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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctgaatttatatgttgattcttctgtatagtttactctgcttgttgtgcaagggttaacctgagtatttaacaaaaatgcttctctgcatacacacagGGACATGGCTTTCGCACAGAACTTATATCCATGATTTTGGATTTAAAACCACGATTCTTGAGATTTCCTG

Basic information

species Zea mays
transcript GRMZM2G077299_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077299_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 6
------------------------------------------------tgctgaatttatatgttgattcttctgtatagtttactctg-----cttgttgtgcaagggttaacctgagtatttaacaaaaatgcttctctgcatacacacagGGACATGGCTTTCGCACAGAACTTATATCCATGATTTTGGATTTAAAACCACGATTCTTGAGATTTCCTG
                                                |||        | |  || |   | |||||||| ||   |       |   | | || ||| |      |||  ||  ||| | | ||| |    | ||| |||||||||||| |||||||||||||||||||| ||||| ||||| ||||||||||||||||||||||| ||||
gtacattatattttgttgtcaaacttcattactggaaaaggaaaacgatgccatgggctttttatgctatctatgtatagtgtatgataacactttaagtcttcatgggctttttcaagtgcttc-caacatttctttt----acacatacagGGACATGGTTTTCGCACAGAACTTATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTG

upper sequence: GRMZM2G077299_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 6
--------------------------------------------------tgctgaatttatatgttgattcttctgtatagtttactctgcttgttgtgcaagggttaacctgagtatttaacaaaaatgcttctctgcatacacacagGGACATGGCTTTCGCACAGAACTTATATCCATGATTTTGGATTTAAAACCACGATTCTTGAGATTTCCTG
                                                  |  || | || |   | | |   ||| |||||| ||   | |   ||         |   | |       |      ||   |||| |  | |||  ||||||||||| |||||||||||||| ||||| ||||| ||||| ||||||||||||||||||||||| ||||
gtacattatattttgttatcaaacttcgttactggaaaaggaaaacgatatcatggactttttcat-gctatctctatatagtgtatgataccacttaaatcttcatgggctttttctactgcttccaacatttcttt-tacacattcagGGACATGGTTTTCGCACAGAACTAATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTG
















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|71441725|gb|DR822775.1|DR822775
EST:     GAGTTGTCTGGTTTGATCAAGTATCACTCATGCCTGAAGACACATACAAG                         GGACATGGCTTTCGCACAGAACTTATATCCATGATTTTGGATTTAAAACCA
genomic: GAGTTGTCTGGTTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgtatattaca ... atacacacagGGACATGGCTTTCGCACAGAACTTATATCCATGATTTTGGATTTAAAACCA
EST: gi|71769433|gb|DR967370.1|DR967370
EST:     GAGTTGTCTGGTTTGATCAAGTATCACTCATGCCTGAAGACACATACAAG                         GGACATGGCTTTCGCACAGAACTTATATCCATGATTTTTGGATTTAAAAC
genomic: GAGTTGTCTGGTTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgtatattaca ... atacacacagGGACATGGCTTTCGCACAGAACTTATATCCATGATTTT-GGATTTAAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgcaagggttaacctgagtatttaacaaaaatgcttctctgcatacacacagGGACATGGCTTTCGCACAGAACTTATATCCATGATTTTGGATTTAAAACCACGATTCTTGAGATTTCCTG
                      atttaac  putative branch site (score: 3)
                   agtatttaacaaaaat  TA-rich tract