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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGGTAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGATCAAGgtaggtgccctttcagtatcttcttaaggctgaatgcttattatgtagtcctcaagtgttgcaatgttggatatgcag

Basic information

species Zea mays
transcript GRMZM5G871336_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G871336_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g05830.1 (Oryza sativa), 5'ss of exon 7
GCTGGTAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGATCAAGgtaggtgccctttcagtatcttcttaaggctgaatgcttattatgtagtcctcaagtgttgcaatgttggatatgcag
||||||||||  |||||||| || ||||| ||||| ||| | |||||||||||||||| ||    ||||   |  |||||    |  | || ||  |||       | ||||| | |||  ||| || |||||
GCTGGTAGAGGTCTTTTCCTCCTCCTCTCGAGATTTATGCTGTTCTATGATCAAGgtatgttatttttctccacgttcttggtcccaattgtttgctat-------tgaagtgatccaagtttgcatgtgcag
















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|71430125|gb|DR811175.1|DR811175
EST:     TAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGATCAAG                         ATCACATGCTTTCTAGTTTCCTAGAGCATTTTCCCCATTTCCCAAATTCCT
genomic: TAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGATCAAGgtaggtgccc ... ggatatgcagATCACATGCTTTCTAGTTTCCTAGAGCATTTTCCCAATTTCCCAAATTCCT
EST: gi|71432140|gb|DR813190.1|DR813190
EST:     TAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGATCAAG                         ATCACATGCTTTCTAGTTTCCTAGAGCATTTTCCCAATTTCCCAAATTCCT
genomic: TAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGATCAAGgtaggtgccc ... ggatatgcagATCACATGCTTTCTAGTTTCCTAGAGCATTTTCCCAATTTCCCAAATTCCT
EST: gi|71311972|gb|DR792494.1|DR792494
EST:     TAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGATCAAG                         ATCACATGCTTTCTAGTTTCCTAGAGCATTTTCTCAATTTCCCAAATTCCT
genomic: TAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGATCAAGgtaggtgccc ... ggatatgcagATCACATGCTTTCTAGTTTCCTAGAGCATTTTCCCAATTTCCCAAATTCCT
EST: gi|148950551|gb|EC896128.2|EC896128
EST:     TAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGATCAAG                         ATCACATGCTTTCTAGTTTCCTAGAGCATTTTCCCAATTTCCCAAATTCCT
genomic: TAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGATCAAGgtaggtgccc ... ggatatgcagATCACATGCTTTCTAGTTTCCTAGAGCATTTTCCCAATTTCCCAAATTCCT
EST: gi|93012464|gb|EB637984.1|EB637984
EST:     TAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGATCAAG                         ATCACATGCTTTCTAGTTTCCTAGAGCATTTTCCCAATTTCCCAATTTC-T
genomic: TAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGATCAAGgtaggtgccc ... ggatatgcagATCACATGCTTTCTAGTTTCCTAGAGCATTTTCCCAATTTCCCAAATTCCT
EST: gi|149059964|gb|EE157094.2|EE157094
EST:     TAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGATCAAG                         ATCACATGCTTTCTAGTTTCCTAGAGCATTTTCCCAATTTCCCAAATTCCT
genomic: TAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGATCAAGgtaggtgccc ... ggatatgcagATCACATGCTTTCTAGTTTCCTAGAGCATTTTCCCAATTTCCCAAATTCCT
EST: gi|149045945|gb|EE047943.2|EE047943
EST:     TAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGATCAAG                         ATCACATGCTTTCTAGTTTCCTAGAGCATTTTCCCAATTTCCCAAATTCCT
genomic: TAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGATCAAGgtaggtgccc ... ggatatgcagATCACATGCTTTCTAGTTTCCTAGAGCATTTTCCCAATTTCCCAAATTCCT

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: 46 (upstream exon), 49 (downstream exon)
Score: 53

GCTGGTAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGATCAAGgtaggtgccc ... ggatatgcagATCACATGCTTTCTAGTTTCCTAGAGCATTTTCCCAATTTCCCAAATTCCTTCTTGGTTGGTGGACCAGCAGATTACTTTGTAATTGAACTCGCTGATCA


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 33

GCTGGTAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGATCAAGgtaggtgccc ... ggatatgcagATCACATGCTTTCTAGTTTCCTAGAGCATTTTCCCAATTTCCCAAATTCCTTCTTGGTTGGTGGACCAGCAGATTACTTTGTAATTGAACTCGCTGATCA


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 44

GCTGGTAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGATCAAGgtaggtgccc ... ggatatgcagATCACATGCTTTCTAGTTTCCTAGAGCATTTTCCCAATTTCCCAAATTCCTTCTTGGTTGGTGGACCAGCAGATTACTTTGTAATTGAACTCGCTGATCA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 22

GCTGGTAGAGACCTTTTCCTTCTGCTCTCTAGATTCATGTTCTTCTATGATCAAGgtaggtgccc ... ggatatgcagATCACATGCTTTCTAGTTTCCTAGAGCATTTTCCCAATTTCCCAAATTCCTTCTTGGTTGGTGGACCAGCAGATTACTTTGTAATTGAACTCGCTGATCA