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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcctcttactcctgttggaagtttggctttgtaaaattttctatccgcatgtgtttgacacttgccttggaatagGATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAG

Basic information

species Zea mays
transcript GRMZM2G109039_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109039_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g48964.1 (Oryza sativa), 3'ss of exon 3
gtttgcctcttactcctgttggaagtttggctttgtaaaattttctatccgcatgtgtttgacacttg---ccttggaatagGATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAG
         |   |||| ||| ||| |   || |||| || | ||| |  |  |||| |||||| |||   | |  | | |||| |||||||| || || ||||| ||||| || ||||| ||||| |||||||||||||| || ||||||||||| ||||||||||||
--------gtgcgtccttttgaaagctca-ctgtgtagaactgtctgt--gtttgtgcttgacagttgacacttgtgtacagGAATGCAAACCGACTGAAAAAGGCGGGATGTATTATGAATTTAGGCGAAATACTAGATCAGTAAAATCAACTATACTACATTTTCAG
















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|5510853|gb|AI857237.1|AI857237
EST:     AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT
genomic: AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT
EST: gi|20301188|gb|BQ164131.1|BQ164131
EST:     AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT
genomic: AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT
EST: gi|20301181|gb|BQ164124.1|BQ164124
EST:     AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT
genomic: AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT
EST: gi|20300911|gb|BQ163854.1|BQ163854
EST:     AAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAACCANCAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT
genomic: AAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT
EST: gi|20300918|gb|BQ163861.1|BQ163861
EST:     AAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT
genomic: AAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttggctttgtaaaattttctatccgcatgtgtttgacacttgccttggaatagGATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAG
                                gtttgac  putative branch site (score: 4)
                                        cttgcctt  CT-rich tract
       tttgtaaaattttcta  TA-rich tract