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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAACAGGGCCGAGGCAAGGGCCCTTGAGCGATCCAGGAGAGGGCTTGGCGATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGGgtaattggaatgtatctcggcacttttcttttgactactagaaagcagtggattgtctgttcctggagatagttgctatcacttttgttcttatcaattttatgtgatcttgctgcctcatttatctcgcgttttttgtag

Basic information

species Zea mays
transcript GRMZM2G540403_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G540403_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g15860.1 (Oryza sativa), 5'ss of exon 4
GGAACAGGGCCGAGGCAAGGGCCCTTGAGCGATCCAGGAGAGGGCTTGGCGATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGGgtaattggaatgtatctcggcacttttcttttgacta--ctagaaagcagtggattgtctgttcctgga---gatagttgcta--tcacttttgttcttatcaattt-tatgtgatcttgctgcctcatttatctcgcgttttttgtag--
||| |||||| |||||   ||| ||  ||||||||||||||||  | |||||||| || ||||| |||||||| || |||||||||||||| || ||||||||||   | | |   |  ||   |  | || |  ||  ||   | ||| ||  |||||| || || |    ||||||||  |  ||| | |||||||||    |||   | ||||       | ||  |  | | |  || ||||     
GGAGCAGGGCGGAGGCCGCGGCTCTCCAGCGATCCAGGAGAGGAATCGGCGATGGATCCGTCGGGATGCTCCAATCCCTCACTGTCGCTGCGCTTTCTGGgtaatcctattttgcttgtgcgtctgccattggcttatgctgttatgcattgtgttgtctttttctcggtatgatagttgtaagctcattcttgttcttaatggtttacttatgatgaacaaccttcggtgctgttgttttgtttgcgcag
















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|78112113|gb|DV530509.1|DV530509
EST:     GATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGG                         GTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTTGT-GTTACACGAA
genomic: GATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGGgtaattggaa ... ttttttgtagCTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTT-GTTGTTACACGAA
EST: gi|149071944|gb|EE160331.2|EE160331
EST:     GATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGG                         CTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAAT
genomic: GATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGGgtaattggaa ... ttttttgtagCTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAAT
EST: gi|78120502|gb|DV538886.1|DV538886
EST:     GATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGG                         CTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAAT
genomic: GATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGGgtaattggaa ... ttttttgtagCTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAAT
EST: gi|88756340|gb|DY540481.1|DY540481
EST:     GATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGG                         CTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAAT
genomic: GATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGGgtaattggaa ... ttttttgtagCTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAAT
EST: gi|148952677|gb|EC898511.2|EC898511
EST:     GATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGG                         CTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAAT
genomic: GATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGGgtaattggaa ... ttttttgtagCTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAAT
EST: gi|91877627|gb|EB407584.1|EB407584
EST:     GATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGG                         CTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAAT
genomic: GATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGGgtaattggaa ... ttttttgtagCTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAAT
EST: gi|71766550|gb|DR964487.1|DR964487
EST:     GATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGG                         CTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAAT
genomic: GATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGGgtaattggaa ... ttttttgtagCTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAAT
EST: gi|148964459|gb|EC905815.2|EC905815
EST:     GATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGG                         CTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAAT
genomic: GATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGGgtaattggaa ... ttttttgtagCTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAAT
EST: gi|76936044|gb|DV174582.1|DV174582
EST:     GATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGG                         CTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAAT
genomic: GATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGGgtaattggaa ... ttttttgtagCTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAAT
EST: gi|148957275|gb|EC903307.2|EC903307
EST:     GATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGG                         CTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAAT
genomic: GATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGGgtaattggaa ... ttttttgtagCTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAAT
EST: gi|149027549|gb|EE046558.2|EE046558
EST:     GATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGG                         CTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAAT
genomic: GATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGGgtaattggaa ... ttttttgtagCTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAAT
EST: gi|71422924|gb|DR805897.1|DR805897
EST:     GATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGG                         CTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAAT
genomic: GATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGGgtaattggaa ... ttttttgtagCTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAAT
EST: gi|149013466|gb|EE042980.2|EE042980
EST:     GATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGG                         CTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAAT
genomic: GATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGGgtaattggaa ... ttttttgtagCTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAAT
EST: gi|71448089|gb|DR829139.1|DR829139
EST:     GATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGG                         CTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAAT
genomic: GATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGGgtaattggaa ... ttttttgtagCTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAAT
EST: gi|91051844|gb|EB162262.1|EB162262
EST:     GATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGG                         CTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAAT
genomic: GATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGGgtaattggaa ... ttttttgtagCTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAAT

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: 42 (upstream exon), 48 (downstream exon)
Score: 71

GGAACAGGGCCGAGGCAAGGGCCCTTGAGCGATCCAGGAGAGGGCTTGGCGATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGGgtaattggaa ... ttttttgtagCTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 97

GGAACAGGGCCGAGGCAAGGGCCCTTGAGCGATCCAGGAGAGGGCTTGGCGATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGGgtaattggaa ... ttttttgtagCTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 111

GGAACAGGGCCGAGGCAAGGGCCCTTGAGCGATCCAGGAGAGGGCTTGGCGATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGGgtaattggaa ... ttttttgtagCTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 99

GGAACAGGGCCGAGGCAAGGGCCCTTGAGCGATCCAGGAGAGGGCTTGGCGATGGGTCTGTCGGCATGCTCCAGTCTCTCACTGTCGCTGCCCTGTCTGGgtaattggaa ... ttttttgtagCTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA