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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGTCTTCGAGCACGCCAACGACAGGCCCATCATCTTCTCCAGCTTCCAACCCGATGCCGCGCAGCTCATCCGCAAGCTGCAAGACAAATACCCTgtaagtgtcactgccaccaccaccgagcacacaatcaacattcaacactggctgattaaccctgctacgaacag

Basic information

species Zea mays
transcript GRMZM5G829946_T04
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G829946_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os04g32320.1 (Oryza sativa), 5'ss of exon 7
GTTGTCTTCGAGCACGCCAACGACAGGCCCATCATCTTCTCCAGCTTCCAACCCGATGCCGCGCAGCTCATCCGCAAGCTGCAAGACAAATACCCTgtaagtgtcactgccaccaccaccgagcacacaatcaacattcaaca--ctggctgattaaccctgctacgaacag------------------------
|| ||||| ||||| ||||| || ||||| ||| |||||||||||||||| ||||| |||||||   | || ||||| |||||||| | |||||||||||||       | | |  ||  |  | |   |  |  |||  |||   | | | ||||  ||  |       |                         
GTCGTCTTTGAGCATGCCAAGGAGAGGCCAATCTTCTTCTCCAGCTTCCAGCCCGACGCCGCGCGAATTATGCGCAAACTGCAAGATAGATACCCTgtaagtaatttcactatctacattgtactctgcaagacaattagacatgttagtttattactccctccgtccctaaatatttagcatctttgattttttt
















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|31355157|gb|CD439514.1|CD439514
EST:     TCCAACCCGATGCCGCGCAGCTCATCCGCAAGCTGCAAGACAAATACCCT                         GTGCTCTTCCTGACCAACGGAGGGACGCAGGTGTACGCCGACCCGCGTCGG
genomic: TCCAACCCGATGCCGCGCAGCTCATCCGCAAGCTGCAAGACAAATACCCTgtaagtgtca ... ctacgaacagGTGCTCTTCCTGACCAACGGAGGGACGCAGGTGTACGCCGACCCGCGTCGG
EST: gi|93017159|gb|EB642679.1|EB642679
EST:     TCCAACCCGATGCCGCGCAGCTCATCCGCAAGCTGCAAGACAAATACCCT                         GTGCTCTTCTTGACCAACGGAGGGACGCAGGTGTACGCCGACCCGCGTCGG
genomic: TCCAACCCGATGCCGCGCAGCTCATCCGCAAGCTGCAAGACAAATACCCTgtaagtgtca ... ctacgaacagGTGCTCTTCCTGACCAACGGAGGGACGCAGGTGTACGCCGACCCGCGTCGG
EST: gi|78180580|gb|DV550908.1|DV550908
EST:     TCCAACCCGATGCCGCGCAGCTCATCCGCAAGCTGCAAGACAAATACCCT                         GTGCTCTTCCTGACCAACGGAGGGACGCAGGTGTACGCCGACCCGCGTCGG
genomic: TCCAACCCGATGCCGCGCAGCTCATCCGCAAGCTGCAAGACAAATACCCTgtaagtgtca ... ctacgaacagGTGCTCTTCCTGACCAACGGAGGGACGCAGGTGTACGCCGACCCGCGTCGG
EST: gi|26455300|gb|CA826883.1|CA826883
EST:     TGCCGCGCAGCTCATCCGCAAGCTGCAAGACAAATACCCT                         GTGCTCTTCCTGACCAACGGAGGGACGCAGGTGTACGCCGACCCGCGTCGG
genomic: TGCCGCGCAGCTCATCCGCAAGCTGCAAGACAAATACCCTgtaagtgtca ... ctacgaacagGTGCTCTTCCTGACCAACGGAGGGACGCAGGTGTACGCCGACCCGCGTCGG
EST: gi|87154706|gb|DY399495.1|DY399495
EST:     TGCCGCGCAGCTCATCCGCAAGCTGCAAGACAAATACCCT                         GTGCTCTTCCTGACCAACGGAGGGACGCAGGTGTACGCCGACCCGCGTCGG
genomic: TGCCGCGCAGCTCATCCGCAAGCTGCAAGACAAATACCCTgtaagtgtca ... ctacgaacagGTGCTCTTCCTGACCAACGGAGGGACGCAGGTGTACGCCGACCCGCGTCGG
EST: gi|71429646|gb|DR810696.1|DR810696
EST:     TCCAACCCGATGCCGCGCAGCTCATCCGCAAGCTGCAAGACAAATACCCT                         GTGCTCTTCCTGACCAACGGAGGGACGCAGGTGTACGCCGACCCGCGTCGG
genomic: TCCAACCCGATGCCGCGCAGCTCATCCGCAAGCTGCAAGACAAATACCCTgtaagtgtca ... ctacgaacagGTGCTCTTCCTGACCAACGGAGGGACGCAGGTGTACGCCGACCCGCGTCGG
EST: gi|6964668|gb|AW433361.1|AW433361
EST:     CCCGATGCCGCGCAGCTCATCCGCAAGCTGCAAGACAAATACCCT                         GTGCTCTTCCTGACCAACGGAGGGACGCAGGTGTACGCCGACCCGCGTCGG
genomic: CCCGATGCCGCGCAGCTCATCCGCAAGCTGCAAGACAAATACCCTgtaagtgtca ... ctacgaacagGTGCTCTTCCTGACCAACGGAGGGACGCAGGTGTACGCCGACCCGCGTCGG
EST: gi|6973514|gb|AW438208.1|AW438208
EST:     TCCAACCCGATGCCGCGCAGCTCATCCGCAAGCTGCAAGACAAATACCCT                         GTGCTCTTCCTGACCAACGGAGGGACGCAGGTG-ACGCCGACCCGCGTCGG
genomic: TCCAACCCGATGCCGCGCAGCTCATCCGCAAGCTGCAAGACAAATACCCTgtaagtgtca ... ctacgaacagGTGCTCTTCCTGACCAACGGAGGGACGCAGGTGTACGCCGACCCGCGTCGG
EST: gi|31349103|gb|CD433460.1|CD433460
EST:     TCCAACCCGATGCCGCGCAGCTCATCCGCTAGCTGCAAGACAAATACCCT                         GTGCTCTTCCTGACCAACGGAGGGACGCAGGTGTACGCCGACCCGCGTCGG
genomic: TCCAACCCGATGCCGCGCAGCTCATCCGCAAGCTGCAAGACAAATACCCTgtaagtgtca ... ctacgaacagGTGCTCTTCCTGACCAACGGAGGGACGCAGGTGTACGCCGACCCGCGTCGG
EST: gi|148964440|gb|EE015554.2|EE015554
EST:     TCCAACCCGATGCCGCGCAGCTCATCCGCAAGGTGCAAGACAAATACCCT                         GTGCTCTTCCTGACCAACGGAGGGACGCAGGTGTACGCCGACCCGCGTCGG
genomic: TCCAACCCGATGCCGCGCAGCTCATCCGCAAGCTGCAAGACAAATACCCTgtaagtgtca ... ctacgaacagGTGCTCTTCCTGACCAACGGAGGGACGCAGGTGTACGCCGACCCGCGTCGG
EST: gi|74237764|gb|DT645678.1|DT645678
EST:     TCCAACCCGATGCCGCGCAGCTCATCCGCAAGCTGCAAGACAAATACCCT                         GTGCTCTTCCTGACCAACGGAGGGACGCAGGTGTACGCCGACCCGCGTCGG
genomic: TCCAACCCGATGCCGCGCAGCTCATCCGCAAGCTGCAAGACAAATACCCTgtaagtgtca ... ctacgaacagGTGCTCTTCCTGACCAACGGAGGGACGCAGGTGTACGCCGACCCGCGTCGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGTCTTCGAGCACGCCAACGACAGGCCCATCATCTTCTCCAGCTTCCAACCCGATGCCGCGCAGCTCATCCGCAAGCTGCAAGACAAATACCCTgtaagtgtcactgccaccaccaccgagcacacaatcaacattcaacactggctgattaaccctgctacgaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA