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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcgaaggccgaatgcagttgagcacacagcttcttgaacatggcttgttctgaaaccttgatgggcaatcgatctcttgtttgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCGAGGGTGCTGTGCTCGACGAACCAGCCCTGCTTCCTGAGCCACGAGGACG

Basic information

species Zea mays
transcript GRMZM2G080375_T06
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G080375_T04 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g09570.1 (Oryza sativa), 3'ss of exon 10
---------------------------gtaagtcg--aaggccgaatgcagttgagcacacagcttcttgaacatggcttgttctga-aaccttgatg--ggcaatcgatctcttgtttgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCGAGGGTGCTGTGCTCGACGAACCAGCCCTGCTTCCTGAGCCACGAGGACG
                            | | ||   |  |   | | ||||| ||  |    |  |    |     | | | |||| || || ||    |  | ||   |  || | | ||||| ||||| |||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||
gtaagtccagaacactctttttcaatgatcaatctttagtgttcagttcagttcagttcttcacaccagacatcaaccatatcctgataatctggacactgaaactccggcgatt-tctacagAGAATCACGGAGAAGCAGAACAAGGTGGTGATCACGGACAGGATGTGGGCGAGGGTGCTGTGCTCGACGAACCAGCCATGCTTCCTGAGCCACGAGGACG

upper sequence: GRMZM2G080375_T04 (Zea mays), 3'ss of exon 10
lower sequence: AT4G29220.1 (Arabidopsis thaliana), 3'ss of exon 12
gtaagtcgaagg-ccgaatgcagttgagcacacagcttcttgaacatggcttgttctgaaaccttgatgggcaatcgatctcttgtt-tgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCGAGGGTGCTGTGCTCGACGAACCAGCCCTGCTTCCTGAGCCACGAGGACG
|| ||||  ||| || ||| |   |       || ||  |  |          ||  | || | | ||     || | |    | || || |||||||||| ||||| |||||||||||||||||||| ||| | |||||||||||| |  |||  ||||||||||| ||  | ||| |||  || |  ||| 
gtgagtctcaggaccaaatactcatacctgagcatctcttacatttatatcaatttgggaatcctaataa--catggtttgaatattgtgtagAGGATCACGGAGAAACAGAACAAGGTGGTGATCACTGACAGAATGTGGGCGAGGCTTTTGTCTTCGACGAACCAACCGAGTTTCATGAAGCAAGCTGACA

upper sequence: GRMZM2G080375_T04 (Zea mays), 3'ss of exon 10
lower sequence: AT4G26270.1 (Arabidopsis thaliana), 3'ss of exon 12
----gtaa-gtcgaaggccg--aatgcagttgagcacacagcttcttgaacatggc--ttgttctgaaaccttgatgggcaatcgatctcttgtttgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCGAGGGTGCTGTGCTCGACGAACCAGCCCTGCTTCCTGAGCCACGAGGACG
     ||  |||    |     |   | ||| |   ||          | |||     |  |  |   || || |||   |    || | |   || |||||||| || ||||| |||||| | ||||||||||| ||| |||||||||| ||| | || |  ||||| ||||||||  | ||| || ||| | | || |
catcatactgtcatcagttatcatcaccgttaaagtcatcatcctcatatcatcataatcatagtatcacttttatgtaaacatcatttttatgttacagAGGATAACGGAGAAACAGAACCATGTGGTGATCACAGACAGGATGTGGGCAAGGCTACTCTCTTCGACAAACCAGCCGAGTTTCTTGGGCCCCAAAGATG

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|74234372|gb|DT642286.1|DT642286
EST:     GCTTCACGGTCGCTCCGGTCAACGGCAGGCACGCCTACATCCCGTTTTAT                         AGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCG
genomic: GCTTCACGGTCGCTCCGGTCAACGGCAGGCACGCCTACATCCCGTTCTATgtaagtcgaa ... ttgtttgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgaacatggcttgttctgaaaccttgatgggcaatcgatctcttgtttgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCGAGGGTGCTGTGCTCGACGAACCAGCCCTGCTTCCTGAGCCACGAGGACG
                        ccttgat  putative branch site (score: 5)
                                         tctcttgttt  putative PPT