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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatacacatacataatatccttgtttgatctagttcatgtttacaactagagctcacctagaaaatactatatcttattggtttctgttgtttcttcagATTGAAGCACGCGGTCTCCCTCTTACTCCAGAGGCACTGCTTTCATTGCCTCCATTCTCTTCAATCACATTTAACTCAGAGGTTGCTAATGGAACAATGA

Basic information

species Zea mays
transcript GRMZM2G019260_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G019260_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g14830.1 (Oryza sativa), 3'ss of exon 5
-ttatacacatacataatatccttgtt-tgatctagttcatgtttacaactagagctcacctagaaaatactatatcttattggtttctgttgtttcttcagATTGAAGCACGCGGTCTCCCTCTTACTCCAGAGGCACTGCTTTCATTGCCTCCATTCTCTTCAATCACATTTAACTCAGAGGTTGCTAATGGAACAATGA
 |   |    ||  | || |     ||   ||  || |||   ||| ||     |  |  ||   ||||| | || |||  |  ||||| | |||||| |||||||||||||| || || ||||| |||||||||| | ||||||| ||||||||||||| |||||| |||||||| ||||| |||||||||||||||||||
ttcccatgtttaacttatgtgtgaattacaatgcagatcaccctta-aagagttgtgccactgttaaataat-tagcttgctattttctatcgtttctccagATTGAAGCACGTGGCCTTCCTCTAACTCCAGAGGTATTGCTTTCGTTGCCTCCATTCTGTTCAATTACATTTAATTCAGAAGTTGCTAATGGAACAATGA

upper sequence: GRMZM2G019260_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g48160.1 (Oryza sativa), 3'ss of exon 7
---ttatacacatacataatatccttgtttgatctagttcatgtttacaactagagctcacctagaaaatactatatcttattggtttctgttgtttcttcagATTGAAGCACGCGGTCTCCCTCTTACTCCAGA-----GGCACTGCTTTCATTGCCTCCATTCTCTTCAATCACATTTAACTCAGAGGTTGCTAATGGAACAATGA
    | |   |||   |||  |   |  |  || ||  |||  |||  | | |  |  |  ||   ||||| | || ||| |   ||||    |||||| |||||||||||||| || |||||||| ||||||||      | | |||||||  |||||||||||| | |||| |||||||| ||||| |||||||||||||      
actctctttccatgattaacttatgt-ctgaatataactcacttttggagc-attgtgccgctgttaaataat-taacttgtctttttccaccgtttctccagATTGAAGCACGTGGCCTCCCTCTAACTCCAGACCAGAAGTATTGCTTTCGCTGCCTCCATTCTGTCCAATTACATTTAATTCAGAAGTTGCTAATGGAAT-----
















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|22489427|gb|BU049350.1|BU049350
EST:     TGAACATTACAATTCTTGGATGCAATGATTTCTATTCTTATAGAAAGCAG                         ATTGAAGCACGTGGTCTCCCTCTTACTCCAGAGGCACTGCTTTCATTGCCT
genomic: TGAACATTACAATTCTTGGATGCAATGATTTCTATTCTTATAGAAAGCAGgtgaaccttc ... gtttcttcagATTGAAGCACGCGGTCTCCCTCTTACTCCAGAGGCACTGCTTTCATTGCCT
EST: gi|17970040|gb|BM276808.1|BM276808
EST:     TGAACATTACAATTCTTGGATGCAATGATTTCTATTCTTATAGAAAGCAG                         ATTGAAGCACGTGGTCTCCCTCTTACTCCAGAGGCACTGCTTTCATTGCCT
genomic: TGAACATTACAATTCTTGGATGCAATGATTTCTATTCTTATAGAAAGCAGgtgaaccttc ... gtttcttcagATTGAAGCACGCGGTCTCCCTCTTACTCCAGAGGCACTGCTTTCATTGCCT
EST: gi|78093392|gb|DV521766.1|DV521766
EST:     TGAACATTACAATTCTTGGATGCAATGATTTCTATTCTTATAGAAAGCAG                         ATTGAAGCACGCGGTCTCCCTCTTACTCCAGAGGCACTGCTTTCATTGCCT
genomic: TGAACATTACAATTCTTGGATGCAATGATTTCTATTCTTATAGAAAGCAGgtgaaccttc ... gtttcttcagATTGAAGCACGCGGTCTCCCTCTTACTCCAGAGGCACTGCTTTCATTGCCT
EST: gi|101392374|gb|EB818116.1|EB818116
EST:     TGAACATTACAATTCTTGGATGCAATGATTTCTATTCTTATAGAAAGCAG                         ATTGAAGCACGCGGTCTCCCTCTTACTCCAGAGGCACTGCTTTCATTGCCT
genomic: TGAACATTACAATTCTTGGATGCAATGATTTCTATTCTTATAGAAAGCAGgtgaaccttc ... gtttcttcagATTGAAGCACGCGGTCTCCCTCTTACTCCAGAGGCACTGCTTTCATTGCCT
EST: gi|76285163|gb|DV024731.1|DV024731
EST:     TGAACATTACAATTCTTGGATGCAATGATTTCTATTCTTATAGAAAGCAG                         ATTGAAGCACGCGGTCTCCCTCTTACTCCAGAGGCACTGCTTTCATTGCCT
genomic: TGAACATTACAATTCTTGGATGCAATGATTTCTATTCTTATAGAAAGCAGgtgaaccttc ... gtttcttcagATTGAAGCACGCGGTCTCCCTCTTACTCCAGAGGCACTGCTTTCATTGCCT
EST: gi|88758554|gb|DY542923.1|DY542923
EST:     TGAACATTACAATTCTTGGATGCAATGATTTCTATTCTTATAGAAAGCAG                         ATTGAAGCACGTGGTCTCCCAGTTACTCCAGAGGCACTGCTTTCATTGCCT
genomic: TGAACATTACAATTCTTGGATGCAATGATTTCTATTCTTATAGAAAGCAGgtgaaccttc ... gtttcttcagATTGAAGCACGCGGTCTCCCTCTTACTCCAGAGGCACTGCTTTCATTGCCT
EST: gi|12047185|gb|BF729324.1|BF729324
EST:     TGAACATTACAATTCTTGGATGCAATGATTTCTATTCTTATAGAAAGCAG                         ATTGAAGCACGTGGTCTCCCTCTTACTCCAGAGGCACTGCTTTCATTGCCT
genomic: TGAACATTACAATTCTTGGATGCAATGATTTCTATTCTTATAGAAAGCAGgtgaaccttc ... gtttcttcagATTGAAGCACGCGGTCTCCCTCTTACTCCAGAGGCACTGCTTTCATTGCCT
EST: gi|74234775|gb|DT642689.1|DT642689
EST:     TGAACATTACAATTCTTGGATGCAATGATTTCTATTCTTATAGAAAGCAG                         ATTGAAGCACGCGGTCTCCCTCTTACTCCAGAGGCACTGCTTTCATTGCCT
genomic: TGAACATTACAATTCTTGGATGCAATGATTTCTATTCTTATAGAAAGCAGgtgaaccttc ... gtttcttcagATTGAAGCACGCGGTCTCCCTCTTACTCCAGAGGCACTGCTTTCATTGCCT
EST: gi|71447563|gb|DR828613.1|DR828613
EST:     TGAACATTACAATTCTTGGATGCAATGATTTCTATTCTTATAGAAAGCAG                         ATTGAAGCACGCGGTCTCCCTCTTACTCCAGAGGCACTGCTTTCATTGCCT
genomic: TGAACATTACAATTCTTGGATGCAATGATTTCTATTCTTATAGAAAGCAGgtgaaccttc ... gtttcttcagATTGAAGCACGCGGTCTCCCTCTTACTCCAGAGGCACTGCTTTCATTGCCT
EST: gi|8576971|gb|BE129608.1|BE129608
EST:     TGAACATTACAATTCTTGGATGCAATGATTTCTATTCTTATAGAAAGCAG                         ATTGAAGCACGTGGTCTCCCTCTTACTCCAGAGGCACTGGTTTCATTGCCT
genomic: TGAACATTACAATTCTTGGATGCAATGATTTCTATTCTTATAGAAAGCAGgtgaaccttc ... gtttcttcagATTGAAGCACGCGGTCTCCCTCTTACTCCAGAGGCACTGCTTTCATTGCCT
EST: gi|101390541|gb|EB817205.1|EB817205
EST:     TGAACATTACAATTCTTGGATGCAATGATTTCTATTCTTATAGAAAGCAG                         ATTGAAGCACGTGGTCTCCCTCTTACTCCAGAGGCACTGCTTTCATTGCCT
genomic: TGAACATTACAATTCTTGGATGCAATGATTTCTATTCTTATAGAAAGCAGgtgaaccttc ... gtttcttcagATTGAAGCACGCGGTCTCCCTCTTACTCCAGAGGCACTGCTTTCATTGCCT
EST: gi|71308540|gb|DR790509.1|DR790509
EST:     TGAACATTACAATTCTTGGATGCAATGATTTCTATTCTTATAGAAAGCAG                         ATTGAAGCACGCGGTCTCCCTCTTACTCCAGAGGCACTGCTTTCATTGCCT
genomic: TGAACATTACAATTCTTGGATGCAATGATTTCTATTCTTATAGAAAGCAGgtgaaccttc ... gtttcttcagATTGAAGCACGCGGTCTCCCTCTTACTCCAGAGGCACTGCTTTCATTGCCT
EST: gi|78180064|gb|DV550437.1|DV550437
EST:     TGAACATTACAATTCTTGGATGCAATGATTTCTATTCTTATAGAAAGCAG                         ATTGAAGCACGTGGTCTCCCTCTTACTCCAGAGGCACTGCTTTCATTGCCT
genomic: TGAACATTACAATTCTTGGATGCAATGATTTCTATTCTTATAGAAAGCAGgtgaaccttc ... gtttcttcagATTGAAGCACGCGGTCTCCCTCTTACTCCAGAGGCACTGCTTTCATTGCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactagagctcacctagaaaatactatatcttattggtttctgttgtttcttcagATTGAAGCACGCGGTCTCCCTCTTACTCCAGAGGCACTGCTTTCATTGCCTCCATTCTCTTCAATCACATTTAACTCAGAGGTTGCTAATGGAACAATGA
      agctcac  putative branch site (score: 3)
                                     tttctgttgtttcttc  putative PPT
              tagaaaatactatatc  TA-rich tract