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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACACTATTGATAGAGCCTAAACCACAGGAACCAACAAAACACCAgtatgctacttactcagtaatgaattagcaaagtatcctacaggattcagaaacatttatccttgtttctctggcag

Basic information

species Zea mays
transcript GRMZM2G081682_T02
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081682_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os07g47290.1 (Oryza sativa), 5'ss of exon 12
GAACACTATTGATAGAGCCTAAACCACAGGAACCAACAAAACACCAgtatgctacttactcagtaatgaattagcaaagtatcctacaggattcagaaacatttatccttgttt---ctctggcag
||||||| |||||||||||||||||||| ||||| ||||||||||||||||||  ||| |      |  |||| |||| | ||| |||||||| |  ||   | | ||||||||   ||||  |||
GAACACTCTTGATAGAGCCTAAACCACAAGAACCCACAAAACACCAgtatgcttattagtt-----tacattaacaaaatgtcc-acaggattaaacaatcctaacccttgtttgtcctctcccag
















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|31349785|gb|CD434142.1|CD434142
EST:     GAACACTATTGATAGAGCCTAAACCACAGGAACCAACAAAACACCA                         GTATGACTGGGATGTTGCGACTACGTTTGCTTTTCTACAGAAGTACGGTCT
genomic: GAACACTATTGATAGAGCCTAAACCACAGGAACCAACAAAACACCAgtatgctact ... tctctggcagGTATGACTGGGATGTTGCGACTACGTTTGCTTTTCTACAGAAGTACGGTCT
EST: gi|33092171|gb|CF052165.1|CF052165
EST:     GAACACTATTGATAGAGCCTAAACCACAGGAACCAACAAAACACCA                         GTATGACTGGGATGTTGCGACTACGTTTGCTTTTCTACAGAAGTAC
genomic: GAACACTATTGATAGAGCCTAAACCACAGGAACCAACAAAACACCAgtatgctact ... tctctggcagGTATGACTGGGATGTTGCGACTACGTTTGCTTTTCTACAGAAGTAC
EST: gi|5846747|gb|AI999830.1|AI999830
EST:     GAACACTATTGATAGAGCCTAAACCACAGGAACCAACAAAACACCA                         GTATGACTGGGATGTTGCGACTACGTTTGCTTTTCTACAGAAGTACGGTCT
genomic: GAACACTATTGATAGAGCCTAAACCACAGGAACCAACAAAACACCAgtatgctact ... tctctggcagGTATGACTGGGATGTTGCGACTACGTTTGCTTTTCTACAGAAGTACGGTCT
EST: gi|5296207|gb|AI782887.1|AI782887
EST:     GAACACTATTGATAGAGCCTAAACCACAGGAACCAACAAAACACCA                         GTATGACTGGGATGTTGCGACTACGTTTGCTTTTCTACAGAAGTACGGTCT
genomic: GAACACTATTGATAGAGCCTAAACCACAGGAACCAACAAAACACCAgtatgctact ... tctctggcagGTATGACTGGGATGTTGCGACTACGTTTGCTTTTCTACAGAAGTACGGTCT

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: 250

GAACACTATTGATAGAGCCTAAACCACAGGAACCAACAAAACACCAgtatgctact ... tctctggcagGTATGACTGGGATGTTGCGACTACGTTTGCTTTTCTACAGAAGTACGGTCTTACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 293

GAACACTATTGATAGAGCCTAAACCACAGGAACCAACAAAACACCAgtatgctact ... tctctggcagGTATGACTGGGATGTTGCGACTACGTTTGCTTTTCTACAGAAGTACGGTCTTACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 219

GAACACTATTGATAGAGCCTAAACCACAGGAACCAACAAAACACCAgtatgctact ... tctctggcagGTATGACTGGGATGTTGCGACTACGTTTGCTTTTCTACAGAAGTACGGTCTTACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 355

GAACACTATTGATAGAGCCTAAACCACAGGAACCAACAAAACACCAgtatgctact ... tctctggcagGTATGACTGGGATGTTGCGACTACGTTTGCTTTTCTACAGAAGTACGGTCTTACAG