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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCATGGATTTGGCGTCGCCCTTGCGAACTCCTGACGTGCAACGGGCCTTGTTTCTGGTTCCAGGTGAAATATTCGACGGAGCCAACCAACCCCACCAAGTgtaagtttttctacggagggtatccatatccatttgtgcatctgctggctttctgattcgcgtgtggttctctttatttcgatgcag

Basic information

species Zea mays
transcript GRMZM2G119169_T04
intron # 1
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|211378381|gb|FL000676.1|FL000676
EST:     TTTCTGGTTCCAGGTGAAATATTCGACGGAGCCAACCAACCCCACCAAGT                         CAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAG
genomic: TTTCTGGTTCCAGGTGAAATATTCGACGGAGCCAACCAACCCCACCAAGTgtaagttttt ... ttcgatgcagCAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAG
EST: gi|211378377|gb|FL000672.1|FL000672
EST:     TTTCTGGTTCCAGGTGAAATATTCGACGGAGCCAACCAACCCCACCAAGT                         CAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAG
genomic: TTTCTGGTTCCAGGTGAAATATTCGACGGAGCCAACCAACCCCACCAAGTgtaagttttt ... ttcgatgcagCAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAG
EST: gi|211381028|gb|FL000688.1|FL000688
EST:     TTTCTGGTTCCAGGTGAAATATTCGACGGAGCCAACCAACCCCACCAAGT                         CAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAG
genomic: TTTCTGGTTCCAGGTGAAATATTCGACGGAGCCAACCAACCCCACCAAGTgtaagttttt ... ttcgatgcagCAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAG
EST: gi|50335900|gb|CO531026.1|CO531026
EST:     GGTGAAATATTCGACGGAGCCAACCAACCCCACCAAGT                         CAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAG
genomic: GGTGAAATATTCGACGGAGCCAACCAACCCCACCAAGTgtaagttttt ... ttcgatgcagCAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAG
EST: gi|30704742|gb|CD058589.1|CD058589
EST:     GGTGAAATATTCGACGGAGCCAACCAACCCCACCAAGT                         CAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAG
genomic: GGTGAAATATTCGACGGAGCCAACCAACCCCACCAAGTgtaagttttt ... ttcgatgcagCAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAG
EST: gi|211381023|gb|FL000683.1|FL000683
EST:     GGTGAAATATTCGACGGAGCCAACCAACCCCACCAAGT                         CAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAG
genomic: GGTGAAATATTCGACGGAGCCAACCAACCCCACCAAGTgtaagttttt ... ttcgatgcagCAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAG
EST: gi|60356912|gb|DN223885.1|DN223885
EST:     GGTGAAATATTCGACGGAGCCAACCAACCCCACCAAGT                         CAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAG
genomic: GGTGAAATATTCGACGGAGCCAACCAACCCCACCAAGTgtaagttttt ... ttcgatgcagCAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAG
EST: gi|29167874|gb|CB411134.1|CB411134
EST:     GACGGAGCCAACCAACCCCACCAAGT                         CAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAG
genomic: GACGGAGCCAACCAACCCCACCAAGTgtaagttttt ... ttcgatgcagCAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAG
EST: gi|67011073|gb|CO439822.1|CO439822
EST:     GGTGAAATATTCGACGGAGCCAACCAACCCCACCAAGT                         CAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAG
genomic: GGTGAAATATTCGACGGAGCCAACCAACCCCACCAAGTgtaagttttt ... ttcgatgcagCAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAG

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), 45 (downstream exon)
Score: 292

CCATGGATTTGGCGTCGCCCTTGCGAACTCCTGACGTGCAACGGGCCTTGTTTCTGGTTCCAGGTGAAATATTCGACGGAGCCAACCAACCCCACCAAGTgtaagttttt ... ttcgatgcagCAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 262

CCATGGATTTGGCGTCGCCCTTGCGAACTCCTGACGTGCAACGGGCCTTGTTTCTGGTTCCAGGTGAAATATTCGACGGAGCCAACCAACCCCACCAAGTgtaagttttt ... ttcgatgcagCAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 267

CCATGGATTTGGCGTCGCCCTTGCGAACTCCTGACGTGCAACGGGCCTTGTTTCTGGTTCCAGGTGAAATATTCGACGGAGCCAACCAACCCCACCAAGTgtaagttttt ... ttcgatgcagCAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 149

CCATGGATTTGGCGTCGCCCTTGCGAACTCCTGACGTGCAACGGGCCTTGTTTCTGGTTCCAGGTGAAATATTCGACGGAGCCAACCAACCCCACCAAGTgtaagttttt ... ttcgatgcagCAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAG