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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgattagtccaaaagtgcatattggatgtgttatcatatttcatattacaatcatgaccaaattcctgttctgcagTCTGGTCATAACATTGAAAAAGTCAGGGAAAAAATGGGGGATCTGATAAAGCAAATGGTCAACATTTATTCTCTTCCCAAATTACTTCCCTATATTCTTG

Basic information

species Zea mays
transcript GRMZM2G009849_T02
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 36
-------------------------------------------------------------------------------------------gtatgattagtccaaaagtgcatattggatgtgt---tatcatatttcatattacaatcatgaccaaat---tcctgttctgcagTCTGGTCATAACATTGAAAAAGTCAGGGAAAAAATGGGGGATCTGATAAAGCAAATGGTCAACATTTATTCTCTTCCCAAATTACTTCCCTATATTCTTG
                                                                                             ||  ||| |    |  |||   |   || | |   ||| || ||  || ||  | ||||  | |||    | ||||  |||||||||| || ||||| ||||||||||| ||||||||||| || ||||||||||||||||||||||| ||||||||||| ||| | || || || ||| | |
gtacatagagtgcacaaatattgattagtgtaatcctgaatcttcccatcagaaacacaggctggagaagtatattcttcagattgatcgaacatatttatttgttatatgccattgcaatctttgcctataattttaaattttcgattcattcctaaacaactgctgtattgcagTCTGGCCACAACATCGAAAAAGTCAGAGAAAAAATGGGAGAGCTGATAAAGCAAATGGTCAACATCTATTCTCTTCCAAAACTTCTCCCATACATTTTGG

upper sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 18
lower sequence: AT2G35630.1 (Arabidopsis thaliana), 3'ss of exon 37
------------------------------------------------gtatgatta--gtccaaaagtgcatattggatgtgttatcatatttcatattacaatcatgaccaaattcctgttct----gcagTCTGGTCATAACATTGAAAAAGTCAGGGAAAAAATGGGGGATCTGATAAAGCAAATGGTCAACATTTATTCTCTTCCCAAATTACTTCCCTATATTCTTG
                                                  || |||   ||  |    |   | || ||       |  |  ||||   |    | ||    || | | ||| ||    |||||  || ||||||||||||||||| || ||||||||| |||| ||||| ||||| ||  |  |    |||||| |    ||      |||||||||| | |
gttaggcatctgatattaatccaatttcctatggtgttggcctctttctaatcattcccgtttatctttctgttttagaaaaagattggtgcttcag--tgtctttatatttaactccttgtccttggtgcagTTGGGGCATAACATTGAAAAAGTAAGAGAAAAAATGCGGGAGCTGATGAAGCAGATCATTCAGGCATATTCTGTAGGAAAGACGTATCCCTATATTTTGG

upper sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 18
lower sequence: EFJ11209 (Selaginella moellendorffii), 3'ss of exon 35
gtatgattagtccaaaagtgcatattggatgtgttatcatatttcata-ttacaatcatgaccaaattcctgttctgcagTCTGGTCATAACATTGAAAAAGTCAGGGAAAAAATGGGGGATCTGATAAAGCAAATGGTCAACATTTATTCTCTTCCCAAATTACTTCCCTATATTCTTG
                                || ||     || ||  || | |   |  |  |     | | ||||||||||||||||| |||||||| ||  ||||||| ||| |||| ||||| |  |  ||      ||| ||  ||    | ||  || || | || |||   |
--------------------------------gtaattgacatttatgcttgcgagtttagctgagcatgtttcctgcagTCTGGTCATAATATTGAAAAGGTTCGGGAAAAGATGCGGGAGCTGATGAGACTCATCTGTTGCATCTACCCTGCATCAAAGCTATTTACGTACATTTGCG

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|28909669|gb|CB331043.1|CB331043
EST:     TGTTGACAGAAGCTGAAGCTGCAATTTTTCTTCCTTGCCTCATAGAGAAG                         TCTGG-CATAAC-TTGAAAAAGTCAGGGAAAAAATGGGGGATCTGATAAAG
genomic: TGTTGACAGAAGCTGAAGCTGCAATTTTTCTTCCTTGCCTCATAGAGAAGgtatgattag ... tgttctgcagTCTGGTCATAACATTGAAAAAGTCAGGGAAAAAATGGGGGATCTGATAAAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggatgtgttatcatatttcatattacaatcatgaccaaattcctgttctgcagTCTGGTCATAACATTGAAAAAGTCAGGGAAAAAATGGGGGATCTGATAAAGCAAATGGTCAACATTTATTCTCTTCCCAAATTACTTCCCTATATTCTTG
                                         ttcctgttct  CT-rich tract
         ttatcatatttcatat  TA-rich tract