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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGCGGACACAATCAGCCTCTGGTGCAGgtaactcctgaatttactgtctgcagtttcgaaacggacttactcagaatttatttgcagtaggacttattgatgtttgtttctttacattctgtatgga...

Basic information

species Zea mays
transcript GRMZM2G057158_T02
intron # 6
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|26558010|gb|CA830245.1|CA830245
EST:     GGAGCGGACACAATCAGCCTCTGGTGCAG                         GCAATGTGAACCTCAACACCTTGATGAACATGTTCAGTGGGCTTGGTGCTG
genomic: GGAGCGGACACAATCAGCCTCTGGTGCAGgtaactcctg ... tgaatcctagGCAATGTGAACCTCAACACCTTGATGAACATGTTCAGTGGGCTTGGTGCTG
EST: gi|21828621|gb|BQ703305.1|BQ703305
EST:     GGAGCGGACACAATCAGCCTCTGGTGCAG                         GCAATGTGAACCTCAACACCTTGATGAACATGTTCAGTGGGCTTGGTGCTG
genomic: GGAGCGGACACAATCAGCCTCTGGTGCAGgtaactcctg ... tgaatcctagGCAATGTGAACCTCAACACCTTGATGAACATGTTCAGTGGGCTTGGTGCTG
EST: gi|67027074|gb|CO455823.1|CO455823
EST:     GGAGCGGACACAATCAGCCTCTGGTGCAG                         GCAATGTGAACCTCAACACCTTGATGAACATGTTCAGTGGGCTTGGTGCTG
genomic: GGAGCGGACACAATCAGCCTCTGGTGCAGgtaactcctg ... tgaatcctagGCAATGTGAACCTCAACACCTTGATGAACATGTTCAGTGGGCTTGGTGCTG
EST: gi|87156460|gb|DY401249.1|DY401249
EST:     GGAGCGGACACAATCAGCCTCTGGTGCAG                         GCAATGTGAACCTCAACACCTTGATGAACATGTTCAGTGGGCTTGGTGCTG
genomic: GGAGCGGACACAATCAGCCTCTGGTGCAGgtaactcctg ... tgaatcctagGCAATGTGAACCTCAACACCTTGATGAACATGTTCAGTGGGCTTGGTGCTG
EST: gi|113704257|gb|EE681761.1|EE681761
EST:     GGAGCGGACACAATCAGCCTCTGGTGCAG                         GCAATGTGAACCTCAACACCTTGATGAACATGTTCAGTGGGCTTGGTGCTG
genomic: GGAGCGGACACAATCAGCCTCTGGTGCAGgtaactcctg ... tgaatcctagGCAATGTGAACCTCAACACCTTGATGAACATGTTCAGTGGGCTTGGTGCTG
EST: gi|78180947|gb|DV551320.1|DV551320
EST:     GGAGCGGACACAATCAGCCTCTGGTGCAG                         GCAATGTGAACCTCAACACCTTGATGAACATGTTCA
genomic: GGAGCGGACACAATCAGCCTCTGGTGCAGgtaactcctg ... tgaatcctagGCAATGTGAACCTCAACACCTTGATGAACATGTTCA
EST: gi|94473208|gb|EB702166.1|EB702166
EST:     GGAGCGGACACAATCAGCCTCTGGTGCAG                         GCAATGTGAACCTCAACACCTTGATGAACATGTTCAGTGGGCTTGGTGCTG
genomic: GGAGCGGACACAATCAGCCTCTGGTGCAGgtaactcctg ... tgaatcctagGCAATGTGAACCTCAACACCTTGATGAACATGTTCAGTGGGCTTGGTGCTG

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), 8 (downstream exon)
Score: 9

GGAGCGGACACAATCAGCCTCTGGTGCAGgtaactcctg ... tgaatcctagGCAATGTGAACCTCAACACCTTGATGAACATGTTCAGTGGGCTTGGTGCTGGTGGTGGCCTAGGTGTTCCAAATGCTCCTAATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 13

GGAGCGGACACAATCAGCCTCTGGTGCAGgtaactcctg ... tgaatcctagGCAATGTGAACCTCAACACCTTGATGAACATGTTCAGTGGGCTTGGTGCTGGTGGTGGCCTAGGTGTTCCAAATGCTCCTAATG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 12

GGAGCGGACACAATCAGCCTCTGGTGCAGgtaactcctg ... tgaatcctagGCAATGTGAACCTCAACACCTTGATGAACATGTTCAGTGGGCTTGGTGCTGGTGGTGGCCTAGGTGTTCCAAATGCTCCTAATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 4

GGAGCGGACACAATCAGCCTCTGGTGCAGgtaactcctg ... tgaatcctagGCAATGTGAACCTCAACACCTTGATGAACATGTTCAGTGGGCTTGGTGCTGGTGGTGGCCTAGGTGTTCCAAATGCTCCTAATG