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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcaacatacattcgatttatttgtattaattgtgcattttatagtcttcaaatgttttctagatcttatgatctcatagacatatctaggtatttagaaccacaattgcttctgttttgtagCATCACTTGCTCCAAGTTTATCAGATGATTTGTTAGCAAAGGCAACTTTGCAAGTTGTCCAGTTGCTGAAAAATAGAGGTGCAAAATCTGAAATTACCCG

Basic information

species Zea mays
transcript GRMZM2G168629_T04
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168629_T05 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g07340.1 (Oryza sativa), 3'ss of exon 5
gtaagtcaacatacattcgatttatttgtattaattgtgcattttatagtcttcaaatgttttctagatcttatgatctcatagacatatctaggtatttagaaccacaattgcttctgttttgtagCATCACTTGCTCCAAGTTTATCAGATGATTTGTTAGCAAAGGCAACTTTGCAAGTTGTCCAGTTGCTGAAAAATAGAGGTGCAAAATCTGAAATTACCCG
                        |  ||   | |  ||   | |    |  |    |||||| |   |    |||  |  || |  | | ||   | | |     |  || |||  | || |  ||||||||||||| || || | || |||||||| ||||| |||||||||||  | |||||||||||||| ||||||||| ||||||||||||||||| ||||
-----------------------gtaagtcgaactgatgtgctgtgctattatatgttgttttttgcgtggcttgagtttgtaaaggtgttta--cactgactgttaacat-gctatttttcttcagCATCACTTGCTGCATGTCTGTCTGATGATTTATTAGCCAAGGCAACTTTTGAGGTTGTCCAGTTGCTTAAAAATAGAAGTGCAAAATCTGAAATTGCCCG

upper sequence: GRMZM2G168629_T05 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 5
gtaagtcaacatacattcgatttatttgtattaattgtgcattttatagtcttcaaatgttttctagatcttatgatctcatagacatatctaggtatttagaaccacaattgcttctgttttgtagCATCACTTGCTCCAAGTTTATCAGATGATTTGTTAGCAAAGGCAACTTTGCAAGTTGTCCAGTTGCTGAAAAATAGAGGTGCAAAATCTGAAATTACCCG
                     | | | | | | || |||| | |  |  | |      ||||| | | |    |||  |  || |  | | ||   | | |     |  || |||  | || |  ||||||||||||| || || | || |||||||| ||||| |||||||||||  | |||||||||||||| ||||||||| ||||||| ||||||||| ||||
--------------------gtaagtcgaactgat-gtgc-tgtgctgttatatgttggttttttgggtggcttgaatttgtaaaggtgttta--cactgactgttaacat-gctatttttcttcagCATCACTTGCTGCATGTCTGTCTGATGATTTATTAGCCAAGGCAACTTTTGAGGTTGTCCAGTTGCTTAAAAATAGAAGTGCAAAGTCTGAAATTGCCCG

upper sequence: GRMZM2G168629_T05 (Zea mays), 3'ss of exon 5
lower sequence: Vv12s0035g01840.t01 (Vitis vinifera), 3'ss of exon 6
gtaagtcaacatacattcgatttatttgtattaattgtgcattttatagtcttcaaatgttttctagatcttatgatctcatagacatatctaggt-atttagaaccacaattgcttctgttttgtagCATCACTTGCTCCAAGTTTATCAGATGATTTGTTAGCAAAGGCAACTTTGCAAGTTGTCCAGTTGCTGAAAAATAGAGGTGCAAAATCTGAAATTACCCG
                            |  |       ||  |   | | | ||| | |  | ||    | |  || |   || || |   |||| || ||     |||| |   | |  | |  |||||| |||||  ||||||| |||||||||||||| ||||| |||||| |  | ||||||| |    ||| || ||  || | |||| ||||||| |||||
--------------------------catggtgccccctcaaat-ggaatttgcaactttgatataagattgaaaattttg-agccagagaaaggtgatataactgaacaaatttctttcatcttcagCATCTCTTGCATCAAGTTTGTCAGATGATTTGTTGGCAAAAGCAACTGTTGAGGTTGTCCGGAACTTGAGAAGTAAGGGAGTAAAACCTGAAATGACCCG

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|149102408|gb|EE188204.2|EE188204
EST:     ATTGGGTTCTAACCCAGCAAGCGTCAGAAAGAAATCTATTTCTTGCATTG                         CATCACTTGCTCCAAAGTT-ATCAGATGATTTGTTAGCCAAGGCCACTTT
genomic: ATTGGGTTCTAACCCAGCAAGCGTCAGAAAGAAATCTATTTCTTGCATTGgtaagtcaac ... tgttttgtagCATCACTTGCTCCAA-GTTTATCAGATGATTTGTTAGCAAAGGCAACTTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgatctcatagacatatctaggtatttagaaccacaattgcttctgttttgtagCATCACTTGCTCCAAGTTTATCAGATGATTTGTTAGCAAAGGCAACTTTGCAAGTTGTCCAGTTGCTGAAAAATAGAGGTGCAAAATCTGAAATTACCCG
                                         cttctgtttt  CT-rich tract
                       tatttagaa  TA-rich tract