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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcactaaatatattaacaacaatgatgaatcgcttaagttgttggtgaatatcatattgtaatttggattacatgatctgcagAGAGGAGCATCAGCAAGCAAGTTCCTCAATTACTTCGTTAAACAAATTGTTCCAGCATTTGAGAAG

Basic information

species Zea mays
transcript GRMZM2G059039_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059039_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g20930.1 (Oryza sativa), 3'ss of exon 8
gtatcactaaatatattaacaacaatgatgaatcgcttaagttgttggtgaatatcatattgtaatttg----------------gattacatgatctgcagAGAGGAGCATCAGCAAGCAAGTTCCTCAATTACTTCGTTAAACAAATTGTTCCAGCATTTGAGAAG
  |   ||| |     | | |||    |      |    | ||||| |||||| |||| || |  | ||                  || ||||||||||||||||| | |||    |||||||||||||| || |||||||| |||||||||||||  ||||| |||
--aatgctagaaggtcttataacctgaaacggaggtagtacttgttagtgaatgtcatcttatcttatgctttttttttcactacatttgcatgatctgcagAGAGGGGGATCGAGCAGCAAGTTCCTCAACTATTTCGTTAAGCAAATTGTTCCAGTTTTTGACAAG
















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|60338080|gb|DN205053.1|DN205053
EST:     ACATTGAGAGGTGGATTTCATGCATGTATATGGCTCTTCCGATCTTCATG                         AGAGGAGCATCAGCAAGCAAGTTCCTCAATTACTTCGTTAAACAAATTGTT
genomic: ACATTGAGAGGTGGATTTCATGCATGTATATGGCTCTTCCGATCTTCATGgtatcactaa ... tgatctgcagAGAGGAGCATCAGCAAGCAAGTTCCTCAATTACTTCGTTAAACAAATTGTT
EST: gi|148943964|gb|EC889044.2|EC889044
EST:     ACATTGAGAGGTGGATTTCATGCATGTATATGGCTCTTCCGATCTTCATG                         AGAGGAGCATCAGCAAGC
genomic: ACATTGAGAGGTGGATTTCATGCATGTATATGGCTCTTCCGATCTTCATGgtatcactaa ... tgatctgcagAGAGGAGCATCAGCAAGC
EST: gi|32933981|gb|CF038793.1|CF038793
EST:     ACATTGAGAGGTGGATTTCATGCATGTATATGGCTCTTCCGATCTTCATG                         AGAGGAGCATCAGCAAGCAAGTTCCTCAATTACTTCGTTAAACAAATTGTT
genomic: ACATTGAGAGGTGGATTTCATGCATGTATATGGCTCTTCCGATCTTCATGgtatcactaa ... tgatctgcagAGAGGAGCATCAGCAAGCAAGTTCCTCAATTACTTCGTTAAACAAATTGTT
EST: gi|76014976|gb|DT942146.1|DT942146
EST:     ACATTGAGAGGTGGATTTCATGCATGTATATGGCTCTTCCGATCTTCATG                         AGAGGAGCATCAG
genomic: ACATTGAGAGGTGGATTTCATGCATGTATATGGCTCTTCCGATCTTCATGgtatcactaa ... tgatctgcagAGAGGAGCATCAG
EST: gi|31356580|gb|CD440937.1|CD440937
EST:     ACATTGAGAGGTGGATTTCATGCATGTATATGGCTCTTCCGATCTTCATG                         AGAGGAGCATCAGCAAGCAAGTTCCTCAATTACTTCGTTAAACAAATTGTT
genomic: ACATTGAGAGGTGGATTTCATGCATGTATATGGCTCTTCCGATCTTCATGgtatcactaa ... tgatctgcagAGAGGAGCATCAGCAAGCAAGTTCCTCAATTACTTCGTTAAACAAATTGTT
EST: gi|31358588|gb|CD442945.1|CD442945
EST:     ACATTGAGAGGTGGATTTCATGCATGTATATGGCTCTTCCGATCTTCATG                         AGAGGAGCATCAGCAAGCAAGTTCCTCAATTACTTCGTTAAACAAATTGTT
genomic: ACATTGAGAGGTGGATTTCATGCATGTATATGGCTCTTCCGATCTTCATGgtatcactaa ... tgatctgcagAGAGGAGCATCAGCAAGCAAGTTCCTCAATTACTTCGTTAAACAAATTGTT

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: 48 (upstream exon), 49 (downstream exon)
Score: 212

GTTTCTGACATTGACCACATTGAGAGGTGGATTTCATGCATGTATATGGCTCTTCCGATCTTCATGgtatcactaa ... tgatctgcagAGAGGAGCATCAGCAAGCAAGTTCCTCAATTACTTCGTTAAACAAATTGTTCCAGCATTTGAGAAG


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 67

GTTTCTGACATTGACCACATTGAGAGGTGGATTTCATGCATGTATATGGCTCTTCCGATCTTCATGgtatcactaa ... tgatctgcagAGAGGAGCATCAGCAAGCAAGTTCCTCAATTACTTCGTTAAACAAATTGTTCCAGCATTTGAGAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 76

GTTTCTGACATTGACCACATTGAGAGGTGGATTTCATGCATGTATATGGCTCTTCCGATCTTCATGgtatcactaa ... tgatctgcagAGAGGAGCATCAGCAAGCAAGTTCCTCAATTACTTCGTTAAACAAATTGTTCCAGCATTTGAGAAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 56

GTTTCTGACATTGACCACATTGAGAGGTGGATTTCATGCATGTATATGGCTCTTCCGATCTTCATGgtatcactaa ... tgatctgcagAGAGGAGCATCAGCAAGCAAGTTCCTCAATTACTTCGTTAAACAAATTGTTCCAGCATTTGAGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcgcttaagttgttggtgaatatcatattgtaatttggattacatgatctgcagAGAGGAGCATCAGCAAGCAAGTTCCTCAATTACTTCGTTAAACAAATTGTTCCAGCATTTGAGAAG
                   aatatcatattgtaat  TA-rich tract