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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGGAGATGCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAGgtctgactggcaaaaaaaaaaaactccagattattcagttctctctacgcaccaaattcatgatcttggcgagtttaagcgtacctgatctctgcatttcggttgtttcgcag

Basic information

species Zea mays
transcript GRMZM2G437859_T03
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G437859_T03 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g55500.4 (Oryza sativa), 5'ss of exon 6
GTTGGGAGATGCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAGgtctgactggcaaaaaaaaaaaactccagattattcagttctct--ctacgcaccaaattcatgatcttggcgagtttaagcgtacctgatctctgcatttcggttgtttcgcag
|||||||||||||||||| |||| || |||||| | || || ||||||||||| |||||||| || |  ||||          ||||| || ||  | |||| |  |||   |||| |||     |   | | |  |   || |     || | ||  |||| |           
GTTGGGAGATGCGTTGAGGTTGGACTTCCAATGTTAATTCTGTTTGTCGTGCTTTCTCAGgtttggcaagcaa----------ctcca-atgatcgaattcttttgctagtgaccatatttgaagttgagtctaactcgtgcattgtcaat-tatgtttttcag-----------
















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|74244049|gb|DT651963.1|DT651963
EST:     GCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAG                         TATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGGTTCTCC
genomic: GCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAGgtctgactgg ... tgtttcgcagTATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGGTTCTCC
EST: gi|78084450|gb|DV512843.1|DV512843
EST:     GCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAG                         TATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGGAAAGGTTCTC
genomic: GCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAGgtctgactgg ... tgtttcgcagTATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGG-AAAGGTTCTC
EST: gi|76923378|gb|DV169457.1|DV169457
EST:     GCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAG                         TATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGGTTCTCC
genomic: GCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAGgtctgactgg ... tgtttcgcagTATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGGTTCTCC
EST: gi|74238882|gb|DT646796.1|DT646796
EST:     GCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAG                         TATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGGGTTCTC
genomic: GCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAGgtctgactgg ... tgtttcgcagTATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGG-TTCTC
EST: gi|71310987|gb|DR791795.1|DR791795
EST:     GCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAG                         TATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGGTTCTCC
genomic: GCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAGgtctgactgg ... tgtttcgcagTATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGGTTCTCC
EST: gi|71438783|gb|DR819833.1|DR819833
EST:     GCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAG                         TATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGGTTCTCC
genomic: GCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAGgtctgactgg ... tgtttcgcagTATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGGTTCTCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGGGAGATGCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAGgtctgactggcaaaaaaaaaaaactccagattattcagttctctctacgcaccaaattcatgatcttggcgagtttaagcgtacctgatctctgcatttcggttgtttcgcag

- - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - GCTGAT