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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGGCCCTTGGCGCGCGCCGCTGGCTCGCCTCGCTCCAGCGCCAGTGCCAGTACCTCGCCATCCTCTGCTCCAACTCTCTCCCTGCCCGCGACCACGCCGgtgagtaataacttactaatcactccatcgttggtgtgagtaacttgcacgagatggttaaccaatggcgacggcggtgagcatggatatatatggatttatgcag

Basic information

species Zea mays
transcript GRMZM2G116658_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116658_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os09g35760.1 (Oryza sativa), 5'ss of exon 7
CAGGCCCTTGGCGCGCGCCGCTGGCTCGCCTCGCTCCAGCGCCAGTGCCAGTACCTCGCCATCCTCTGCTCCAACTCTCTCCCTGCCCGCGACCACGCCGgtgagtaataacttactaatcactccatcgttggtgtgagtaacttgcacgagatggttaaccaatggcgacggcggtga-gcatggatatatatggatttatgcag
|||||||| ||||| |||||||||||||||||||||||||| ||||||||||| ||||||||||||||||||||||| ||||| |||||||||||||| ||||||      ||  |   ||   | |  | | |     ||  |  |     |||   | || |||||     | |||   |||                       
CAGGCCCTCGGCGCCCGCCGCTGGCTCGCCTCGCTCCAGCGACAGTGCCAGTATCTCGCCATCCTCTGCTCCAACTCCCTCCCCGCCCGCGACCACGCTGgtgag------ctcgccgttcgtgctagtgctagctccggtggccggagttcgat--cttactaatggttcttgtggttttgcag----------------------
















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|148946498|gb|EC891809.2|EC891809
EST:     GTACCTCGCCATCCTCTGCTCCCACTCTCTCCCTGCCCGCGACCACGCCG                         CGATCACGCCGGTGGGGCGGAGGAGCATGCTGAAGCTGGCGCAGCGG
genomic: GTACCTCGCCATCCTCTGCTCCAACTCTCTCCCTGCCCGCGACCACGCCGgtgagtaata ... atttatgcagCGATCACGCCGGTGGGGCGGAGGAGCATGCTGAAGCTGGCGCAGCGG
EST: gi|149098428|gb|EE184407.2|EE184407
EST:     GTACCTCGCCATCCTCTGCTCCAACTCTCTCCCTGCCCGCGACCACGCCG                         CGATCACGCGGGTGGGGCGGAGGAGCATG
genomic: GTACCTCGCCATCCTCTGCTCCAACTCTCTCCCTGCCCGCGACCACGCCGgtgagtaata ... atttatgcagCGATCACGCCGGTGGGGCGGAGGAGCATG
EST: gi|149008252|gb|EE040406.2|EE040406
EST:     GTACCTCGCCATCCTCTGCTCCAACTCTCTCCCTGCCCGCGACCACGCCG                         CGATCACGCCGGTGGGGCGGAGGAGCATGCTGAAGCTGGCGCAGCGGATGA
genomic: GTACCTCGCCATCCTCTGCTCCAACTCTCTCCCTGCCCGCGACCACGCCGgtgagtaata ... atttatgcagCGATCACGCCGGTGGGGCGGAGGAGCATGCTGAAGCTGGCGCAGCGGATGA
EST: gi|88756928|gb|DY541069.1|DY541069
EST:     GTACCTCGCCATCCTCTGCTCCAACTCTCTCCCTGCCCGCGACCACGCCG                         CGATCACGCCGGTGGGGCGGAGGAGCATGCTGAAGCTGGCGCAGCGGATGA
genomic: GTACCTCGCCATCCTCTGCTCCAACTCTCTCCCTGCCCGCGACCACGCCGgtgagtaata ... atttatgcagCGATCACGCCGGTGGGGCGGAGGAGCATGCTGAAGCTGGCGCAGCGGATGA

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 3 RNA-Seq libraries.


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 50

CAGGCCCTTGGCGCGCGCCGCTGGCTCGCCTCGCTCCAGCGCCAGTGCCAGTACCTCGCCATCCTCTGCTCCAACTCTCTCCCTGCCCGCGACCACGCCGgtgagtaata ... atttatgcagCGATCACGCCGGTGGGGCGGAGGAGCATGCTGAAGCTGGCGCAGCGGATGACGGACAACTTCTGCGCCGGTGTGTGTGCGTCGGCGGCGCAGAAGTGGCG


Block sizes: 37 (upstream exon), 40 (downstream exon)
Score: 6

CAGGCCCTTGGCGCGCGCCGCTGGCTCGCCTCGCTCCAGCGCCAGTGCCAGTACCTCGCCATCCTCTGCTCCAACTCTCTCCCTGCCCGCGACCACGCCGgtgagtaata ... atttatgcagCGATCACGCCGGTGGGGCGGAGGAGCATGCTGAAGCTGGCGCAGCGGATGACGGACAACTTCTGCGCCGGTGTGTGTGCGTCGGCGGCGCAGAAGTGGCG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 26

CAGGCCCTTGGCGCGCGCCGCTGGCTCGCCTCGCTCCAGCGCCAGTGCCAGTACCTCGCCATCCTCTGCTCCAACTCTCTCCCTGCCCGCGACCACGCCGgtgagtaata ... atttatgcagCGATCACGCCGGTGGGGCGGAGGAGCATGCTGAAGCTGGCGCAGCGGATGACGGACAACTTCTGCGCCGGTGTGTGTGCGTCGGCGGCGCAGAAGTGGCG