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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctatatcttggagatgggtggcactgtttctaatcaactctggttgtaacatgaatatctagtgttctacaatgttttcctttttctttttcagTGCTACACTTCTGCCAAACCTGTAATATTAGAACCTGTGATGAAGGTGGAACTCAAATTTCCAACTGAGTTTCAGGGCACAGTAACTGGTGATATGAACA

Basic information

species Zea mays
transcript GRMZM2G056393_T02
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os03g36780.1 (Oryza sativa), 3'ss of exon 16
gtgagctatatcttgg--agatgggtggcactgtttctaatcaactctggttgtaa---catgaatat-ctagtgttctacaatgtttt---cctttt-----tcttttt--cagTGCTACACTTCTGCCAAACCTGTAATATTAGAACCTGTGATGAAGGTGGAACTCAAATTTCCAACTGAGTTTCAGGGCACAGTAACTGGTGATATGAACA
|||||   | |  |      |      ||| | |||| | | |||  ||    ||     ||||| || | | | || || | || |||   ||||||     || ||||  ||||| ||  || |||| | |||||||||||| ||||| |||||||| |||||||| ||| |||| || ||||| |||||||| ||||| ||||| |||||||
gtgagacttgttatatttgtacaatcagcattctttcaagtaaacagtgacattagagtgatgaaaatacaaatcttataaattgatttgctccttttgtctctccttttgccagTGTTATGCTGCTGCTAGACCTGTAATATTGGAACCAGTGATGAAAGTGGAACTAAAAGTTCCTACAGAGTTCCAGGGCACGGTAACCGGTGACATGAACA
















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|32932818|gb|CF037630.1|CF037630
EST:     ATTCCAGTGAACTTGCTTTTAAGCTAGCTGCTATCTATGCTTTTCGACAG                         TGCTACACTTCTGCCAAACCTGTAATATTAGAACCTGTGATGAAGGTGGAA
genomic: ATTCCAGTGAACTTGCTTTTAAGCTAGCTGCTATCTATGCTTTTCGACAGgtgagctata ... tctttttcagTGCTACACTTCTGCCAAACCTGTAATATTAGAACCTGTGATGAAGGTGGAA
EST: gi|211184463|gb|FL030548.1|FL030548
EST:     ATTCCAGTGAACTTGCTTTTAAGCTAGCTGCTATCTATGCTTTTCGACAG                         TGCTACACTTCTGCCAAACCTGTAATATTAGAACCTGTGATGAAGGTGGAA
genomic: ATTCCAGTGAACTTGCTTTTAAGCTAGCTGCTATCTATGCTTTTCGACAGgtgagctata ... tctttttcagTGCTACACTTCTGCCAAACCTGTAATATTAGAACCTGTGATGAAGGTGGAA
EST: gi|6194594|gb|AW146698.1|AW146698
EST:     ATTCCAGTGAACTTGCTTTTAAGCTAGCTGCTATCTATGCTTTTCGACAG                         TGCTACACTTCTGCCAAACCTGTAATATTAGAACCT
genomic: ATTCCAGTGAACTTGCTTTTAAGCTAGCTGCTATCTATGCTTTTCGACAGgtgagctata ... tctttttcagTGCTACACTTCTGCCAAACCTGTAATATTAGAACCT
EST: gi|6020648|gb|AW065681.1|AW065681
EST:     ATTCCAGTGAACTTGCTTTTAAGCTAGCTGCTATCTATGCTTTTCGACAG                         TGCTACACTTCTGCCAAACCTGTAATATTAGAACCTGTGATGAAGGTGGAA
genomic: ATTCCAGTGAACTTGCTTTTAAGCTAGCTGCTATCTATGCTTTTCGACAGgtgagctata ... tctttttcagTGCTACACTTCTGCCAAACCTGTAATATTAGAACCTGTGATGAAGGTGGAA
EST: gi|33093919|gb|CF053913.1|CF053913
EST:     ATTCCAGTGAACTTGCTTTTAAGCTAGCTGCTATCTATGCTTTTCGACAG                         TGCTACACTTCTGCCAAACCTGTAATATTAGAACCTGTGATGAAGGTGGAA
genomic: ATTCCAGTGAACTTGCTTTTAAGCTAGCTGCTATCTATGCTTTTCGACAGgtgagctata ... tctttttcagTGCTACACTTCTGCCAAACCTGTAATATTAGAACCTGTGATGAAGGTGGAA
EST: gi|69351603|gb|DR452190.1|DR452190
EST:     ATTCCAGTGAACTTGCTTTTAAGCTAGCTGCTATCTATGCTTTTCGACAG                         TGCTACACTTCTGCCAAACCTGTAATATTAGAACCTGTGATGAAGGTGGAA
genomic: ATTCCAGTGAACTTGCTTTTAAGCTAGCTGCTATCTATGCTTTTCGACAGgtgagctata ... tctttttcagTGCTACACTTCTGCCAAACCTGTAATATTAGAACCTGTGATGAAGGTGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggttgtaacatgaatatctagtgttctacaatgttttcctttttctttttcagTGCTACACTTCTGCCAAACCTGTAATATTAGAACCTGTGATGAAGGTGGAACTCAAATTTCCAACTGAGTTTCAGGGCACAGTAACTGGTGATATGAACA
    ttgtaac  putative branch site (score: 2)
                         ttctacaatgttttcc  putative PPT
                                         tttttcttttt  TA-rich tract