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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGATGCTCATGGGGAGGGTCTCACATGAAGGGAGGGAGAACATCCGTGTCAAGCATGATATTACGGACAACCTTTCTTTAAAGATAAATGCTCAGgtaaattgattttaaactgctagtaaattgatgattatttggattcagctttgcttgaagccacctttaaaaatccttagttgaccgattttgtgctcttgcag

Basic information

species Zea mays
transcript GRMZM2G120876_T01
intron # 4
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|211134090|gb|FL422145.1|FL422145
EST:     TGATATTACGGACAACCTTTCTTTAAAGATAAATGCTCAG                         TTGACAAGTGAGCCCCACTACTCCCAAGGGATGCTGAATTTTGATTATAAG
genomic: TGATATTACGGACAACCTTTCTTTAAAGATAAATGCTCAGgtaaattgat ... gctcttgcagTTGACAAGTGAGCCCCACTACTCCCAAGGGATGCTGAATTTTGATTATAAG
EST: gi|32836655|gb|CD976333.1|CD976333
EST:     GTGTCAAGCATGATATTACGGACAACCTTTCTTTAAAGATAAATGCTCAG                         TTGACAAGTGAGCCCCACTACTCCCAAGGGATGCTGAATTTTGATTATAAG
genomic: GTGTCAAGCATGATATTACGGACAACCTTTCTTTAAAGATAAATGCTCAGgtaaattgat ... gctcttgcagTTGACAAGTGAGCCCCACTACTCCCAAGGGATGCTGAATTTTGATTATAAG
EST: gi|211538850|gb|FL377090.1|FL377090
EST:     TGATATTACGGACAACCTTTCTTTAAAGATAAATGCTCAG                         TTGACAAGTGAGCCCCACTACTCCCAAGGGATGCTGAATTTTGATTATAAG
genomic: TGATATTACGGACAACCTTTCTTTAAAGATAAATGCTCAGgtaaattgat ... gctcttgcagTTGACAAGTGAGCCCCACTACTCCCAAGGGATGCTGAATTTTGATTATAAG
EST: gi|211045137|gb|FL385512.1|FL385512
EST:     TGATATTACGGACAACCTTTCTTTAAAGATAAATGCTCAG                         TTGACAAGTGAGCCCCACTACTCCCAAGGGATGCTGAATATTTGATTATAA
genomic: TGATATTACGGACAACCTTTCTTTAAAGATAAATGCTCAGgtaaattgat ... gctcttgcagTTGACAAGTGAGCCCCACTACTCCCAAGGGATGCTGAAT-TTTGATTATAA

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: 1022

ACGATGCTCATGGGGAGGGTCTCACATGAAGGGAGGGAGAACATCCGTGTCAAGCATGATATTACGGACAACCTTTCTTTAAAGATAAATGCTCAGgtaaattgat ... gctcttgcagTTGACAAGTGAGCCCCACTACTCCCAAGGGATGCTGAATTTTGATTATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 646

ACGATGCTCATGGGGAGGGTCTCACATGAAGGGAGGGAGAACATCCGTGTCAAGCATGATATTACGGACAACCTTTCTTTAAAGATAAATGCTCAGgtaaattgat ... gctcttgcagTTGACAAGTGAGCCCCACTACTCCCAAGGGATGCTGAATTTTGATTATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 589

ACGATGCTCATGGGGAGGGTCTCACATGAAGGGAGGGAGAACATCCGTGTCAAGCATGATATTACGGACAACCTTTCTTTAAAGATAAATGCTCAGgtaaattgat ... gctcttgcagTTGACAAGTGAGCCCCACTACTCCCAAGGGATGCTGAATTTTGATTATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 572

ACGATGCTCATGGGGAGGGTCTCACATGAAGGGAGGGAGAACATCCGTGTCAAGCATGATATTACGGACAACCTTTCTTTAAAGATAAATGCTCAGgtaaattgat ... gctcttgcagTTGACAAGTGAGCCCCACTACTCCCAAGGGATGCTGAATTTTGATTATAAG