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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGACCTTAACCGTAGACGAGCTTTTCTACCTGAAATCACAGTTTTCTCTATTGGAACCAGACAGGAATGGGTGCATCACTCTTGACAATATCAGAATGgttagctcatagctacagctaattccagactggttaatgctagaatatagtccgtacttttttttgtgtaattctaatggctcctgttgcttcacgctgtttag

Basic information

species Zea mays
transcript GRMZM2G109843_T02
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|211220514|gb|FL333416.1|FL333416
EST:     TATTGGAACCAGACAGGAATGGGTGCATCACTCTTGACAATATCAGAATG                         GCCTTAACGAGAGAAGCTACTGATGCAATGAAGGAATCGCGAGTTCAAGAT
genomic: TATTGGAACCAGACAGGAATGGGTGCATCACTCTTGACAATATCAGAATGgttagctcat ... cgctgtttagGCCTTAACGAGAGAAGCTACTGATGCAATGAAGGAATCGCGAGTTCAAGAT
EST: gi|67012906|gb|CO441655.1|CO441655
EST:     TATTGGAACCAGACAGGAATGGGTGCATCACTCTTGACAATATCAGAATG                         GCCTTAACGAGAGAAGCTACTGATGCAATGAAGGAATCGCGAGTTCAAGAT
genomic: TATTGGAACCAGACAGGAATGGGTGCATCACTCTTGACAATATCAGAATGgttagctcat ... cgctgtttagGCCTTAACGAGAGAAGCTACTGATGCAATGAAGGAATCGCGAGTTCAAGAT
EST: gi|211442907|gb|FL470068.1|FL470068
EST:     TATTGGAACCAGACAGGAATGGATGCATCACTCTTGACAATATCAGAATG                         GCCTTAACGAGAGAAGCTACTGATGCAATGAAGGAATCGCGAGTTCAAGAT
genomic: TATTGGAACCAGACAGGAATGGGTGCATCACTCTTGACAATATCAGAATGgttagctcat ... cgctgtttagGCCTTAACGAGAGAAGCTACTGATGCAATGAAGGAATCGCGAGTTCAAGAT
EST: gi|211425736|gb|FL365893.1|FL365893
EST:     TATTGGAACCAGACAGGAATGGATGCATCACTCTTGACAATATCAGAATG                         GCCTTAACGAGAGAAGCTACTGATGCAATGAAGGAATCGCGAGTTCAAGAT
genomic: TATTGGAACCAGACAGGAATGGGTGCATCACTCTTGACAATATCAGAATGgttagctcat ... cgctgtttagGCCTTAACGAGAGAAGCTACTGATGCAATGAAGGAATCGCGAGTTCAAGAT

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: 46 (upstream exon), 42 (downstream exon)
Score: 121

AAAGACCTTAACCGTAGACGAGCTTTTCTACCTGAAATCACAGTTTTCTCTATTGGAACCAGACAGGAATGGGTGCATCACTCTTGACAATATCAGAATGgttagctcat ... cgctgtttagGCCTTAACGAGAGAAGCTACTGATGCAATGAAGGAATCGCGAGTTCAAGATATTCTTGTTTCG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 24

AAAGACCTTAACCGTAGACGAGCTTTTCTACCTGAAATCACAGTTTTCTCTATTGGAACCAGACAGGAATGGGTGCATCACTCTTGACAATATCAGAATGgttagctcat ... cgctgtttagGCCTTAACGAGAGAAGCTACTGATGCAATGAAGGAATCGCGAGTTCAAGATATTCTTGTTTCG


Block sizes: 45 (upstream exon), 42 (downstream exon)
Score: 18

AAAGACCTTAACCGTAGACGAGCTTTTCTACCTGAAATCACAGTTTTCTCTATTGGAACCAGACAGGAATGGGTGCATCACTCTTGACAATATCAGAATGgttagctcat ... cgctgtttagGCCTTAACGAGAGAAGCTACTGATGCAATGAAGGAATCGCGAGTTCAAGATATTCTTGTTTCG


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 26

AAAGACCTTAACCGTAGACGAGCTTTTCTACCTGAAATCACAGTTTTCTCTATTGGAACCAGACAGGAATGGGTGCATCACTCTTGACAATATCAGAATGgttagctcat ... cgctgtttagGCCTTAACGAGAGAAGCTACTGATGCAATGAAGGAATCGCGAGTTCAAGATATTCTTGTTTCG