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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATGCTGGCGAGCAGGCTGGCGAAACACAGGACGCGCCCGAGGGTGTACGTCGGCTGCATGAAGTCCGGGCCTGTCCTGTCACAGAAgtgagcagagatcatttttcttcttcttcttctcacagccgagttagttctgttctgtcgagtgagaccggcctgtactgtactgtgtctctgtatctgttgttgcag

Basic information

species Zea mays
transcript GRMZM2G119265_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G119265_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g65590.1 (Oryza sativa), 5'ss of exon 6
GGATGCTGGCGAGCAGGCTGGCGAAACACAGGACGCGCCCGAGGGTGTACGTCGGCTGCATGAAGTCCGGGCCTGTCCTGTCACAGAAgtgagcagagatcatttttcttcttcttcttctcacagccgagttagttctgttctgtcgagtgagaccggcctgtactgtactgtgtctctgtatctgttgttgcag
|||||||| ||||||||||||| ||  ||||||| || |||||||||||||||||||||||||||||||| ||||| ||||| |||||||||||| |      ||    |||| |  ||            ||  |  |   |||  |  || ||      ||| | ||  | |||   |||    ||||||||||
GGATGCTGACGAGCAGGCTGGCCAAGTACAGGACACGACCGAGGGTGTACGTCGGCTGCATGAAGTCCGGACCTGTTCTGTCGCAGAAgtgagcaaatggagattaaaatcttgtgttttgt---------ttgttggtagcctgatgcatg-gatgaatttgt-cggtgttttgttgttgt--tcgttgttgcag
















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|148946206|gb|EC891501.2|EC891501
EST:     CCGAGGGTGTACGTCGGCTGCATGAAGTCCGGGCCTGTCCTGTCACAGAA                         AGGAGTCAAGTACCACGAGCCAGAGTACTGGAAGTTCGGCGACGAGGGCAA
genomic: CCGAGGGTGTACGTCGGCTGCATGAAGTCCGGGCCTGTCCTGTCACAGAAgtgagcagag ... gttgttgcagAGGAGTCAAGTACCACGAGCCAGAGTACTGGAAGTTCGGCGACGAGGGCAA
EST: gi|148982796|gb|EE028625.2|EE028625
EST:     CCGAGGGTGTACGTCGGCTGCATGAAGTCCGGGCCTGTCCTGTCACAGAA                         AGGAGTCAAGTACCACGAGCCAGAGTACTGGAAGTTCGGCGACGAGGGCAA
genomic: CCGAGGGTGTACGTCGGCTGCATGAAGTCCGGGCCTGTCCTGTCACAGAAgtgagcagag ... gttgttgcagAGGAGTCAAGTACCACGAGCCAGAGTACTGGAAGTTCGGCGACGAGGGCAA
EST: gi|94472474|gb|EB701432.1|EB701432
EST:     CCGAGGGTGTACGTCGGCTGCATGAAGTCCGGGCCTGTCCTGTCACAGAA                         AGGAGTCAAGTACCACGAGCCAGAGTACTGGAAGTTCGGCGACGAGGGCAA
genomic: CCGAGGGTGTACGTCGGCTGCATGAAGTCCGGGCCTGTCCTGTCACAGAAgtgagcagag ... gttgttgcagAGGAGTCAAGTACCACGAGCCAGAGTACTGGAAGTTCGGCGACGAGGGCAA
EST: gi|211026937|gb|FL261354.1|FL261354
EST:     CCGAGGGTGTACGTCGGCTGCATGAAGTCCGGGCCTGTCCTGTCACAGAA                         AGGA-TCAAGTACCACGAGCCAGAGTACTGGAAGTTCGGCGACGAGGGCAA
genomic: CCGAGGGTGTACGTCGGCTGCATGAAGTCCGGGCCTGTCCTGTCACAGAAgtgagcagag ... gttgttgcagAGGAGTCAAGTACCACGAGCCAGAGTACTGGAAGTTCGGCGACGAGGGCAA
EST: gi|149105464|gb|EE290981.2|EE290981
EST:     CCGAGGGTGTACGTCGGCTGCATGAAGTCCGGGCCTGTCCTGTCACAGAA                         AGGAGTCAAGTACCACGAGCCAGAGTACTGGAAGTTCGGCGACGAGGGCAA
genomic: CCGAGGGTGTACGTCGGCTGCATGAAGTCCGGGCCTGTCCTGTCACAGAAgtgagcagag ... gttgttgcagAGGAGTCAAGTACCACGAGCCAGAGTACTGGAAGTTCGGCGACGAGGGCAA
EST: gi|149009309|gb|EE153896.2|EE153896
EST:     CCGAGGGTGTACGTCGGCTGCATGAAGTCCGGGCCTGTCCTGTCACAGAA                         AGGAGTCAAGTACCACGAGCCAGAGTACTGGAAGTTTGGCGACGAGGGCAA
genomic: CCGAGGGTGTACGTCGGCTGCATGAAGTCCGGGCCTGTCCTGTCACAGAAgtgagcagag ... gttgttgcagAGGAGTCAAGTACCACGAGCCAGAGTACTGGAAGTTCGGCGACGAGGGCAA
EST: gi|211026936|gb|FL261353.1|FL261353
EST:     CCGAGGGTGTACGTCGGCTGCATGAAGTCCGGGCCTGTCCTGTCACAGAA                         AGGAGTCAAGTACCACGAGCCAGAGTACTGGAAGTTCGGCGACGAGGGCAA
genomic: CCGAGGGTGTACGTCGGCTGCATGAAGTCCGGGCCTGTCCTGTCACAGAAgtgagcagag ... gttgttgcagAGGAGTCAAGTACCACGAGCCAGAGTACTGGAAGTTCGGCGACGAGGGCAA
EST: gi|101401735|gb|EB822520.1|EB822520
EST:     CCGAGGGTGTACGTCGGCTGCATGAAGTCCGGGCCTGTCCTGTCCCAGAA                         AGGAGTCAAGTACCACGAGCCAGAGTACTGGAAGTTCGGCGTCGAGGGCAA
genomic: CCGAGGGTGTACGTCGGCTGCATGAAGTCCGGGCCTGTCCTGTCACAGAAgtgagcagag ... gttgttgcagAGGAGTCAAGTACCACGAGCCAGAGTACTGGAAGTTCGGCGACGAGGGCAA
EST: gi|148930010|gb|EE285878.2|EE285878
EST:     CCGAGGGTGTACGTCGGCTGCATGAAGTCCGGGCCTGTCCTGTCACAGAA                         AGGAGTCAAGTACCACGAGCCAGAGTACTGGAAGTTCGGCGACGAGGGCAA
genomic: CCGAGGGTGTACGTCGGCTGCATGAAGTCCGGGCCTGTCCTGTCACAGAAgtgagcagag ... gttgttgcagAGGAGTCAAGTACCACGAGCCAGAGTACTGGAAGTTCGGCGACGAGGGCAA

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 1 RNA-Seqlibrary.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 684

GGATGCTGGCGAGCAGGCTGGCGAAACACAGGACGCGCCCGAGGGTGTACGTCGGCTGCATGAAGTCCGGGCCTGTCCTGTCACAGAAgtgagcagag ... gttgttgcagAGGAGTCAAGTACCACGAGCCAGAGTACTGGAAGTTCGGCGACGAGGGCAACAAGTACTTCCGCCACGCCACCGGCCAAATCTACGCCATCTCCAAGGAC




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