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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGATTCTTTTGTCAAAACTCAAGCTCTGACAGAGGATGTAATTGCTGGATGGCGCCCAAAAGTCATGGGTTAAATTCATTTCTAAAGTTAGACGTTAAGgtaaactgcataataagtgcatatatccccttttaatagaatgaataaatttggcatgcttagatttccttggttcgctattttgtgtctatggaaataa...

Basic information

species Zea mays
transcript GRMZM5G826194_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G826194_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os06g12630.2 (Oryza sativa), 5'ss of exon 6
-----------TGGATTCTTTTGTCAAAACTCAAGCTCTGACAGAGGATGTAATTGCTGGATGGCGCCCAAAAGTCATGGGTTAAATT--CATTTCTAAAGTTAGACGTTAAGgtaaactgcataataagtg-catatatccccttttaatagaatgaataaatttggcatgcttagatttccttggttcgctattttgtgtctatggaaataa
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TATCTTTTCAATGGATTCATTTGTCAAGACTATAGCTCTGCAAGAGGATGTCATTGCTGGATGGCGCCCAAAGGTCATGGGTTAAATTGTAGCTGTAAAAgtaaggcactctgataaactataaactatacatcatactttcttcagtaaagctagaattataccacacacaaacaattttcgtatgattaccacttgtt--------------
















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|93017050|gb|EB642570.1|EB642570
EST:     TGGCGCCCAAAAGTCATGGGTTAAATTCATTTCTAAAGTTAGACGTTAAG                         GGGCGGATGTAGTACAGGTGCATGGGGATACAGGTACAAGCAGAACAGAAC
genomic: TGGCGCCCAAAAGTCATGGGTTAAATTCATTTCTAAAGTTAGACGTTAAGgtaaactgca ... tatatagcagGGGCGGATGTAGTACAGGTGCATGGGGATACAGGTACAAGCAGAACAGAAC




















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), 47 (downstream exon)
Score: 31

TGGATTCTTTTGTCAAAACTCAAGCTCTGACAGAGGATGTAATTGCTGGATGGCGCCCAAAAGTCATGGGTTAAATTCATTTCTAAAGTTAGACGTTAAGgtaaactgca ... tatatagcagGGGCGGATGTAGTACAGGTGCATGGGGATACAGGTACAAGCAGAACAGAACAGGCTCTTGATCAGTTCATTAAGGATAACAAAGAAGCAAAAAAACTCAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 134

TGGATTCTTTTGTCAAAACTCAAGCTCTGACAGAGGATGTAATTGCTGGATGGCGCCCAAAAGTCATGGGTTAAATTCATTTCTAAAGTTAGACGTTAAGgtaaactgca ... tatatagcagGGGCGGATGTAGTACAGGTGCATGGGGATACAGGTACAAGCAGAACAGAACAGGCTCTTGATCAGTTCATTAAGGATAACAAAGAAGCAAAAAAACTCAT


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

TGGATTCTTTTGTCAAAACTCAAGCTCTGACAGAGGATGTAATTGCTGGATGGCGCCCAAAAGTCATGGGTTAAATTCATTTCTAAAGTTAGACGTTAAGgtaaactgca ... tatatagcagGGGCGGATGTAGTACAGGTGCATGGGGATACAGGTACAAGCAGAACAGAACAGGCTCTTGATCAGTTCATTAAGGATAACAAAGAAGCAAAAAAACTCAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 44

TGGATTCTTTTGTCAAAACTCAAGCTCTGACAGAGGATGTAATTGCTGGATGGCGCCCAAAAGTCATGGGTTAAATTCATTTCTAAAGTTAGACGTTAAGgtaaactgca ... tatatagcagGGGCGGATGTAGTACAGGTGCATGGGGATACAGGTACAAGCAGAACAGAACAGGCTCTTGATCAGTTCATTAAGGATAACAAAGAAGCAAAAAAACTCAT