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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCTTGGTAAGCATGTTCCACGACGTACAGAAGAGgtgagaaattattagggtgtgcaagatatcatttttatgcaatgggtgccgtcatgatatttttgctatcctgacgtgcag

Basic information

species Zea mays
transcript GRMZM2G045241_T05
intron # 16
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|76294030|gb|DV033598.1|DV033598
EST:     ACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG                         GAAATTCTCCTGTACCCGGGATTTGAGAATACCCCTGTGAAGTCCG
genomic: ACCTTGGTAAGCATGTTCCACGACGTACAGAAGAGgtgagaaatt ... tgacgtgcagGAAATTCTCCTGTACCCGGGATTTGAGAATACCCCTGTGAAGTCCG
EST: gi|47961462|gb|CN844171.1|CN844171
EST:     CGACGTACAGAAGAG                         GAAATTCTCCTGTACCCGGGATTTGAGAATACCCCTGTGAAGTCCG
genomic: CGACGTACAGAAGAGgtgagaaatt ... tgacgtgcagGAAATTCTCCTGTACCCGGGATTTGAGAATACCCCTGTGAAGTCCG
EST: gi|78081455|gb|DV509867.1|DV509867
EST:     ACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG                         GAAATTCTCCTGTACCCGGGATTTGAGAATACCCCTGTGAAGTCCG
genomic: ACCTTGGTAAGCATGTTCCACGACGTACAGAAGAGgtgagaaatt ... tgacgtgcagGAAATTCTCCTGTACCCGGGATTTGAGAATACCCCTGTGAAGTCCG
EST: gi|211252583|gb|FL430692.1|FL430692
EST:     ACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG                         GAAATTCTCCTGTACCCGGGATTTGAGAATACCCCTGTGAAGTCCG
genomic: ACCTTGGTAAGCATGTTCCACGACGTACAGAAGAGgtgagaaatt ... tgacgtgcagGAAATTCTCCTGTACCCGGGATTTGAGAATACCCCTGTGAAGTCCG
EST: gi|76908596|gb|DV163020.1|DV163020
EST:     ACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG                         GAAATTCTCCTGTACCCGGGATTTGAGAATACCCCTGTGAAGTCCG
genomic: ACCTTGGTAAGCATGTTCCACGACGTACAGAAGAGgtgagaaatt ... tgacgtgcagGAAATTCTCCTGTACCCGGGATTTGAGAATACCCCTGTGAAGTCCG
EST: gi|211489896|gb|FL473954.1|FL473954
EST:     ACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG                         GAAATTCTCCTGTACCCGGGATTTGAGAATACCCCTGTGAAGTCCG
genomic: ACCTTGGTAAGCATGTTCCACGACGTACAGAAGAGgtgagaaatt ... tgacgtgcagGAAATTCTCCTGTACCCGGGATTTGAGAATACCCCTGTGAAGTCCG
EST: gi|15080211|gb|BI388982.1|BI388982
EST:     ACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG                         GAAATTCTCCTGTACCCGGGATTTGAGAATACCCCTGTGAAGTCCG
genomic: ACCTTGGTAAGCATGTTCCACGACGTACAGAAGAGgtgagaaatt ... tgacgtgcagGAAATTCTCCTGTACCCGGGATTTGAGAATACCCCTGTGAAGTCCG
EST: gi|211489897|gb|FL473955.1|FL473955
EST:     ACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG                         GAAATTCTCCTGTACCCGGGATTTGAGAATACCCCTGTGAAGTCCG
genomic: ACCTTGGTAAGCATGTTCCACGACGTACAGAAGAGgtgagaaatt ... tgacgtgcagGAAATTCTCCTGTACCCGGGATTTGAGAATACCCCTGTGAAGTCCG
EST: gi|78117446|gb|DV535833.1|DV535833
EST:     ACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG                         GAAATTCTCCTGTACCCGGGATTTGAGAATACCCCTGTGAAGTCCG
genomic: ACCTTGGTAAGCATGTTCCACGACGTACAGAAGAGgtgagaaatt ... tgacgtgcagGAAATTCTCCTGTACCCGGGATTTGAGAATACCCCTGTGAAGTCCG
EST: gi|211260967|gb|FL474891.1|FL474891
EST:     ACCTTGGTAAGCATGTTCCACGACGTACAGAAGAG                         GAAATTCTCCTGTACCCGGGATTTGAGAATACCCCTGTGAAGTCCG
genomic: ACCTTGGTAAGCATGTTCCACGACGTACAGAAGAGgtgagaaatt ... tgacgtgcagGAAATTCTCCTGTACCCGGGATTTGAGAATACCCCTGTGAAGTCCG

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: 40 (upstream exon), 46 (downstream exon)
Score: 181

ACCTTGGTAAGCATGTTCCACGACGTACAGAAGAGgtgagaaatt ... tgacgtgcagGAAATTCTCCTGTACCCGGGATTTGAGAATACCCCTGTGAAGTCCG


Block sizes: 35 (upstream exon), 49 (downstream exon)
Score: 157

ACCTTGGTAAGCATGTTCCACGACGTACAGAAGAGgtgagaaatt ... tgacgtgcagGAAATTCTCCTGTACCCGGGATTTGAGAATACCCCTGTGAAGTCCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 191

ACCTTGGTAAGCATGTTCCACGACGTACAGAAGAGgtgagaaatt ... tgacgtgcagGAAATTCTCCTGTACCCGGGATTTGAGAATACCCCTGTGAAGTCCG


Block sizes: 35 (upstream exon), 49 (downstream exon)
Score: 224

ACCTTGGTAAGCATGTTCCACGACGTACAGAAGAGgtgagaaatt ... tgacgtgcagGAAATTCTCCTGTACCCGGGATTTGAGAATACCCCTGTGAAGTCCG