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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaaaacggatttgcagctctgagtaggggcaaccatgcaattccccctttccatttcattttgtatggtgggtaaccttattttgttcatgtttgacagCTTAAACTGGCAGCACCAGCTTTGCAAGAACCCTAGACCTAATCCTGACATCAAGACCCTTTTTGTTGATCATTCATGTGGACAACCGAATGGTGCACGT

Basic information

species Zea mays
transcript GRMZM2G030422_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030422_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g14980.2 (Oryza sativa), 3'ss of exon 4
taaaaacg-gatttgcagctctgagtaggggcaaccatgcaattccccctttccatttcattttgtatggtgggtaaccttattttgttcatgtttgacagCTTAAACTGGCAGCACCAGCTTTGCAAGAACCCTAGACCTAATCCTGACATCAAGACCCTTTTTGTTGATCATTCATGTGGACAACCGAATGGTGCACGT
 |  | |  | | |  |  | ||| |      |    |  ||||     | |  |       |  |     |          ||||  | || | |  |||||||||||||||||||||||||||||| || ||||||||||| ||||| |||||||| || |||||||||||||| ||||||||||| |||||||| |||
-agcaccatgctgtatacttttgatttatcatatgtttaaaatttttaatgtggaggagggataatgcatggacctttgacttttttataatatgttgcagCTTAAACTGGCAGCACCAGCTTTGCAAAAATCCTAGACCTAACCCTGATATCAAGACTCTGTTTGTTGATCATTCTTGTGGACAACCAAATGGTGCTCGT

upper sequence: GRMZM2G030422_T03 (Zea mays), 3'ss of exon 6
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 4
------------------------------------------------------------taaaaacggatttgcagctctgagtaggggcaaccatgcaattccccctttccat----ttcat-------tttgtatggtgggtaaccttat-tttgttcatgt-ttgacagCTTAAACTGGCAGCACCAGCTTTGCAAGAACCCTAGACCTAATCCTGACATCAAGACCCTTTTTGTTGATCATTCATGTGGACAACCGAATGGTGCACGT
                                                            |       | |  |||    ||       |||||   ||| ||     ||||| |    ||||        ||   |||  || |     | | || ||| || | ||  |||  | || |||||||| ||||||||||| ||||| || || ||||||||||| ||||| || ||  |||||||  |||| || |  || ||||| || || 
gtaataaatagcccatgtgttctaccttgagctcctcaagattatccaggtggtggcttctgcttgtagttgagcattgttggtggcatgcaacaccgcactttgtattttccttcgaattcaccagagtattgacatgaaggatttttatgtgttcgtttatctatttgcagTCTCAATTGGCAGCATCAGCTTTGCAAAAACCCAAGGCCGAATCCTGACATTAAGACACTCTTCATTGATCACACATGCGGGCCTCCTAATGGGGCTCGA

upper sequence: GRMZM2G030422_T03 (Zea mays), 3'ss of exon 6
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 4
taaaaacggatttgcagctctgagtaggggcaaccatgcaattccccctttccatttcat-----tttgtatggtgggtaaccttattttgttcatgtt------tgacagCTTAAACTGGCAGCACCAGCTTTGCAAGAACCCTAGACCTAATCCTGACATCAAGACCCTTTTTGTTGATCATTCATGTGGACAACCGAATGGTGCACGT
          ||| || |  |   |  |       |   | |     | ||  | || ||     |||  ||   |  |  | || || || | || ||         |||  | ||||||||||||||||||||||||||||| || || ||||||||||||||||| || ||| |||||||  | |||||||  || |||||||| |||
----------ttttcaacgtttcatgtgttgttttaaatattcttttcattgtacttaatgagaatttaaataa-gaattgctttcttgtgcttattttgttaccctgcagTCTCAACTGGCAGCACCAGCTTTGCAAGAACCCAAGGCCGAATCCTGACATCAAGACACTGTTTATTGATCACACTTGTGGACCTCCTAATGGTGCCCGT

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|19057857|gb|BM736524.1|BM736524
EST:     AATTTCCCAGCCTGAAGACTTCTAGGTTGCGGACACTTATTAACCAGAG                         CTTAAACTGGCAGCACCAGCTTTGCAAGAACCCTAGACCTAATCCTGACAT
genomic: AATTTCCCAGCCTGAAGACTTCTAGGTTGCGGACACTTATTAACCAGAGgtagccccat ... tgtttgacagCTTAAACTGGCAGCACCAGCTTTGCAAGAACCCTAGACCTAATCCTGACAT
EST: gi|22490728|gb|BU050651.1|BU050651
EST:     CAATTTCCCAGCCTGAAGACTTCTAGGTTGCGGACACTTATTAACCAGAG                         CTTAAACTGGCAGCACCAGCTTTGCAAGAACCCTAGACCTAATCCTGACAT
genomic: CAATTTCCCAGCCTGAAGACTTCTAGGTTGCGGACACTTATTAACCAGAGgtagccccat ... tgtttgacagCTTAAACTGGCAGCACCAGCTTTGCAAGAACCCTAGACCTAATCCTGACAT
EST: gi|71766923|gb|DR964860.1|DR964860
EST:     CAATTTCCCAGCCTGAAGACTTCTAGGTTGCGGACACTTATTAACCAGAG                         CTTAAACTGGCAGCACCAGCTTTGCAAGAACCCTAGACCTAATCCTGACAT
genomic: CAATTTCCCAGCCTGAAGACTTCTAGGTTGCGGACACTTATTAACCAGAGgtagccccat ... tgtttgacagCTTAAACTGGCAGCACCAGCTTTGCAAGAACCCTAGACCTAATCCTGACAT
EST: gi|32928255|gb|CF033067.1|CF033067
EST:     CAATTTCCCAGCCTGAAGACTTCTAGGTTGCGGACACTTATTAACCAGAG                         CTTAAATTGGCAGCACCAGCTTTGCAAGAACCCTAGACCTAATCCTGACAT
genomic: CAATTTCCCAGCCTGAAGACTTCTAGGTTGCGGACACTTATTAACCAGAGgtagccccat ... tgtttgacagCTTAAACTGGCAGCACCAGCTTTGCAAGAACCCTAGACCTAATCCTGACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctttccatttcattttgtatggtgggtaaccttattttgttcatgtttgacagCTTAAACTGGCAGCACCAGCTTTGCAAGAACCCTAGACCTAATCCTGACATCAAGACCCTTTTTGTTGATCATTCATGTGGACAACCGAATGGTGCACGT
                         gggtaac  putative branch site (score: 3)
        atttcattttgtat  TA-rich tract