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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCGCGCGCGCCGCCCCCATCGCCGGCAAGGCGGCGGTGCTGCTGCATATTCTCCCGGTCCCCCCTCCGGAGCCACCCTCCCCTTCTCCGGGACCTTGAGgtatttccgtctcccagtgacgctactttttgctgttgcgctggctggattcctgcgtcggtttagcacttcagcttatggcgcgcttgctctggattgt...

Basic information

species Zea mays
transcript GRMZM5G825110_T01
intron # 1
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|211033695|gb|FL002056.1|FL002056
EST:     TCTCCCGGTCCCCCCTCCGGAGCCACCCTCCCCTTCTCCGGGACCTTGAG                         TAACTTTGGAGTACCAGTGATGCAAAGGGACACTAGCTCTAGCGATGTTTC
genomic: TCTCCCGGTCCCCCCTCCGGAGCCACCCTCCCCTTCTCCGGGACCTTGAGgtatttccgt ... ttctttttagTAACTTTGGAGTACCAGTGATGCAAAGGGACACTAGCTCTAGCGATGTTTC
EST: gi|78079230|gb|DV507642.1|DV507642
EST:     TCTCCCGGTCCCCCCTCCGGAGCCACCCTCCCCTTCTCCGGGACCTTGAG                         TAACTTTGGAGTACCAGTGATGCAAAGGGACACTAGCTCTAGCGATGTTTC
genomic: TCTCCCGGTCCCCCCTCCGGAGCCACCCTCCCCTTCTCCGGGACCTTGAGgtatttccgt ... ttctttttagTAACTTTGGAGTACCAGTGATGCAAAGGGACACTAGCTCTAGCGATGTTTC
EST: gi|76021501|gb|DT948671.1|DT948671
EST:     TCTCCCGGTCCCCCCTCCGGAGCCACCCTCCCCTTCTCCGGGACCTTGAG                         TAACTTTGGAGTACCAGTGATGCAAAGGGACACTAGCTCTAGCGATGTTTC
genomic: TCTCCCGGTCCCCCCTCCGGAGCCACCCTCCCCTTCTCCGGGACCTTGAGgtatttccgt ... ttctttttagTAACTTTGGAGTACCAGTGATGCAAAGGGACACTAGCTCTAGCGATGTTTC

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), 49 (downstream exon)
Score: 130

TCCGCGCGCGCCGCCCCCATCGCCGGCAAGGCGGCGGTGCTGCTGCATATTCTCCCGGTCCCCCCTCCGGAGCCACCCTCCCCTTCTCCGGGACCTTGAGgtatttccgt ... ttctttttagTAACTTTGGAGTACCAGTGATGCAAAGGGACACTAGCTCTAGCGATGTTTCTGCTTCTCATGTAGGGCGTGTAAGACGTCGCAAACATCCATCTGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 75

TCCGCGCGCGCCGCCCCCATCGCCGGCAAGGCGGCGGTGCTGCTGCATATTCTCCCGGTCCCCCCTCCGGAGCCACCCTCCCCTTCTCCGGGACCTTGAGgtatttccgt ... ttctttttagTAACTTTGGAGTACCAGTGATGCAAAGGGACACTAGCTCTAGCGATGTTTCTGCTTCTCATGTAGGGCGTGTAAGACGTCGCAAACATCCATCTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 79

TCCGCGCGCGCCGCCCCCATCGCCGGCAAGGCGGCGGTGCTGCTGCATATTCTCCCGGTCCCCCCTCCGGAGCCACCCTCCCCTTCTCCGGGACCTTGAGgtatttccgt ... ttctttttagTAACTTTGGAGTACCAGTGATGCAAAGGGACACTAGCTCTAGCGATGTTTCTGCTTCTCATGTAGGGCGTGTAAGACGTCGCAAACATCCATCTGAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 116

TCCGCGCGCGCCGCCCCCATCGCCGGCAAGGCGGCGGTGCTGCTGCATATTCTCCCGGTCCCCCCTCCGGAGCCACCCTCCCCTTCTCCGGGACCTTGAGgtatttccgt ... ttctttttagTAACTTTGGAGTACCAGTGATGCAAAGGGACACTAGCTCTAGCGATGTTTCTGCTTCTCATGTAGGGCGTGTAAGACGTCGCAAACATCCATCTGAG