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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAAACgtaagttgaagtcctttcttgaaacggaaagatctctgcatttcttaatatcaattacaaagatgcatactactaaaattaagaaacttctaatttgagctgttatacctcctccatatttgttccacttggtacctattgtaagtttgaaggctgattcaaaaagttttttttgcag

Basic information

species Zea mays
transcript GRMZM2G330650_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G330650_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g25390.1 (Oryza sativa), 5'ss of exon 4
ATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAAACgtaagttgaagtcctttcttgaaacggaaagatctctgcatttcttaatatcaattacaaagatgcatactactaaaattaagaaacttctaatttgagctgttatacctcctccatatttgttccacttggtacctattgtaagtttgaaggctgattcaaaaagttttttttgcag
||||||||||||||||||||||||||||||||||| ||||||||        | ||||||     ||| || | |      |  ||  || | |  |    |   |  || || |  |||  || | |    ||| |  |  |  |                                                                      
ATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAGACgtaagtcagcaagttctcttgatgaataaatatgttt----cacagaacctctagtttagtc-tctgttgtattatatataaccaattcca---ttgggaggaaaccc----------------------------------------------------------------------
















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|71774532|gb|DR972410.1|DR972410
EST:     ATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAAAC                         ATACCAAAGTAGCCTTGGTAACAACAATAAGAGGGTTGAGCTCTTTGATAT
genomic: ATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAAACgtaagttgaa ... ttttttgcagATACCAAAGTAGCCTTGGTAACAACAATAAGAGGGTTGAGCTCTTTGATAT
EST: gi|78122353|gb|DV540737.1|DV540737
EST:     ATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAAAC                         ATACCAAAGTAGCCTTGGTAACAACAATAAGAGGGTTGAGCTCTTTGATAT
genomic: ATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAAACgtaagttgaa ... ttttttgcagATACCAAAGTAGCCTTGGTAACAACAATAAGAGGGTTGAGCTCTTTGATAT
EST: gi|211019324|gb|FL371811.1|FL371811
EST:     ATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAAAC                         ATACCAAAGTAGCCTTGGTAACAACAATAAGAGGGTTGAGCTCTTTGATAT
genomic: ATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAAACgtaagttgaa ... ttttttgcagATACCAAAGTAGCCTTGGTAACAACAATAAGAGGGTTGAGCTCTTTGATAT
EST: gi|211320442|gb|FL345947.1|FL345947
EST:     ATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAAAC                         ATACCAAAGTAGCCTTGGTAACAACAATAAGAGGGTTGAGCTCTTTGATAT
genomic: ATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAAACgtaagttgaa ... ttttttgcagATACCAAAGTAGCCTTGGTAACAACAATAAGAGGGTTGAGCTCTTTGATAT
EST: gi|32827094|gb|CD966772.1|CD966772
EST:     ATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAAAC                         ATACCAAAGTAGCCTTGGTAACAACAATAAGAGGGTTGAGCTCTTTGATAT
genomic: ATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAAACgtaagttgaa ... ttttttgcagATACCAAAGTAGCCTTGGTAACAACAATAAGAGGGTTGAGCTCTTTGATAT
EST: gi|148961350|gb|EE012080.2|EE012080
EST:     ATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAAAC                         ATACCAAAGTAGCCTTGGTAACAACAATAAGAGGGTTGAGCTCTTTGATAT
genomic: ATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAAACgtaagttgaa ... ttttttgcagATACCAAAGTAGCCTTGGTAACAACAATAAGAGGGTTGAGCTCTTTGATAT

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: 45 (upstream exon), 49 (downstream exon)
Score: 70

ATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAAACgtaagttgaa ... ttttttgcagATACCAAAGTAGCCTTGGTAACAACAATAAGAGGGTTGAGCTCTTTGATATGGGTGCTGGAAGTAGTGAGCCTGCTGCTGAGGACAATATTCAAATGGCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 85

ATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAAACgtaagttgaa ... ttttttgcagATACCAAAGTAGCCTTGGTAACAACAATAAGAGGGTTGAGCTCTTTGATATGGGTGCTGGAAGTAGTGAGCCTGCTGCTGAGGACAATATTCAAATGGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 150

ATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAAACgtaagttgaa ... ttttttgcagATACCAAAGTAGCCTTGGTAACAACAATAAGAGGGTTGAGCTCTTTGATATGGGTGCTGGAAGTAGTGAGCCTGCTGCTGAGGACAATATTCAAATGGCA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 141

ATCAAAGAGTTGAATTCCTATGTCACCTTGAGGAAAACgtaagttgaa ... ttttttgcagATACCAAAGTAGCCTTGGTAACAACAATAAGAGGGTTGAGCTCTTTGATATGGGTGCTGGAAGTAGTGAGCCTGCTGCTGAGGACAATATTCAAATGGCA