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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaactagctgatggcttggtcagggctcctagtccccccccccccccccccaatcttatttgagtttgacctacttatgttgctactctcagGCAGAGGGAGTATTAAATTCAAGATTACAACAAATAGTGCATACACTTGACAAG

Basic information

species Zea mays
transcript GRMZM5G812144_T01
intron # 2
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|60337036|gb|DN204009.1|DN204009
EST:     TCCTTATAGAAATAAACATGGATTCTGAGAAGAATGATGCTGAGGTTCAG                         GCAGAGGGAGTATTAAATTCAAGATTACAACAAATAGTGCATACACTTGAC
genomic: TCCTTATAGAAATAAACATGGATTCTGAGAAGAATGATGCTGAGGTTCAGgtaaactagc ... ctactctcagGCAGAGGGAGTATTAAATTCAAGATTACAACAAATAGTGCATACACTTGAC
EST: gi|76285995|gb|DV025563.1|DV025563
EST:     TCCTTATAGAAATAAACATGGATTCTGAGAAGAATGATGCTGAGGTTCAG                         GCAGAGGGAGTATTAAATTCAAGATTACAACAAATAGTGCATACACTTGAC
genomic: TCCTTATAGAAATAAACATGGATTCTGAGAAGAATGATGCTGAGGTTCAGgtaaactagc ... ctactctcagGCAGAGGGAGTATTAAATTCAAGATTACAACAAATAGTGCATACACTTGAC
EST: gi|6851505|gb|AW352515.1|AW352515
EST:     TCCTTATAGAAATAAACATGGATTCTGAGAAGAATGATGCTGAGGTTCAG                         TCAGAGGGAGTATTAAATTCAAGATTACAGCAAATAGTGCATACACTTGAC
genomic: TCCTTATAGAAATAAACATGGATTCTGAGAAGAATGATGCTGAGGTTCAGgtaaactagc ... ctactctcagGCAGAGGGAGTATTAAATTCAAGATTACAACAAATAGTGCATACACTTGAC

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), 49 (downstream exon)
Score: 143

GAAACTCCCTGATGAGATCTTAAGGCACAATGTGGATGAGAAGCGCCAGTTCCTTATAGAAATAAACATGGATTCTGAGAAGAATGATGCTGAGGTTCAGgtaaactagc ... ctactctcagGCAGAGGGAGTATTAAATTCAAGATTACAACAAATAGTGCATACACTTGACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 83

GAAACTCCCTGATGAGATCTTAAGGCACAATGTGGATGAGAAGCGCCAGTTCCTTATAGAAATAAACATGGATTCTGAGAAGAATGATGCTGAGGTTCAGgtaaactagc ... ctactctcagGCAGAGGGAGTATTAAATTCAAGATTACAACAAATAGTGCATACACTTGACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 91

GAAACTCCCTGATGAGATCTTAAGGCACAATGTGGATGAGAAGCGCCAGTTCCTTATAGAAATAAACATGGATTCTGAGAAGAATGATGCTGAGGTTCAGgtaaactagc ... ctactctcagGCAGAGGGAGTATTAAATTCAAGATTACAACAAATAGTGCATACACTTGACAAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 138

GAAACTCCCTGATGAGATCTTAAGGCACAATGTGGATGAGAAGCGCCAGTTCCTTATAGAAATAAACATGGATTCTGAGAAGAATGATGCTGAGGTTCAGgtaaactagc ... ctactctcagGCAGAGGGAGTATTAAATTCAAGATTACAACAAATAGTGCATACACTTGACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccccccccccccccaatcttatttgagtttgacctacttatgttgctactctcagGCAGAGGGAGTATTAAATTCAAGATTACAACAAATAGTGCATACACTTGACAAG
                          gtttgac  putative branch site (score: 138)
                                             ctactctc  putative PPT
              aatcttattt  TA-rich tract