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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAGgtgagagattcctacctgcctcccgacctagattctgttcaagagatctcatgatatgtttgtgtcctacctgcttcccgatcgagatcctattcaagag...

Basic information

species Zea mays
transcript GRMZM2G119169_T04
intron # 2
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:     CAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAG                         AACACCCGTGAGACAGCTTTTGCCCTTAGGAAGTTGTCACTCACCAAGGCC
genomic: CAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAGgtgagagatt ... atacttgtagAACACCCGTGAGACAGCTTTTGCCCTTAGGAAGTTGTCACTCACCAAGGCC
EST: gi|211378377|gb|FL000672.1|FL000672
EST:     CAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAG                         AACACCCGTGAGACAGCTTTTGCCCTTAGGAAGTTGTCACTCACCAAGGCC
genomic: CAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAGgtgagagatt ... atacttgtagAACACCCGTGAGACAGCTTTTGCCCTTAGGAAGTTGTCACTCACCAAGGCC
EST: gi|211381028|gb|FL000688.1|FL000688
EST:     CAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAG                         AACACCCGTGAGACAGCTTTTGCCCTTAGGAAGTTGTCACTCACCAAGGCC
genomic: CAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAGgtgagagatt ... atacttgtagAACACCCGTGAGACAGCTTTTGCCCTTAGGAAGTTGTCACTCACCAAGGCC
EST: gi|50335900|gb|CO531026.1|CO531026
EST:     CAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAG                         AACACCCGTGAGACAGCTTTTGCCCTTAGGAAGTTGTCACTCACCAAGGCC
genomic: CAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAGgtgagagatt ... atacttgtagAACACCCGTGAGACAGCTTTTGCCCTTAGGAAGTTGTCACTCACCAAGGCC
EST: gi|30704742|gb|CD058589.1|CD058589
EST:     CAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAG                         AACACCCGTGAGACAGCTTTTGCCCTTAGGAAGTTGTCACTCACCAAGGCC
genomic: CAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAGgtgagagatt ... atacttgtagAACACCCGTGAGACAGCTTTTGCCCTTAGGAAGTTGTCACTCACCAAGGCC
EST: gi|211381023|gb|FL000683.1|FL000683
EST:     CAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAG                         AACACCCGTGAGACAGCTTTTGCCCTTAGGAAGTTGTCACTCACCAAGGCC
genomic: CAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAGgtgagagatt ... atacttgtagAACACCCGTGAGACAGCTTTTGCCCTTAGGAAGTTGTCACTCACCAAGGCC
EST: gi|60356912|gb|DN223885.1|DN223885
EST:     CAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAG                         AACACCCGTGAGACAGCTTTTGCCCTTAGGAAGTTGTCACTCACCAAGGCC
genomic: CAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAGgtgagagatt ... atacttgtagAACACCCGTGAGACAGCTTTTGCCCTTAGGAAGTTGTCACTCACCAAGGCC
EST: gi|29167874|gb|CB411134.1|CB411134
EST:     CAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAG                         AACACCCGTGAGACAGCTTTTGCCCTTAGGAAGTTGTCACTCACCAAGGCC
genomic: CAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAGgtgagagatt ... atacttgtagAACACCCGTGAGACAGCTTTTGCCCTTAGGAAGTTGTCACTCACCAAGGCC
EST: gi|67011073|gb|CO439822.1|CO439822
EST:     CAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAG                         AACACCCGTGAGACAGCTTTTGCCCTTAGGAAGTTGTCACTCACCAAGGCC
genomic: CAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAGgtgagagatt ... atacttgtagAACACCCGTGAGACAGCTTTTGCCCTTAGGAAGTTGTCACTCACCAAGGCC

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), 49 (downstream exon)
Score: 270

CAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAGgtgagagatt ... atacttgtagAACACCCGTGAGACAGCTTTTGCCCTTAGGAAGTTGTCACTCACCAAGGCCAAAAGGTACCTTGAGGATGTGATTGCCCACAAGCAGGCCATCCCGTTCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 303

CAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAGgtgagagatt ... atacttgtagAACACCCGTGAGACAGCTTTTGCCCTTAGGAAGTTGTCACTCACCAAGGCCAAAAGGTACCTTGAGGATGTGATTGCCCACAAGCAGGCCATCCCGTTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 254

CAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAGgtgagagatt ... atacttgtagAACACCCGTGAGACAGCTTTTGCCCTTAGGAAGTTGTCACTCACCAAGGCCAAAAGGTACCTTGAGGATGTGATTGCCCACAAGCAGGCCATCCCGTTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 182

CAACCAAGGCCATGGGCCGTGACCTACGTGTTCACTTCAAGgtgagagatt ... atacttgtagAACACCCGTGAGACAGCTTTTGCCCTTAGGAAGTTGTCACTCACCAAGGCCAAAAGGTACCTTGAGGATGTGATTGCCCACAAGCAGGCCATCCCGTTCC