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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAGgtacttggttgttctgctgactgcactatattagttctaaagaaatgtgttaagtagggtttttctatttccatgtattgaatggatttgctttgctgacag

Basic information

species Zea mays
transcript GRMZM2G151916_T01
intron # 8
splice site 5'
intron type U2

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|32908149|gb|CF012962.1|CF012962
EST:     CTCTCTTTCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAG                         GTTCTTGGTACTCCAACACGTGAGGAAATCCGTTGTATGAATCCAAACTAC
genomic: CTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAGgtacttggtt ... ttgctgacagGTTCTTGGTACTCCAACACGTGAGGAAATCCGTTGTATGAATCCAAACTAC
EST: gi|31363416|gb|CD447773.1|CD447773
EST:     CTCTCTTTTCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAG                         GTTCTTGGTACTCCAACACGTGAGGAAATCCGTTGTATGAATCCAAACTAC
genomic: CTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAGgtacttggtt ... ttgctgacagGTTCTTGGTACTCCAACACGTGAGGAAATCCGTTGTATGAATCCAAACTAC
EST: gi|60398307|gb|DN231123.1|DN231123
EST:     CTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAG                         GTTCTTGGTACTCCAACACGTGAGGAAATCCGTTGTATGAATCCAAACTAC
genomic: CTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAGgtacttggtt ... ttgctgacagGTTCTTGGTACTCCAACACGTGAGGAAATCCGTTGTATGAATCCAAACTAC
EST: gi|211015494|gb|FL335940.1|FL335940
EST:     CTCTCTTTCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAG                         GTTCTTGGTACTCCAACACGTGAGGAAATCCGTTGTATGAATCCAAACTAC
genomic: CTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAGgtacttggtt ... ttgctgacagGTTCTTGGTACTCCAACACGTGAGGAAATCCGTTGTATGAATCCAAACTAC
EST: gi|211033507|gb|FL333369.1|FL333369
EST:     CTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAG                         GTTCTTGGTACTCCAACACGTGAGGAAATCCGTTGTATGAATCCAAACTAC
genomic: CTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAGgtacttggtt ... ttgctgacagGTTCTTGGTACTCCAACACGTGAGGAAATCCGTTGTATGAATCCAAACTAC
EST: gi|91875587|gb|EB405544.1|EB405544
EST:     CTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAG                         GTTCTTGGTACTCCAACACGTGAGGAAATCCGTTGTATGAATCCAAACTAC
genomic: CTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAGgtacttggtt ... ttgctgacagGTTCTTGGTACTCCAACACGTGAGGAAATCCGTTGTATGAATCCAAACTAC
EST: gi|211159258|gb|FL355922.1|FL355922
EST:     CTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAG                         GTTCTTGGTACTCCAACACGTGAGGAAATCCGTTGTATGAATCCAAACTAC
genomic: CTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAGgtacttggtt ... ttgctgacagGTTCTTGGTACTCCAACACGTGAGGAAATCCGTTGTATGAATCCAAACTAC

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), 49 (downstream exon)
Score: 184

CCTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAGgtacttggtt ... ttgctgacagGTTCTTGGTACTCCAACACGTGAGGAAATCCGTTGTATGAATCCAAACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 149

CCTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAGgtacttggtt ... ttgctgacagGTTCTTGGTACTCCAACACGTGAGGAAATCCGTTGTATGAATCCAAACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 152

CCTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAGgtacttggtt ... ttgctgacagGTTCTTGGTACTCCAACACGTGAGGAAATCCGTTGTATGAATCCAAACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 111

CCTCTCTTCCCTGGCGAAAGTGCTGTGGATCAACTTGTTGAGATAATAAAGgtacttggtt ... ttgctgacagGTTCTTGGTACTCCAACACGTGAGGAAATCCGTTGTATGAATCCAAACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAG