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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgagtgctaaatttacagcagctacaactgtctcagtgagctggaatgcatgtgcctgacttgcggcggcatggttttgaaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGAAGAGTAGCAGAGAAGGCACTAGACCTGCCAATGTATGCCAAGTACAAAG

Basic information

species Zea mays
transcript GRMZM2G027115_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027115_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os10g14814.1 (Oryza sativa), 3'ss of exon 9
gtaattgagtgctaa---atttacagcagctacaactgtctcagtgagctg-gaatgcatgtgcctgacttgcggcggcatggttttgaaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGAAGAGTAGCAGAGAAGGCACTAGACCTGCCAATGTATGCCAAGTACAAAG
|||||| ||  | |    ||||| | | || | | |  || || |     | |||| ||||| |||||||||   ||   |  | |  |||| |  |||||||||||||||| || ||||||||||||||||| ||||||||||||| |||  ||||||||||||| ||  |  | ||| | || |||||||| | ||
gtaatttagaaccagactatttata-ctgcaaaagccatcccactatatggtgaattcatgttcctgacttgtcacgttgt--tatgaaaatgcctagGCCAACTTTCCTTCACTAGAGAGCTTGATAGAGAGGATTCACGAGGATGCAAGGATAGCAGAGAAGGCCCTGAATTTACCATTATACGCCAAGTATACAG

upper sequence: GRMZM2G027115_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os10g32730.2 (Oryza sativa), 3'ss of exon 10
gtaattgagtgctaa---atttacagcagctacaactgtctcagtgagctggaatgcatgtgcctgacttgcggcggcatggttttgaaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGAAGAGTAGCAGAGAAGGCACTAGACCTGCCAATGTATGCCAAGTACAAAG
|||||| ||  | |    ||||| | | ||   | |  || || |        |||||||| |||||||||   ||   |  | |  |||| |  |||||||||||||||| || ||||||||||||||||| ||||||||||||| |||  || |||| ||||| ||  |  | ||| | || |||||||| ||||
gtaatttaggaccagactatttata-ctgcagaagccatcccactatatgttgatgcatgttcctgacttgtcacgttgt--tatgaaaatgcctagGCCAACTTTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCAAGGATATCAGATAAGGCCCTGAATTTACCATTATACGCCAAGTATAAAG
















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|32921306|gb|CF026118.1|CF026118
EST:     TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAG                         GCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGA
genomic: TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAGgtaattgagt ... aaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGA
EST: gi|15426986|gb|BI542808.1|BI542808
EST:     TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAG                         GCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGA
genomic: TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAGgtaattgagt ... aaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGA
EST: gi|211114263|gb|FL244774.1|FL244774
EST:     TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAG                         GCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGA
genomic: TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAGgtaattgagt ... aaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgagctggaatgcatgtgcctgacttgcggcggcatggttttgaaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGAAGAGTAGCAGAGAAGGCACTAGACCTGCCAATGTATGCCAAGTACAAAG
                   gcctgac  putative branch site (score: 3)
                                                ttctc  putative PPT
                                        ttttgaaatt  TA-rich tract