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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACTGCCAAAATCGTTGATTGTCTTCAGGACCGTGGCATTAACCAGGTCTATATTATCGGAGGCGATGGCACTCAGAAAGGCGCTTCTGTAATTTATGAGgtaacacatgcatccagacggttctgggaattgttgttagatgcggaaacgatgtgtgactcaaaatttctgaaacatggtttcag

Basic information

species Zea mays
transcript GRMZM2G080375_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G080375_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g09570.1 (Oryza sativa), 5'ss of exon 5
CACTGCCAAAATCGTTGATTGTCTTCAGGACCGTGGCATTAACCAGGTCTATATTATCGGAGGCGATGGCACTCAGAAAGGCGCTTCTGTAATTTATGAGgtaacacatgcatccagacggttctgg--gaattgttgttagatgcggaa-acgatgtgtgactcaaaatttctgaaacatggtttcag
||| | |||||| |||||  || || |||| || || ||||||||||| |||||||| ||||| ||||| || |||||||| ||||| ||||||||||||||||| ||       | |  | | |     |||  ||||  |||||  ||  | || | | || |||| ||  ||||| ||| ||||||
CACCGGCAAAATAGTTGACAGTATTAAGGATCGCGGTATTAACCAGGTGTATATTATTGGAGGTGATGGTACCCAGAAAGGTGCTTCCGTAATTTATGAGgtaactcacaggctgataatgatgtaaataaatgtttgtgggatgcccaatgctatctataacacaaacttgttgaaa-atgatttcag
















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|74234373|gb|DT642287.1|DT642287
EST:     ATATTATCGGAGGCGATGGCACTCAGAAAGGCGCTTCTGTAATTTATGAG                         GAAGTCCGGAGACGGGGTCTCAAGTGCTCTGTTGTCGGTGT
genomic: ATATTATCGGAGGCGATGGCACTCAGAAAGGCGCTTCTGTAATTTATGAGgtaacacatg ... atggtttcagGAAGTCCGGAGACGGGGTCTCAAGTGCTCTGTTGTCGGTGT
EST: gi|116813643|gb|EC856113.1|EC856113
EST:     ATATTATCGGAGGCGATGGCACTCAGAAAGGCGCTTCTGTAATTTATGAG                         GAAGTCCGGAGACGGGGTCTCAAGTGCTCTGTTGTCGGTGTCCCAAAGACT
genomic: ATATTATCGGAGGCGATGGCACTCAGAAAGGCGCTTCTGTAATTTATGAGgtaacacatg ... atggtttcagGAAGTCCGGAGACGGGGTCTCAAGTGCTCTGTTGTCGGTGTCCCAAAGACT
EST: gi|33099629|gb|CF059589.1|CF059589
EST:     ATATTATCGGAGGCGATGGCACTCAGAAAGGCGCTTCTGTAATTTATGAG                         GAAGTCCGGAGACGGGGCCTCAAGTGCTCTGTTGTCGGTGTCCCAAAGACT
genomic: ATATTATCGGAGGCGATGGCACTCAGAAAGGCGCTTCTGTAATTTATGAGgtaacacatg ... atggtttcagGAAGTCCGGAGACGGGGTCTCAAGTGCTCTGTTGTCGGTGTCCCAAAGACT
EST: gi|149087521|gb|EE176918.2|EE176918
EST:     TATTATCGGAGGCGATGGCACTCAGAAAGGCGCTTTCTGTA-TTTATGAG                         GAAGTCCGGAGACGGGGTCTCAAGTGCTCTGGTGTCCGTGTCCCAAAGACT
genomic: TATTATCGGAGGCGATGGCACTCAGAAAGGCGCTT-CTGTAATTTATGAGgtaacacatg ... atggtttcagGAAGTCCGGAGACGGGGTCTCAAGTGCTCTGTTGTCGGTGTCCCAAAGACT
EST: gi|87153260|gb|DY398049.1|DY398049
EST:     ATATTATCGGAGGCGACGGGACTCAGAAAGGCGCTTCTGTAATTTATGAG                         GAAGTCCGGAGACGCGGCCTCAAGTGCTCTGTTGTCGGTGTCCCAAAGACT
genomic: ATATTATCGGAGGCGATGGCACTCAGAAAGGCGCTTCTGTAATTTATGAGgtaacacatg ... atggtttcagGAAGTCCGGAGACGGGGTCTCAAGTGCTCTGTTGTCGGTGTCCCAAAGACT
EST: gi|211450005|gb|FL281917.1|FL281917
EST:     ATATTATCGGAGACGACGGCACTCAGAAAGGCGCTTCTGTAATTTATGAG                         GAAGTCCGGAGACGCGGCCTCAAGTGCTCTGTTGTCGGTGTCCCAAAGACT
genomic: ATATTATCGGAGGCGATGGCACTCAGAAAGGCGCTTCTGTAATTTATGAGgtaacacatg ... atggtttcagGAAGTCCGGAGACGGGGTCTCAAGTGCTCTGTTGTCGGTGTCCCAAAGACT
EST: gi|211450006|gb|FL281918.1|FL281918
EST:     ATATTATCGGAGACGACGGCACTCAGAAAGGCGCTTCTGTAATTTATGAG                         GAAGTCCGGAGACGCGGCCTCAAGTGCTCTGTTGTCGGTGTCCCAAAGACT
genomic: ATATTATCGGAGGCGATGGCACTCAGAAAGGCGCTTCTGTAATTTATGAGgtaacacatg ... atggtttcagGAAGTCCGGAGACGGGGTCTCAAGTGCTCTGTTGTCGGTGTCCCAAAGACT

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: 48 (upstream exon), 46 (downstream exon)
Score: 48

CACTGCCAAAATCGTTGATTGTCTTCAGGACCGTGGCATTAACCAGGTCTATATTATCGGAGGCGATGGCACTCAGAAAGGCGCTTCTGTAATTTATGAGgtaacacatg ... atggtttcagGAAGTCCGGAGACGGGGTCTCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 380

CACTGCCAAAATCGTTGATTGTCTTCAGGACCGTGGCATTAACCAGGTCTATATTATCGGAGGCGATGGCACTCAGAAAGGCGCTTCTGTAATTTATGAGgtaacacatg ... atggtttcagGAAGTCCGGAGACGGGGTCTCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 391

CACTGCCAAAATCGTTGATTGTCTTCAGGACCGTGGCATTAACCAGGTCTATATTATCGGAGGCGATGGCACTCAGAAAGGCGCTTCTGTAATTTATGAGgtaacacatg ... atggtttcagGAAGTCCGGAGACGGGGTCTCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 112

CACTGCCAAAATCGTTGATTGTCTTCAGGACCGTGGCATTAACCAGGTCTATATTATCGGAGGCGATGGCACTCAGAAAGGCGCTTCTGTAATTTATGAGgtaacacatg ... atggtttcagGAAGTCCGGAGACGGGGTCTCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCG