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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTTTACAGTGAAACGGCAGCATGCAGTTCTTATTCTTGCTGACACCCTTTACTATGGGAAGTTCAAGCGTTACTGTAAGgtggtcccttactcccacaccccccaaaaaaagaatttctaggataccttgtcttattaagagcaccgtcaagttatttttcatatgtaacaaacagacctttggacaccttgtcccccccattttcccttgatatttatgtcgttgctgatgttgtgattgcaaccgtacag

Basic information

species Zea mays
transcript GRMZM2G114337_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114337_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os06g48700.1 (Oryza sativa), 5'ss of exon 7
TGGTTTACAGTGAAACGGCAGCATGCAGTTCTTATTCTTGCTGACACCCTTTACTATGGGAAGTTCAAGCGTTACTGTAAGgtggtcccttactcccacaccccccaaaaaaagaatttctaggataccttgtcttattaagagcaccgtcaagttatttttcatatgtaacaaacagacctttggacaccttgtcccccccattttcccttgatatttatgtcgttgctgatgttgtgattgcaaccgtacag
||||| ||||||||||| ||||||||||||||||||||| | ||   |||||||||||  ||||||||||| |||||||||||        | ||  |          |||  ||||||  | | |     || ||  ||  ||      | | |||  |   || | | ||| |||| | |         ||                                                             
TGGTTCACAGTGAAACGTCAGCATGCAGTTCTTATTCTTTCCGATTTCCTTTACTATGCAAAGTTCAAGCGGTACTGTAAGgtaaaattgcattcaaatgggt-----aaagtgaatttaaaaggt-----gtattggtagaagtgtaagcca-ttagataatat-tattacagacag-catcgtattggttta------------------------------------------------------------
















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|78544029|gb|DV621527.1|DV621527
EST:     TTATTCTTGCTGACACCCTTTACTATGGGAAGTTCAAGCGTTACTGTAAG                         CCAGGAAATGAGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACT
genomic: TTATTCTTGCTGACACCCTTTACTATGGGAAGTTCAAGCGTTACTGTAAGgtggtccctt ... aaccgtacagCCAGGAAATGAGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACT
EST: gi|211112077|gb|FL283002.1|FL283002
EST:     TTATTCTTGCTGACACCCTTTACTATGGGAAGTTCAAGCGTTACTGTAAG                         CCAGGAAATGAGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACT
genomic: TTATTCTTGCTGACACCCTTTACTATGGGAAGTTCAAGCGTTACTGTAAGgtggtccctt ... aaccgtacagCCAGGAAATGAGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACT
EST: gi|22818980|gb|BU499070.1|BU499070
EST:     TTATTCTTGCTGACACCCTTTACTATGGGAAGTTCAAGCGTTACTGTAAG                         CCAGGAAATGAGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACT
genomic: TTATTCTTGCTGACACCCTTTACTATGGGAAGTTCAAGCGTTACTGTAAGgtggtccctt ... aaccgtacagCCAGGAAATGAGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACT
EST: gi|71762012|gb|DR959949.1|DR959949
EST:     TTATTCTTGCTGACACCCTTTACTATGGGAAGTTCAAGCGTTACTGTAAG                         CCAGGAAATGAGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACT
genomic: TTATTCTTGCTGACACCCTTTACTATGGGAAGTTCAAGCGTTACTGTAAGgtggtccctt ... aaccgtacagCCAGGAAATGAGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACT
EST: gi|71773585|gb|DR971483.1|DR971483
EST:     TTATTCTTGCTGACACCCTTTACTATGGGAAGTTCAAGCGTTACTGTAAG                         CCAGGAAATGAGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACT
genomic: TTATTCTTGCTGACACCCTTTACTATGGGAAGTTCAAGCGTTACTGTAAGgtggtccctt ... aaccgtacagCCAGGAAATGAGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACT
EST: gi|20802912|gb|BQ293962.1|BQ293962
EST:     TTATTCTTGCTGACACCCTTTACTATGGGAAGTTCAAGCGTTACTGTAAG                         CCAGGAAATGAGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACT
genomic: TTATTCTTGCTGACACCCTTTACTATGGGAAGTTCAAGCGTTACTGTAAGgtggtccctt ... aaccgtacagCCAGGAAATGAGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACT
EST: gi|76284047|gb|DV023615.1|DV023615
EST:     TTATTCTTGCTGACACCCTTTACTATGGGAAGTTCAAGCGTTACTGTAAG                         CCAGGAAATGAGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACT
genomic: TTATTCTTGCTGACACCCTTTACTATGGGAAGTTCAAGCGTTACTGTAAGgtggtccctt ... aaccgtacagCCAGGAAATGAGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACT
EST: gi|60358070|gb|DN225043.1|DN225043
EST:     AAGCGTTACTGTAAG                         CCAGGAAAATGAGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAAC
genomic: AAGCGTTACTGTAAGgtggtccctt ... aaccgtacagCCAGG-AAATGAGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAAC
EST: gi|20506952|gb|BQ279416.1|BQ279416
EST:     TTATTCTTGCTGACACCCTTTACTATGGGATGTTCAAGCGTTACTGTAAG                         CCAGGAAATGAGTGGCATAACTGTTTATTCAGATGATCACTACTTGCCAAC
genomic: TTATTCTTGCTGACACCCTTTACTATGGGAAGTTCAAGCGTTACTGTAAGgtggtccctt ... aaccgtacagCCAGGAAATGAGTGGCATAACTG-CTATTCAGATGAGCACTACTTGCCAAC
EST: gi|101389977|gb|EB816920.1|EB816920
EST:     GGGAAGTTCAAGCGTTACTGTAAG                         CCAGGAAATGAGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACT
genomic: GGGAAGTTCAAGCGTTACTGTAAGgtggtccctt ... aaccgtacagCCAGGAAATGAGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACT
EST: gi|26456599|gb|CA828182.1|CA828182
EST:     TTATTCTTGCTGACACCCTTTACTATGGGAAGTTCAAGCGTTACTGTAAG                         CCAGGAAATGAGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACT
genomic: TTATTCTTGCTGACACCCTTTACTATGGGAAGTTCAAGCGTTACTGTAAGgtggtccctt ... aaccgtacagCCAGGAAATGAGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACT
EST: gi|211112078|gb|FL283003.1|FL283003
EST:     TTATTCTTGCTGACACCCTTTACTATGGGAAGTTCAAGCGTTACTGTAAG                         CCAGGAAATGAGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACT
genomic: TTATTCTTGCTGACACCCTTTACTATGGGAAGTTCAAGCGTTACTGTAAGgtggtccctt ... aaccgtacagCCAGGAAATGAGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACT
EST: gi|20336928|gb|BQ172558.1|BQ172558
EST:     TTATTCTTGCTGACACCCTTTACTATGGGAAGTTCAAGCGTTACTGTAAG                         CCAGGAAATGAGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACT
genomic: TTATTCTTGCTGACACCCTTTACTATGGGAAGTTCAAGCGTTACTGTAAGgtggtccctt ... aaccgtacagCCAGGAAATGAGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACT

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), 44 (downstream exon)
Score: 144

TGGTTTACAGTGAAACGGCAGCATGCAGTTCTTATTCTTGCTGACACCCTTTACTATGGGAAGTTCAAGCGTTACTGTAAGgtggtccctt ... aaccgtacagCCAGGAAATGAGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAAT


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 57

TGGTTTACAGTGAAACGGCAGCATGCAGTTCTTATTCTTGCTGACACCCTTTACTATGGGAAGTTCAAGCGTTACTGTAAGgtggtccctt ... aaccgtacagCCAGGAAATGAGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAAT


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 47

TGGTTTACAGTGAAACGGCAGCATGCAGTTCTTATTCTTGCTGACACCCTTTACTATGGGAAGTTCAAGCGTTACTGTAAGgtggtccctt ... aaccgtacagCCAGGAAATGAGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAAT


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 9

TGGTTTACAGTGAAACGGCAGCATGCAGTTCTTATTCTTGCTGACACCCTTTACTATGGGAAGTTCAAGCGTTACTGTAAGgtggtccctt ... aaccgtacagCCAGGAAATGAGTGGCATAACTGCTATTCAGATGAGCACTACTTGCCAACTCTCTTCAAT