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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGGACAACCGGAACAATGGGTGAAATCACACCGgtgagttgactttcttgcactatatggtcatgttagtgttttacctagtcattcattcactgtcaaatagttctcataaacttgaaaagtatagttagat...

Basic information

species Zea mays
transcript GRMZM2G108416_T01
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108416_T01 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os03g24460.3 (Oryza sativa), 5'ss of exon 17
GTATGGACAACCGGAACAATGGGTGAAATCACACCGgtgagttgactttcttgcactatatggtcatgttagtgttttacctagtcattcattca-ctgtcaaatagttctcataaacttga-aaagtatagttagat
|||||||| || ||||| ||||||||||||||||||||||||| || || |||||||||  | |||||||  |   ||| | | | |      || || ||  || ||| |  | || || | ||   |||  |||  
GTATGGACTACTGGAACGATGGGTGAAATCACACCGgtgagtttacatttttgcactatgcgctcatgttt-tcccttagccatttaacagcacagctatctgatggttttgttgaatttaataataaatatctagt-
















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|60357806|gb|DN224779.1|DN224779
EST:     GTATGGACAACCGGAACAATGGGTGAAATCACACCG                         GTTGTAATGATTGATGGACGTGAAATCGGCGACGGGAAAATTGGTCCAGTC
genomic: GTATGGACAACCGGAACAATGGGTGAAATCACACCGgtgagttgac ... tttacatcagGTTGTAATGATTGATGGACGTGAAATCGGCGACGGGAAAATTGGTCCAGTC
EST: gi|148969666|gb|EE020531.2|EE020531
EST:     GTATGGACAACCGGAACAATGGGTGAAATCACACCG                         GTTGTAATGATTGATGGACGTGAAATCGGCGACGGGAAAATTGGTCCAGTC
genomic: GTATGGACAACCGGAACAATGGGTGAAATCACACCGgtgagttgac ... tttacatcagGTTGTAATGATTGATGGACGTGAAATCGGCGACGGGAAAATTGGTCCAGTC
EST: gi|6827209|gb|AW330852.1|AW330852
EST:     GTATGGACAACCGGAACAATGGGTGAAATTACACCG                         GTTGTAATGATTGATGGACGTGAAATCGGCGACGGGAAAATTGGTCCAGTC
genomic: GTATGGACAACCGGAACAATGGGTGAAATCACACCGgtgagttgac ... tttacatcagGTTGTAATGATTGATGGACGTGAAATCGGCGACGGGAAAATTGGTCCAGTC
EST: gi|211381070|gb|FL456665.1|FL456665
EST:     GTATGGACAACCGGAACAATGGGTGAAATCACACCG                         GTTGTAATGATTGATGGACGTGAAATCGGCGACGGGAAAATTGGTCCAGTC
genomic: GTATGGACAACCGGAACAATGGGTGAAATCACACCGgtgagttgac ... tttacatcagGTTGTAATGATTGATGGACGTGAAATCGGCGACGGGAAAATTGGTCCAGTC
EST: gi|149084134|gb|EE173537.2|EE173537
EST:     GTATGGACAACCGGAACAATGGGTGAAATCACACCG                         GTTGTAATGATTGATGGACGTGAAATCGGCGACGGGAAAATTGGTCCAGTC
genomic: GTATGGACAACCGGAACAATGGGTGAAATCACACCGgtgagttgac ... tttacatcagGTTGTAATGATTGATGGACGTGAAATCGGCGACGGGAAAATTGGTCCAGTC
EST: gi|60352318|gb|DN219291.1|DN219291
EST:     GTATGGACAACCGGAACAATGGGTGAAATCACACCG                         GTTGTAATGATTGATGGACGTGAAATCGGCGACGGGAAAATTGGTCCAGTC
genomic: GTATGGACAACCGGAACAATGGGTGAAATCACACCGgtgagttgac ... tttacatcagGTTGTAATGATTGATGGACGTGAAATCGGCGACGGGAAAATTGGTCCAGTC
EST: gi|12058174|gb|BF733074.1|BF733074
EST:     GTATGGACAACCGGAACAATGGGTGAAATTACACCG                         GTTGTAATGATTGATGGACGTGAAATCGGCGACGGGAAAATTGGTCCAGTC
genomic: GTATGGACAACCGGAACAATGGGTGAAATCACACCGgtgagttgac ... tttacatcagGTTGTAATGATTGATGGACGTGAAATCGGCGACGGGAAAATTGGTCCAGTC

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: 47 (upstream exon), 44 (downstream exon)
Score: 70

GTATGGACAACCGGAACAATGGGTGAAATCACACCGgtgagttgac ... tttacatcagGTTGTAATGATTGATGGACGTGAAATCGGCGACGGGAAAATTGGTCCAGTCACTAGACAAATCCAGAAGGCATACAAGATCCTGACAGCAGGGCAAGGAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 82

GTATGGACAACCGGAACAATGGGTGAAATCACACCGgtgagttgac ... tttacatcagGTTGTAATGATTGATGGACGTGAAATCGGCGACGGGAAAATTGGTCCAGTCACTAGACAAATCCAGAAGGCATACAAGATCCTGACAGCAGGGCAAGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 59

GTATGGACAACCGGAACAATGGGTGAAATCACACCGgtgagttgac ... tttacatcagGTTGTAATGATTGATGGACGTGAAATCGGCGACGGGAAAATTGGTCCAGTCACTAGACAAATCCAGAAGGCATACAAGATCCTGACAGCAGGGCAAGGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 90

GTATGGACAACCGGAACAATGGGTGAAATCACACCGgtgagttgac ... tttacatcagGTTGTAATGATTGATGGACGTGAAATCGGCGACGGGAAAATTGGTCCAGTCACTAGACAAATCCAGAAGGCATACAAGATCCTGACAGCAGGGCAAGGAG