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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGGCACTCTACAGGTCGCAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGAAGgttgactttcaccatgacagcagtatgctttcacatgctgtgttggtttattctatggttacccttatttgcaggtttcccttgcgtctcatttggttacccttatttgcag

Basic information

species Zea mays
transcript GRMZM2G043983_T03
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G043983_T03 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g20750.1 (Oryza sativa), 5'ss of exon 8
GTGGGCACTCTACAGGTCGCAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGAAGgttgactttcaccatgacagcagtatgctttcacatgctgtgttggtttattctatggttacccttatttgcaggtttcccttgcgtctcatttggttacccttatttgcag
||||| ||||||||||| || || ||||| ||||||||||| || |||||||||||  |||| |||||||| |     ||||| |||  |  | |  |||||   |  || |      | | |||  | | |    | |   | | |    |||                           
GTGGGTACTCTACAGGTTGCCAGTACTGGTATAGTTGCCTTGAGCTATGTCCAGAAAGTTTCCGAGAAGgtagggccccaccaagaccaccat-tattttcaacagaagtttca---cactttattttaatctgattgtaaggatatggtatgcag-------------------------
















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|32911846|gb|CF016658.1|CF016658
EST:     CAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGTA-                         GTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACT
genomic: CAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGAAGgttgactttc ... ttatttgcagGTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACT
EST: gi|149065576|gb|EE286698.2|EE286698
EST:     CAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGAAG                         GTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACT
genomic: CAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGAAGgttgactttc ... ttatttgcagGTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACT
EST: gi|211255903|gb|FL358694.1|FL358694
EST:     CAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGAAG                         GTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACT
genomic: CAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGAAGgttgactttc ... ttatttgcagGTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACT
EST: gi|76280767|gb|DV020335.1|DV020335
EST:     CAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGAAG                         GTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACT
genomic: CAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGAAGgttgactttc ... ttatttgcagGTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACT
EST: gi|113702734|gb|EE680238.1|EE680238
EST:     CAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGAAG                         GTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACT
genomic: CAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGAAGgttgactttc ... ttatttgcagGTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACT
EST: gi|32867645|gb|CF007327.1|CF007327
EST:     CAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGAAG                         GTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACT
genomic: CAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGAAGgttgactttc ... ttatttgcagGTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACT
EST: gi|78025625|gb|DV494012.1|DV494012
EST:     CCAGAAGATTTCTGAGAAG                         GTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACT
genomic: CCAGAAGATTTCTGAGAAGgttgactttc ... ttatttgcagGTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACT
EST: gi|76016907|gb|DT944077.1|DT944077
EST:     CAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGAAG                         GTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACT
genomic: CAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGAAGgttgactttc ... ttatttgcagGTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACT

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), 47 (downstream exon)
Score: 293

GTGGGCACTCTACAGGTCGCAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGAAGgttgactttc ... ttatttgcagGTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACTTCCAGCTTTGGTTACGATTACTTGCTTAGGCAG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 57

GTGGGCACTCTACAGGTCGCAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGAAGgttgactttc ... ttatttgcagGTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACTTCCAGCTTTGGTTACGATTACTTGCTTAGGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 53

GTGGGCACTCTACAGGTCGCAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGAAGgttgactttc ... ttatttgcagGTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACTTCCAGCTTTGGTTACGATTACTTGCTTAGGCAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 72

GTGGGCACTCTACAGGTCGCAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGAAGgttgactttc ... ttatttgcagGTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACTTCCAGCTTTGGTTACGATTACTTGCTTAGGCAG