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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaataaaaattatttttatgcatatatttattaaaaaaggtacgacaggagaaagaatatgatttgatttttgtttatttaaatagGTGAGGCGGCTCTCGTCATGTGAAACAATGGGATCAGCTACTACAATATGCAGTGATAAGACAGGAACCCTTACATTGAATAAG

Basic information

species Zea mays
transcript GRMZM2G132712_T01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G132712_T03 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os08g40530.1 (Oryza sativa), 3'ss of exon 1
gtaaataaaaatt--atttttatgcatatatttattaaaaaaggtacgacaggagaaagaatatgatttgatttttgtttatttaaatagGTGAGGCGGCTCTCGTCATGTGAAACAATGGGATCAGCTACTACAATATGCAGTGATAAGACAGGAACCCTTACATTGAATAAG
|||||  ||||||  ||| ||||||| ||  |    | |  | | | |    || ||   | ||   |  |||| ||| ||        |||||| || ||||| || || |||||||||||||| || |||||||||||||||||||| ||||| || ||||| |||||||||
gtaaaagaaaattctattcttatgca-attctagaaagatgatgcatgttctgaaaattgacattgctccatttctgtcta--------gGTGAGACGTCTCTCATCCTGCGAAACAATGGGATCTGCAACTACAATATGCAGTGATAAAACAGGGACACTTACCTTGAATAAG

upper sequence: GRMZM2G132712_T03 (Zea mays), 3'ss of exon 17
lower sequence: EFJ25508 (Selaginella moellendorffii), 3'ss of exon 14
gtaaataaaaattatttttatgcatatatttattaaaaaaggtacgacaggagaaagaatatgatttgatttttgtttatttaaatagGTGAGGCGGCTCTCGTCATGTGAAACAATGGGATCAGCTACTACAATATGCAGTGATAAGACAGGAACCCTTACATTGAATAAG
                        ||  |    |||     ||        || | |  | |||||  |||||||||       | ||||  | |   |  |  | || |||||||||||||| || || || || |||||||||||||| |||||||| || |||||  ||
-----------------------gtaagtcccctaa-----gtgttttgtaagtatggttttgattc-atttttgtt-------acagGTCCGTCATTTGGCTGCCTGCGAAACAATGGGATCTGCAACGACTATCTGCAGTGATAAGACCGGAACCCTGACCTTGAACCAG
















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|71443249|gb|DR824299.1|DR824299
EST:     GCTTGCATATTCCATGAAAAAGATGATGCGAGACAAAGCTCTG                         GTGAGGCGGCTCTCGTCATGTGAAACAATGGGATCAGCTACTACAATATGC
genomic: GCTTGCATATTCCATGAAAAAGATGATGCGAGACAAAGCTCTGgtaaataaaa ... atttaaatagGTGAGGCGGCTCTCGTCATGTGAAACAATGGGATCAGCTACTACAATATGC
EST: gi|31350151|gb|CD434508.1|CD434508
EST:     GCTTGCATATTCCATGAAAAAGATGATGCGAGACAAAGCTCTG                         GTGAGGCGGCTCTCGTCATGTGAAACAATGGGATCAGCTACTACAATATGC
genomic: GCTTGCATATTCCATGAAAAAGATGATGCGAGACAAAGCTCTGgtaaataaaa ... atttaaatagGTGAGGCGGCTCTCGTCATGTGAAACAATGGGATCAGCTACTACAATATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaaaaggtacgacaggagaaagaatatgatttgatttttgtttatttaaatagGTGAGGCGGCTCTCGTCATGTGAAACAATGGGATCAGCTACTACAATATGCAGTGATAAGACAGGAACCCTTACATTGAATAAG
                              atttgat  putative branch site (score: 5)
                                          tttattt  putative PPT
                  agaaagaatatgattt  TA-rich tract