAAGTCAATGATGACCCAGTCAGCACCA
genomic: TACCACGGTCTCTTCCATGTTAAAGgtgagctcac ... tctgttgcagAGATATGCCATGCAACAAGCATTTAAGTCAATGATGACCCAGTCAGCACCA

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), 46 (downstream exon)
Score: 64

GTCTCTTCCATGTTAAAGgtgagctcac ... tctgttgcagAGATATGCCATGCAACAAGCATTTAAGTCAATGATGACCCAGTCAGCACCAAACTCATTTGGCTCCAACTCGCCTTTCCCATTTAGCATGCCGCCACAGG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 80

GTCTCTTCCATGTTAAAGgtgagctcac ... tctgttgcagAGATATGCCATGCAACAAGCATTTAAGTCAATGATGACCCAGTCAGCACCAAACTCATTTGGCTCCAACTCGCCTTTCCCATTTAGCATGCCGCCACAGG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 65

GTCTCTTCCATGTTAAAGgtgagctcac ... tctgttgcagAGATATGCCATGCAACAAGCATTTAAGTCAATGATGACCCAGTCAGCACCAAACTCATTTGGCTCCAACTCGCCTTTCCCATTTAGCATGCCGCCACAGG


Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 81

GTCTCTTCCATGTTAAAGgtgagctcac ... tctgttgcagAGATATGCCATGCAACAAGCATTTAAGTCAATGATGACCCAGTCAGCACCAAACTCATTTGGCTCCAACTCGCCTTTCCCATTTAGCATGCCGCCACAGG