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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtttagctgcttcacgacctgctagatttctgtctatgctgttgcaatgtaaagggatcctaatgtttttattgtgcagGTAAAAAAGAATGCAAGAGCATATTTGGTTGGACTGAGAGGTTCAGCGTGGCTATGGGAGTTGCTCGTGCTCTGGATTATCTCCATAGTGATAACAACAG

Basic information

species Zea mays
transcript GRMZM2G032337_T01
intron # 6
splice site 3'
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|76909167|gb|DV163255.1|DV163255
EST:     GTTAGTGTATGAGTATTTGCAACGAGGCAGCCTGGAAGAGATACTGCATG                         GTAAAAAAGAATGCAAGAGCATATTTGGTTGGACTGAGAGGTTCAGCGTGG
genomic: GTTAGTGTATGAGTATTTGCAACGAGGCAGCCTGGAAGAGATACTGCATGgtgcgtttag ... tattgtgcagGTAAAAAAGAATGCAAGAGCATATTTGGTTGGACTGAGAGGTTCAGCGTGG




















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: 49 (upstream exon), 44 (downstream exon)
Score: 58

AAGAATGTGATATCCCTCGTTGGTTTCTGCTTCAAGAATGATGACCTTCTGTTAGTGTATGAGTATTTGCAACGAGGCAGCCTGGAAGAGATACTGCATGgtgcgtttag ... tattgtgcagGTAAAAAAGAATGCAAGAGCATATTTGGTTGGACTGAGAGGTTCAGCGTGGCTATGGGAGTTGCTCGTGCTCTGGATTATCTCCATAGTGATAACAACAG


Block sizes: 39 (upstream exon), 42 (downstream exon)
Score: 15

AAGAATGTGATATCCCTCGTTGGTTTCTGCTTCAAGAATGATGACCTTCTGTTAGTGTATGAGTATTTGCAACGAGGCAGCCTGGAAGAGATACTGCATGgtgcgtttag ... tattgtgcagGTAAAAAAGAATGCAAGAGCATATTTGGTTGGACTGAGAGGTTCAGCGTGGCTATGGGAGTTGCTCGTGCTCTGGATTATCTCCATAGTGATAACAACAG


Block sizes: 39 (upstream exon), 36 (downstream exon)
Score: 15

AAGAATGTGATATCCCTCGTTGGTTTCTGCTTCAAGAATGATGACCTTCTGTTAGTGTATGAGTATTTGCAACGAGGCAGCCTGGAAGAGATACTGCATGgtgcgtttag ... tattgtgcagGTAAAAAAGAATGCAAGAGCATATTTGGTTGGACTGAGAGGTTCAGCGTGGCTATGGGAGTTGCTCGTGCTCTGGATTATCTCCATAGTGATAACAACAG


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 51

AAGAATGTGATATCCCTCGTTGGTTTCTGCTTCAAGAATGATGACCTTCTGTTAGTGTATGAGTATTTGCAACGAGGCAGCCTGGAAGAGATACTGCATGgtgcgtttag ... tattgtgcagGTAAAAAAGAATGCAAGAGCATATTTGGTTGGACTGAGAGGTTCAGCGTGGCTATGGGAGTTGCTCGTGCTCTGGATTATCTCCATAGTGATAACAACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttctgtctatgctgttgcaatgtaaagggatcctaatgtttttattgtgcagGTAAAAAAGAATGCAAGAGCATATTTGGTTGGACTGAGAGGTTCAGCGTGGCTATGGGAGTTGCTCGTGCTCTGGATTATCTCCATAGTGATAACAACAG
                                 tcctaat  putative branch site (score: 51)
                                         tttttatt  CT-rich tract
                                    taatgtttttattgt  TA-rich tract