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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGTCGTGGCGGCGGCGGCTGCCGCTGGCGCCGGCGGCGAGGCATCTTCGGCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccccaccttgcccgccgaaatgcggcctccttgtttcttaatctctcgcggcgcgcgggatttctccgttcctttttcttcttctgatgacgctgctcgggttttctggcgtcaaatgcag

Basic information

species Zea mays
transcript GRMZM2G407044_T01
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|211258838|gb|FL034314.1|FL034314
EST:     GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAA                         GGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
genomic: GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
EST: gi|211261271|gb|FL034325.1|FL034325
EST:     CCCCCGTGGCTGTGGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAA                         GGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
genomic: CCCCCGTGGCTGTG-TCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
EST: gi|148959834|gb|EE153063.2|EE153063
EST:     GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAA                         GGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
genomic: GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
EST: gi|211258845|gb|FL034321.1|FL034321
EST:     GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAA                         GGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
genomic: GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
EST: gi|211258848|gb|FL034324.1|FL034324
EST:     GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAA                         GGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
genomic: GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
EST: gi|76285096|gb|DV024664.1|DV024664
EST:     GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAA                         GGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
genomic: GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
EST: gi|149075260|gb|EE163764.2|EE163764
EST:     GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAA                         GGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
genomic: GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
EST: gi|211258839|gb|FL034315.1|FL034315
EST:     GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAA                         GGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
genomic: GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
EST: gi|211261273|gb|FL034327.1|FL034327
EST:     GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAA                         GGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
genomic: GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
EST: gi|211258836|gb|FL034312.1|FL034312
EST:     CCCCCGTGGCTGTGTCGGCTGTCGCNNCCCGCGGGCGCTGCCAGGGACAA                         GGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
genomic: CCCCCGTGGCTGTGTCGGCTGTCGCC-CCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
EST: gi|211258843|gb|FL034319.1|FL034319
EST:     GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAA                         GGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
genomic: GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
EST: gi|148949305|gb|EC894756.2|EC894756
EST:     GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAA                         GGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
genomic: GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
EST: gi|149087824|gb|EE177122.2|EE177122
EST:     GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAA                         GGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT
genomic: GCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGAT

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: 88

CCGTCGTGGCGGCGGCGGCTGCCGCTGGCGCCGGCGGCGAGGCATCTTCGGCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGATCAACCGGATCGCAGGGGTGTTCGCCAGGAGAGGCTACAACATCGAGTCG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 56

CCGTCGTGGCGGCGGCGGCTGCCGCTGGCGCCGGCGGCGAGGCATCTTCGGCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGATCAACCGGATCGCAGGGGTGTTCGCCAGGAGAGGCTACAACATCGAGTCG


Block sizes: 47 (upstream exon), 34 (downstream exon)
Score: 21

CCGTCGTGGCGGCGGCGGCTGCCGCTGGCGCCGGCGGCGAGGCATCTTCGGCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGATCAACCGGATCGCAGGGGTGTTCGCCAGGAGAGGCTACAACATCGAGTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 76

CCGTCGTGGCGGCGGCGGCTGCCGCTGGCGCCGGCGGCGAGGCATCTTCGGCCCCCGTGGCTGTGTCGGCTGTCGCCCCCGCGGGCGCTGCCAGGGACAAgtaagcaccc ... tcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGATCAACCGGATCGCAGGGGTGTTCGCCAGGAGAGGCTACAACATCGAGTCG