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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGCAGCTTGTTCCAGTTGCGGTTTGCCATGCCATTGGCCATGTAACAAGCACTGTGTCATTTGCTGCTGTAGCTGTGTCATTTGCCCACACTATTAAAGgtgattctatgataagttgattttctatttctattattatccctctacctcctgtttacttgtgctaagatgtttccagttttacaaattacaacacag

Basic information

species Zea mays
transcript GRMZM2G083344_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083344_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g15160.1 (Oryza sativa), 5'ss of exon 5
AAGCAGCTTGTTCCAGTTGCGGTTTGCCATGCCATTGGCCATGTAACAAGCACTGTGTCATTTGCTGCTGTAGCTGTGTCATTTGCCCACACTATTAAAGgtgattctatgataagttgattttctatttctattattatccctctacctcctgtttacttgtgctaagatgtttccagttttacaaattacaacacag
||||  ||  | |||||||| || |||||||| ||||| |||||||||||||| ||||| ||||||||||||||||| |||||||||||||| |||||||||  | | |   ||  |||||||| | ||| |||| ||  || | | | |    | |  || |||| |||| ||||| |      |||| |   ||   
AAGCTACTGTTCCCAGTTGCTGTCTGCCATGCTATTGGTCATGTAACAAGCACCGTGTCCTTTGCTGCTGTAGCTGTCTCATTTGCCCACACCATTAAAGgtactgcaacagtatcttgattttatttttgtatttttggccttttgcgtttcttct--ttatgctgagatttttcctgcaaataaaatgattgcag--
















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|78104083|gb|DV522501.1|DV522501
EST:     CACTGTGTCATTTGCTGCTGTAGCTGTGTCATTTGCCCACACTATTAAAG                         CTCTCGAGCCATTCTTCAATGCGGCTGCTTCCCAGTTTATCCTTGGACAAC
genomic: CACTGTGTCATTTGCTGCTGTAGCTGTGTCATTTGCCCACACTATTAAAGgtgattctat ... tacaacacagCTCTCGAGCCATTCTTCAATGCGGCTGCTTCCCAGTTTATCCTTGGACAAC
EST: gi|149009525|gb|EE041508.2|EE041508
EST:     CACTGTGTCATTTGCTGCTGTAGCTGTGTCATTTGCCCACACTATTAAAG                         CTCTCGAGCCATTCTTCAATGCGGCTGCTTCCCAGTTTATCCTTGGACAAC
genomic: CACTGTGTCATTTGCTGCTGTAGCTGTGTCATTTGCCCACACTATTAAAGgtgattctat ... tacaacacagCTCTCGAGCCATTCTTCAATGCGGCTGCTTCCCAGTTTATCCTTGGACAAC
EST: gi|71439302|gb|DR820352.1|DR820352
EST:     CACTGTGTCATTTGCTGCTGTAGCTGTGTCATTTGCCCACACTATTAAAG                         CTCTCGAGCCATTCTTCAATGCGGCTGCTTCCCAGTTTATCCTTGGACAAC
genomic: CACTGTGTCATTTGCTGCTGTAGCTGTGTCATTTGCCCACACTATTAAAGgtgattctat ... tacaacacagCTCTCGAGCCATTCTTCAATGCGGCTGCTTCCCAGTTTATCCTTGGACAAC
EST: gi|78087779|gb|DV516172.1|DV516172
EST:     CACTGTGTCATTTGCTGCTGTAGCTGTGTCATTTGCCCACACTATTAAAG                         CTCTCGAGCCATTCTTCAATGCGGCTGCTTCCCAGTTTATCCTTGGACAAC
genomic: CACTGTGTCATTTGCTGCTGTAGCTGTGTCATTTGCCCACACTATTAAAGgtgattctat ... tacaacacagCTCTCGAGCCATTCTTCAATGCGGCTGCTTCCCAGTTTATCCTTGGACAAC
EST: gi|148961156|gb|EE011865.2|EE011865
EST:     CACTGTGTCATTTGCTGCTGTAGCTGTGTCATTTGCCCACACTATTAAAG                         CTCTCGAGCCATTCTTCAATGCGGCTGCTTCCCAGTTTATCCTTGGACAAC
genomic: CACTGTGTCATTTGCTGCTGTAGCTGTGTCATTTGCCCACACTATTAAAGgtgattctat ... tacaacacagCTCTCGAGCCATTCTTCAATGCGGCTGCTTCCCAGTTTATCCTTGGACAAC
EST: gi|71768356|gb|DR966293.1|DR966293
EST:     CACTGTGTCATTTGCTGCTGTAGCTGTGTCATTTGCCCACACTATTAAAG                         CTCTCGAGCCATTCTTCAATGCGGCTGCTTCCCAGTTTATCCTTGGACAAC
genomic: CACTGTGTCATTTGCTGCTGTAGCTGTGTCATTTGCCCACACTATTAAAGgtgattctat ... tacaacacagCTCTCGAGCCATTCTTCAATGCGGCTGCTTCCCAGTTTATCCTTGGACAAC
EST: gi|91055754|gb|EB166172.1|EB166172
EST:     CACTGTGTCATTTGCTGCTGTAGCTGTGTCATTTGCCCACACTATTAAAG                         CTCTCGAGCCATTCTTCAATGCGGCTGCTTCCCAGTTTATCCTTGGACAAC
genomic: CACTGTGTCATTTGCTGCTGTAGCTGTGTCATTTGCCCACACTATTAAAGgtgattctat ... tacaacacagCTCTCGAGCCATTCTTCAATGCGGCTGCTTCCCAGTTTATCCTTGGACAAC
EST: gi|76930051|gb|DV172256.1|DV172256
EST:     CACTGTGTCATTTGCTGCTGTAGCTGTGTCATTTGCCCACACTATTAAAG                         CTCTCGAGCCATTCTTCAATGCGGCTGCTTCCCAGTTTATCCTTGGACAAC
genomic: CACTGTGTCATTTGCTGCTGTAGCTGTGTCATTTGCCCACACTATTAAAGgtgattctat ... tacaacacagCTCTCGAGCCATTCTTCAATGCGGCTGCTTCCCAGTTTATCCTTGGACAAC
EST: gi|166562787|gb|EG307350.1|EG307350
EST:     GCTGTGTCATTTGCCCACACTATTAAAG                         CTCTCGAGCCATTCTTCAATGCGGCTGCTTCCCAGTTTATCCTTGGACAAC
genomic: GCTGTGTCATTTGCCCACACTATTAAAGgtgattctat ... tacaacacagCTCTCGAGCCATTCTTCAATGCGGCTGCTTCCCAGTTTATCCTTGGACAAC
EST: gi|94477389|gb|EB706347.1|EB706347
EST:     CACTGTGTCATTTGCTGCTGTAGCTGTGTCATTTGCCCACACTATTTAAG                         CTCTCGAGCCATTCTTCAATGCGGCTGCTTCCCAGTTTATCC
genomic: CACTGTGTCATTTGCTGCTGTAGCTGTGTCATTTGCCCACACTATTAAAGgtgattctat ... tacaacacagCTCTCGAGCCATTCTTCAATGCGGCTGCTTCCCAGTTTATCC
EST: gi|149095075|gb|EE180680.2|EE180680
EST:     CACTGTGTCATTTGCTGCTGTAGCTGTGTCATTTGCCCACACTATTAAAG                         CTCTCGAGCCATTCTTCAATGCGGCTGCTTCCCAGTTTATCCTTGGACAAC
genomic: CACTGTGTCATTTGCTGCTGTAGCTGTGTCATTTGCCCACACTATTAAAGgtgattctat ... tacaacacagCTCTCGAGCCATTCTTCAATGCGGCTGCTTCCCAGTTTATCCTTGGACAAC
EST: gi|148962629|gb|EE013519.2|EE013519
EST:     CACTGTGTCATTTGCTGCTGTAGCTGTGTCATTTGCCCACACTATTAAAG                         CTCTCGAGCCATTCTTCAATGCGGCTGCTTCCCAGTTTATCCTTGGACAAC
genomic: CACTGTGTCATTTGCTGCTGTAGCTGTGTCATTTGCCCACACTATTAAAGgtgattctat ... tacaacacagCTCTCGAGCCATTCTTCAATGCGGCTGCTTCCCAGTTTATCCTTGGACAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGCAGCTTGTTCCAGTTGCGGTTTGCCATGCCATTGGCCATGTAACAAGCACTGTGTCATTTGCTGCTGTAGCTGTGTCATTTGCCCACACTATTAAAGgtgattctatgataagttgattttctatttctattattatccctctacctcctgtttacttgtgctaagatgtttccagttttacaaattacaacacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT