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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAGAAGAGAAGCTTGAGTCGGGTCAAGGGAAATCAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgttgccttatggaagtgtgtcagatgcttttgttgctcttgtataagtcagtccacaacaaacttcatatcctcgacaccttgggtttaacatttgaactctttatcctggttgcag

Basic information

species Zea mays
transcript GRMZM2G151863_T04
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151863_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os11g28300.1 (Oryza sativa), 5'ss of exon 7
GTAGAAGAGAAGCTTGAGTCGGGTCAAGGGAAATCAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttag--tttgttgccttatggaagtgtgtcagatgcttttg-ttgctcttgtataagtcagtccacaacaaacttcatatcctcgacaccttgggtttaacatttgaactctttatcctggttgcag
|| ||||||||||||||||| |||||||| ||||||||| | ||  ||||||||| |||||| |||||||| |||||||||||||| |   |||||  ||||||  | || ||| | ||| |      ||    || ||  || | ||   |   |  |||| ||  |  |    |||  |  || |                         
GTGGAAGAGAAGCTTGAGTCAGGTCAAGGAAAATCAACCCTTCGCCGGTTCTTTGGAAGATTTTGTACACCGATCTTTTTGGAGgtcatcttttgtcaccttataaatgtttgttaaatgttccaaactgggactgcatgcgt-attcagtacttatattcagatgttaaatgtgttg--tacaata-------------------------

upper sequence: GRMZM2G151863_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA18G47670.1 (Glycine max), 5'ss of exon 7
GTAGAAGAGAAGCTTGAGTCGGGTCAAGGGAAATCAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagt----ttgttgccttatggaagtgtgtcagatgcttttgttgctcttgtataagtcagtccacaacaaacttcatatcctcgacaccttgggtttaacatttgaactctttatcctggttgcag
|| ||||| || || ||    || ||||||||| |  |  | ||  | |||||| ||||||||||||||||||| ||||||||||  |||     | |||| | ||  |  ||    |    | ||||     | ||||  | |   |   |       | ||                                                  
GTTGAAGAAAAACTGGATGGTGGACAAGGGAAAACTTCAGTTCGGCGCTTCTTTTCAAGATTCTGTACACCAATATTTTTGGAGgcaagtacaacttttgcatcatttatttgaaataaccacatttgcactacatgtaatattatcttttcttttttatgcag-------------------------------------------------

upper sequence: GRMZM2G151863_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA09G38640.1 (Glycine max), 5'ss of exon 7
GTAGAAGAGAAGCTTGAGTCGGGTCAAGGGAAATCAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagt----ttgttgccttatggaagtgtgtcagatgcttttgttgctcttgtataagtcagtccacaacaaacttcatatcctcgacaccttgggtttaacatttgaactctttatcctggttgcag
|| ||||| || || ||    || ||||||||| |  |  |  |  | |||||| ||||||| ||||||||||| ||||||||||  |||     | |||| | ||  |  | || | ||     |     |  ||||   |  ||    | | ||   ||  | |  |   ||                                       
GTTGAAGAAAAACTGGATGGTGGACAAGGGAAAACTTCAGTTAGGCGCTTCTTTTCAAGATTTTGTACACCAATATTTTTGGAGgcaagtacaacttttgcatcattta--tttgactgagaaaataaccacatttgtgcta--catgtaatatcatcttttcttttttatgcag--------------------------------------

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|32801015|gb|CD953251.1|CD953251
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTTTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTA
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTA
EST: gi|78073958|gb|DV502392.1|DV502392
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCCTCTTAGCTGAATGAGGCGACCGGAGCCAAATAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|71770353|gb|DR968290.1|DR968290
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|74239214|gb|DT647128.1|DT647128
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|60356718|gb|DN223691.1|DN223691
EST:     ACCATCGGTAGGGTTCTTTGCAAAGATTCTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: ACCATCCGTA-GGTTCTTTGC-AAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|211282108|gb|FL480844.1|FL480844
EST:     GTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: GTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|88747529|gb|DY531670.1|DY531670
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GCTTTCATTTTAACCTTTTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|50336723|gb|CO531849.1|CO531849
EST:     GTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTTTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: GTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|60358343|gb|DN225316.1|DN225316
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|60348226|gb|DN215199.1|DN215199
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|40335107|gb|CK369177.1|CK369177
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTTTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|33466756|gb|CF243805.1|CF243805
EST:     GTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTTTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: GTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
EST: gi|89754829|gb|DY685473.1|DY685473
EST:     CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAG                         GCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG
genomic: CAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgt ... ctggttgcagGCTTTCATCTTAACCTTCTTAGCTGAATGGGGCGACCGGAGCCAAATAGCG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAGAAGAGAAGCTTGAGTCGGGTCAAGGGAAATCAACCATCCGTAGGTTCTTTGCAAGATTCTGTACACCAATCTTTTTGGAGgttagtttgttgccttatggaagtgtgtcagatgcttttgttgctcttgtataagtcagtccacaacaaacttcatatcctcgacaccttgggtttaacatttgaactctttatcctggttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG