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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtattgccatgtgggtagcacttctttctcaatagcttgattgtagtctcatattctcatttgctcaacagACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAACACCCATCTTGCATCAAACACATTCCTTGTTGGGCATTCAGTGACACTTG

Basic information

species Zea mays
transcript GRMZM2G029559_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G029559_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g12800.1 (Oryza sativa), 3'ss of exon 6
gtatgtattgccatgtgggtagcact---tctttctcaatagcttgattgtagtctcatattctcatttgctcaacagACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAACACCCATCTTGCATCAAACACATTCCTTGTTGGGCATTCAGTGACACTTG
||| |||| | || ||||||| |  |   |  | ||   ||||    ||||  ||| || || |  | |||  ||||||  || ||| |||| |||||||||||||||||| |||| ||| |||| ||||| || |||||||||||||||| ||||||||| ||||||||||| ||||
gtaagtatggtcaagtgggtatcgttgtgttctccttgttagca-atttgtgatctaatcttgtt-tctgcctaacagAGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAACACACACCTTGCATCAAACACATACCTTGTTGGCCATTCAGTGACTCTTG

upper sequence: GRMZM2G029559_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g12794.3 (Oryza sativa), 3'ss of exon 5
gtatgtattgccatgtgggtagcacttctttctcaatagcttga----ttgtagtctcatattctcatttgctcaacagACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAACACCCATCTTGCATCAAACACATTCCTTGTTGGGCATTCAGTGACACTTG
||| |||| | || ||||||  ||     || ||  |   |       |||| |||| || || |  | ||| |||||||  || ||| |||| |||||||||||||||||| |||| ||| |||| ||||| || |||||||||||||||| ||||||||| ||||| ||||| ||||
gtaagtatggtcaagtgggtgtcatagtgttttccttgtgtcagcaatttgttgtctaatcttatt-tctgcccaacagAGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAACACACACCTTGCATCAAACACATACCTTGTTGGCCATTCGGTGACTCTTG
















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|32823439|gb|CD963161.1|CD963161
EST:     TGGAAAGTGGTTGGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTG                         ACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC
genomic: TGGAAAGTGGTT-GTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTGgtatgtattg ... tgctcaacagACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC
EST: gi|211221751|gb|FL290080.1|FL290080
EST:     TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTG                         ACAGAAGAATCAG
genomic: TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTGgtatgtattg ... tgctcaacagACAGAAGAATCAG
EST: gi|7216701|gb|AW562823.1|AW562823
EST:     TTGGAAAGTGGTTGNACCCACGTATGGGGTTTTATCCCTATGCTGCTGTG                         ACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC
genomic: TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTGgtatgtattg ... tgctcaacagACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC
EST: gi|32807718|gb|CD959952.1|CD959952
EST:     TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTG                         ACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC
genomic: TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTGgtatgtattg ... tgctcaacagACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC
EST: gi|213175370|gb|FM190159.1|FM190159
EST:     TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTG                         ACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC
genomic: TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTGgtatgtattg ... tgctcaacagACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcacttctttctcaatagcttgattgtagtctcatattctcatttgctcaacagACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAACACCCATCTTGCATCAAACACATTCCTTGTTGGGCATTCAGTGACACTTG
                  gcttgat  putative branch site (score: 5)
                                     ttctcattt  putative PPT
                                tcatatt  TA-rich tract