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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACAACCAGAGTTGTATGCATCCACTTGACACGACGTTTTGCCTGGCGATAAATCCGCAGTATCATTTCCTCAACGGTGTTAGCGATGCATCGTCTCAGgtaaaaaatgcaaccattgtcttgtgactcttaaccagcttagaccatattcatgcagtgacactgatggtgaacatcgatacgtcacataggttgggaa...

Basic information

species Zea mays
transcript GRMZM2G085916_T02
intron # 13
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|78022621|gb|DV491008.1|DV491008
EST:     TAAATCCGCAGTATCATTTCCTCAACGGTGTTAGCGATGCATCGTCTCAG                         TTGCAGCTAATTTGATGCTTGTGTTTATGGAAACCAAGAGGTGGCGCTGAT
genomic: TAAATCCGCAGTATCATTTCCTCAACGGTGTTAGCGATGCATCGTCTCAGgtaaaaaatg ... ttcttttcagTTGCAGCTAATTTGATGCTTGTGTTTATGGAAACCAAGAGGTGGCGCTGAT
EST: gi|12968748|gb|BG265694.1|BG265694
EST:     TAAATCCGCAGTATCATTTCCTCAACGGTGTTAGCGATGCATCGTCTCAG                         TTGCAGCTAATTTGATGCTTGTGTTTATGGAAACCAAGAGGTGGCGCTGAT
genomic: TAAATCCGCAGTATCATTTCCTCAACGGTGTTAGCGATGCATCGTCTCAGgtaaaaaatg ... ttcttttcagTTGCAGCTAATTTGATGCTTGTGTTTATGGAAACCAAGAGGTGGCGCTGAT
EST: gi|5871680|gb|AW018151.1|AW018151
EST:     TAAATCCGCAGTATCATTTCCTCAACGGTGTTAGCGATGCATCGTCTCAG                         TTGCAGCTAATTTGATGCTTGTGTTTATGGAAACCAAGAGGTGGCGCTGAT
genomic: TAAATCCGCAGTATCATTTCCTCAACGGTGTTAGCGATGCATCGTCTCAGgtaaaaaatg ... ttcttttcagTTGCAGCTAATTTGATGCTTGTGTTTATGGAAACCAAGAGGTGGCGCTGAT
EST: gi|32942143|gb|CF046962.1|CF046962
EST:     TAAATCCGCAGTATCATTTCCTCAACGGTGTTAGCGATGCATCGTCTCAG                         TTGCAGCTAATTTGATGCTTGTGTTTATGGAAACCAAGAGGTGGCGCTGAT
genomic: TAAATCCGCAGTATCATTTCCTCAACGGTGTTAGCGATGCATCGTCTCAGgtaaaaaatg ... ttcttttcagTTGCAGCTAATTTGATGCTTGTGTTTATGGAAACCAAGAGGTGGCGCTGAT
EST: gi|78084502|gb|DV512895.1|DV512895
EST:     TAAATCCGCAGTATCATTTCCTCAACGGTGTTAGCGATGCATCGTCTCAG                         TTGCAGCTAATTTGATGCTTGTGTTTATGGAAACCAAGAGGTGGCGCTGAT
genomic: TAAATCCGCAGTATCATTTCCTCAACGGTGTTAGCGATGCATCGTCTCAGgtaaaaaatg ... ttcttttcagTTGCAGCTAATTTGATGCTTGTGTTTATGGAAACCAAGAGGTGGCGCTGAT
EST: gi|32846870|gb|CD986551.1|CD986551
EST:     TAAATCCGCACTATCATTTCCTCAACGGAGTTAGCGATGCATCGTCTCAG                         TTGCAGCTAATTTGATGCTTGTGTTTATGGAAACCAAGAGGTGGCGCTGAT
genomic: TAAATCCGCAGTATCATTTCCTCAACGGTGTTAGCGATGCATCGTCTCAGgtaaaaaatg ... ttcttttcagTTGCAGCTAATTTGATGCTTGTGTTTATGGAAACCAAGAGGTGGCGCTGAT
EST: gi|32845897|gb|CD985578.1|CD985578
EST:     TAAATCCGCAGTATCATTTCCTCAACGGTGTTAGCGATGCATCGTCTCAG                         TTGCAGCTAATTTGATGCTTGTGTTTATGGAAACCAAGAGGTGGCGCTGAT
genomic: TAAATCCGCAGTATCATTTCCTCAACGGTGTTAGCGATGCATCGTCTCAGgtaaaaaatg ... ttcttttcagTTGCAGCTAATTTGATGCTTGTGTTTATGGAAACCAAGAGGTGGCGCTGAT
EST: gi|6056473|gb|AW090863.1|AW090863
EST:     TAAATCCGCAGTATCATTTCCTCAACGGTGTTAGCGATGCATCGTCTCAG                         TTGCAGCTAATTTGATGCTTGTGTTTATGGAAACCAAGAGGTGGCGCTGAT
genomic: TAAATCCGCAGTATCATTTCCTCAACGGTGTTAGCGATGCATCGTCTCAGgtaaaaaatg ... ttcttttcagTTGCAGCTAATTTGATGCTTGTGTTTATGGAAACCAAGAGGTGGCGCTGAT

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), 46 (downstream exon)
Score: 64

GGACAACCAGAGTTGTATGCATCCACTTGACACGACGTTTTGCCTGGCGATAAATCCGCAGTATCATTTCCTCAACGGTGTTAGCGATGCATCGTCTCAGgtaaaaaatg ... ttcttttcagTTGCAGCTAATTTGATGCTTGTGTTTATGGAAACCAAGAGGTGGCGCTGATCCATTGGAAACCTGGTTGTGTATGAATGGGTTTCCAGCTACTTCTATTC


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 27

GGACAACCAGAGTTGTATGCATCCACTTGACACGACGTTTTGCCTGGCGATAAATCCGCAGTATCATTTCCTCAACGGTGTTAGCGATGCATCGTCTCAGgtaaaaaatg ... ttcttttcagTTGCAGCTAATTTGATGCTTGTGTTTATGGAAACCAAGAGGTGGCGCTGATCCATTGGAAACCTGGTTGTGTATGAATGGGTTTCCAGCTACTTCTATTC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 31

GGACAACCAGAGTTGTATGCATCCACTTGACACGACGTTTTGCCTGGCGATAAATCCGCAGTATCATTTCCTCAACGGTGTTAGCGATGCATCGTCTCAGgtaaaaaatg ... ttcttttcagTTGCAGCTAATTTGATGCTTGTGTTTATGGAAACCAAGAGGTGGCGCTGATCCATTGGAAACCTGGTTGTGTATGAATGGGTTTCCAGCTACTTCTATTC


Block sizes: 45 (upstream exon), 45 (downstream exon)
Score: 22

GGACAACCAGAGTTGTATGCATCCACTTGACACGACGTTTTGCCTGGCGATAAATCCGCAGTATCATTTCCTCAACGGTGTTAGCGATGCATCGTCTCAGgtaaaaaatg ... ttcttttcagTTGCAGCTAATTTGATGCTTGTGTTTATGGAAACCAAGAGGTGGCGCTGATCCATTGGAAACCTGGTTGTGTATGAATGGGTTTCCAGCTACTTCTATTC