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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcttgtgctctttgtttgcttttttgctgtaagaacatttgtggaacaggttgtcaagttcgcctctcacaacctttttcctatttacactttttgcagGTGCTGATGTGGCTGGTGGTAGGGGTTTCTATTTAAAGGATGAAGGTGTCCTCCTTAACCTGGCATTGATAAATTTTGGGCTAGCCTTTCTGAGAAAACG

Basic information

species Zea mays
transcript GRMZM2G172101_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G172101_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g37837.1 (Oryza sativa), 3'ss of exon 4
tgcttgtgctctttgtttgcttttttgctgtaagaacatttgtggaacaggttgtcaagttcgcct-ctcacaacctttttcctattta--cactttttgcagGTGCTGATGTGGCTGGTGGTAGGGGTTTCTATTTAAAGGATGAAGGTGTCCTCCTTAACCTGGCATTGATAAATTTTGGGCTAGCCTTTCTGAGAAAACG
   ||        | |||| | | ||     ||   || |  ||  |    ||       || |    | | |   |  || ||   ||  || ||||||||||||||||||| || ||||| ||||||| |||||||||||||||||||||||| || ||| ||||||||||||||||||| || || ||||||||||| ||
---ttaaaaatgatctttgatctattcacagaatcccactgttgccattttttcctggtctctcaaatttataggttacttactgcctatccaatttttgcagGTGCTGATGTAGCAGGTGGAAGGGGTTACTATTTAAAGGATGAAGGTGTCCTACTGAACTTGGCATTGATAAATTTTGGACTCGCTTTTCTGAGAAAGCG

upper sequence: GRMZM2G172101_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g10190.1 (Oryza sativa), 3'ss of exon 4
tgcttgtgctctttgtttgcttttttgctgtaagaacatttgtggaacaggttgtcaagttcgc-ctctcacaacctttttcctattta--cactttttgcagGTGCTGATGTGGCTGGTGGTAGGGGTTTCTATTTAAAGGATGAAGGTGTCCTCCTTAACCTGGCATTGATAAATTTTGGGCTAGCCTTTCTGAGAAAACG
       | |||||| |  | | ||  | | ||   || |  ||  |    ||       || | |  | | |   |  || ||   ||  || |||||||||||| |||||| || ||||| ||||||| ||||||||||||||||||||| || || ||| ||||||||||||||||||| || || ||||||||||| ||
-aaaaaggatctttgatc-cctattcacag-aatcccactgttgccatttttttctgttctctcacatttataggttacttactgcctatccaatttttgcagGTGTTGATGTAGCAGGTGGAAGGGGTTACTATTTAAAGGATGAAGGTGTGCTACTGAACTTGGCATTGATAAATTTTGGACTTGCTTTTCTGAGAAAGCG
















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|211021857|gb|FL368551.1|FL368551
EST:     GAATCACGTGGACCTTTGCAGGATGCTTGACATTGTCGCATTGGAGAAGG                         GTGCTGATGTGGCTGGTGGTAGGGGTTTCTATTTAAAGGAT
genomic: GAATCACGTGGACCTTTGCAGGATGCTTGACATTGTCGCATTGGAGAAGGgtatatgctc ... ctttttgcagGTGCTGATGTGGCTGGTGGTAGGGGTTTCTATTTAAAGGAT
EST: gi|148937654|gb|EC881846.2|EC881846
EST:     GAATCACGTGGACCTTTGCAGGATGCTTGACATTGTCGCATTGGAGAAGG                         GTGCTGATGTGGCTGGTGGTAGGGGTTTCTATTTAAAGGATGAAGGTGTCC
genomic: GAATCACGTGGACCTTTGCAGGATGCTTGACATTGTCGCATTGGAGAAGGgtatatgctc ... ctttttgcagGTGCTGATGTGGCTGGTGGTAGGGGTTTCTATTTAAAGGATGAAGGTGTCC
EST: gi|31351150|gb|CD435507.1|CD435507
EST:     GAATCACGTGGACCTTTGCAGGATGCTTGACATTGTCGCATTGGAGAAGG                         GTGCTGATGTGGCTGGTGGTAGGGGTTTCTATTTAAAGGATGAAGGTGTCC
genomic: GAATCACGTGGACCTTTGCAGGATGCTTGACATTGTCGCATTGGAGAAGGgtatatgctc ... ctttttgcagGTGCTGATGTGGCTGGTGGTAGGGGTTTCTATTTAAAGGATGAAGGTGTCC
EST: gi|37421408|gb|CF648402.1|CF648402
EST:     GAATCACGTGGACCTTTGCAGGATGCTTGACATTGTCGCATTGGAGAAGG                         GTGCTGATGTGGCTGGTGGTANGGGTTTCTATTTAAAGGATGAAGGTGTCC
genomic: GAATCACGTGGACCTTTGCAGGATGCTTGACATTGTCGCATTGGAGAAGGgtatatgctc ... ctttttgcagGTGCTGATGTGGCTGGTGGTAGGGGTTTCTATTTAAAGGATGAAGGTGTCC
EST: gi|148931370|gb|EC874280.2|EC874280
EST:     GAATCACGTGGACCTTTGCAGGATGCTTGACATTGTCGCATTGGAGAAGG                         GTGCTGATGTGGCTGGTGGTAGGGGTTTCTATTTAAAGGATGAAGGTGTCC
genomic: GAATCACGTGGACCTTTGCAGGATGCTTGACATTGTCGCATTGGAGAAGGgtatatgctc ... ctttttgcagGTGCTGATGTGGCTGGTGGTAGGGGTTTCTATTTAAAGGATGAAGGTGTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacaggttgtcaagttcgcctctcacaacctttttcctatttacactttttgcagGTGCTGATGTGGCTGGTGGTAGGGGTTTCTATTTAAAGGATGAAGGTGTCCTCCTTAACCTGGCATTGATAAATTTTGGGCTAGCCTTTCTGAGAAAACG
                   ctctcac  putative branch site (score: 3)
                            cctttttcctatttac  putative PPT
                                     tatttacacttttt  TA-rich tract