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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGGGAAGAATGATCCGCAGTACATCCTGGACACGAGCGTGTACCCGCGGGAGCCGGAGAGCATGAAGGAGCTGCGCGAGATCACCGCCAAGCACCCATGgtatgtcccgctagcttttcgccctgtcgtacgtggtggattcgagtgtgtgggcctgctggacgtggacagaccgagatctgagaacgaacgtggcgtggcgtgcag

Basic information

species Zea mays
transcript GRMZM2G099363_T03
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099363_T03 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os06g06980.3 (Oryza sativa), 5'ss of exon 1
-GGGGGAAGAATGATCCGCAGTACATCCTGGACACGAGCGTGTACCCGCGGGAGCCGGAGAGCATGAAGGAGCTGCGCGAGATCACCGCCAAGCACCCATGgtatgtcccgctagcttttcgccctgtcgtacgtggtggattcgagtgtgtgggcctgctggacgtggacagaccgagatctgagaacgaacgtggcgtggcgtgcag
  || |     |  |||||||||||||||||| ||||||||||||||||| ||||  ||| ||||||||||||| |||||| |||||||||| ||||||||||| | | ||    |  | | ||   || |  |    | ||  |||   |  | | |    ||  ||    ||  | ||   | || |||   ||   | ||      
TCGGTGCTTCGTT-TCCGCAGTACATCCTGGAGACGAGCGTGTACCCGCGCGAGCACGAGTGCATGAAGGAGCTCCGCGAGGTCACCGCCAACCACCCATGgtacgccacgaatcccctcctcctcctcttgggccccgaatcggagctcggcgacatc---gatttgattcgattggga---gggatcgatgttgttcttgcag----

upper sequence: GRMZM2G099363_T03 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os06g06980.2 (Oryza sativa), 5'ss of exon 2
GGGGGAAGAATGATCCGCAGTACATCCTGGACACGAGCGTGTACCCGCGGGAGCCGGAGAGCATGAAGGAGCTGCGCGAGATCACCGCCAAGCACCCATGgtatgtcccgctagcttttcgccctgtcgtacgtggtggattcgagtgtgtgggcctgctggacgtggacagaccgagatctgagaacgaacgtggcgtggcgtgcag
                    ||||||||||| ||||||||||||||||| ||||  ||| ||||||||||||| |||||| |||||||||| ||||||||||| | | ||    |  | | ||   || |  |    | ||  |||   |  | | |    ||  ||    ||  | ||   | || |||   ||   | ||      
--------------------TACATCCTGGAGACGAGCGTGTACCCGCGCGAGCACGAGTGCATGAAGGAGCTCCGCGAGGTCACCGCCAACCACCCATGgtacgccacgaatcccctcctcctcctcttgggccccgaatcggagctcggcgacatc---gatttgattcgattggga---gggatcgatgttgttcttgcag----
















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|211150565|gb|FL189863.1|FL189863
EST:     GAGCCGGAGAGCATGAAGGAGCTGCGCGAGATCACCGCCAAGCACCCATG                         GAACCTGATGACCACCTCCGCCGACGAGGGCCAGTTCCTCAACATGCTCAT
genomic: GAGCCGGAGAGCATGAAGGAGCTGCGCGAGATCACCGCCAAGCACCCATGgtatgtcccg ... tggcgtgcagGAACCTGATGACCACCTCCGCCGACGAGGGCCAGTTCCTCAACATGCTCAT
EST: gi|5510830|gb|AI857214.1|AI857214
EST:     CGGAGAGCATGAAGGAGCTGCGCGAGATNNNNNNNAAGCACCCATG                         GAACCTGATGACCACCTCCGCCGACGAGGGCCAGTTCCTCAACATGCTCAT
genomic: CGGAGAGCATGAAGGAGCTGCGCGAGATCACCGCCAAGCACCCATGgtatgtcccg ... tggcgtgcagGAACCTGATGACCACCTCCGCCGACGAGGGCCAGTTCCTCAACATGCTCAT
EST: gi|74238429|gb|DT646343.1|DT646343
EST:     GAGCCCGAGAGCATGAAGGAGCTGCGCGAGATCACCGCCAAGCACCCATG                         GAACCTGATGACCACCTCCGCCGACGAGGGCCAGTTCCTCAACATGCTCAT
genomic: GAGCCGGAGAGCATGAAGGAGCTGCGCGAGATCACCGCCAAGCACCCATGgtatgtcccg ... tggcgtgcagGAACCTGATGACCACCTCCGCCGACGAGGGCCAGTTCCTCAACATGCTCAT
EST: gi|149014739|gb|EE044420.2|EE044420
EST:     CCGCCAAGCACCCATG                         GAACCTGATGACCACCTCCGCCGACGAGGGCCAGTTCCTCAACATGCTCAT
genomic: CCGCCAAGCACCCATGgtatgtcccg ... tggcgtgcagGAACCTGATGACCACCTCCGCCGACGAGGGCCAGTTCCTCAACATGCTCAT
EST: gi|86474833|gb|DY241203.1|DY241203
EST:     GAGCCGGAGAGCATGAAGGAGCTGCGCGAGATCACCGCCAAGCACCCATG                         GAACCTGATGACCACCTCCGCCGACGAGGGCCAGTTCCTCAACATGCTCAT
genomic: GAGCCGGAGAGCATGAAGGAGCTGCGCGAGATCACCGCCAAGCACCCATGgtatgtcccg ... tggcgtgcagGAACCTGATGACCACCTCCGCCGACGAGGGCCAGTTCCTCAACATGCTCAT
EST: gi|16916553|gb|BM072891.1|BM072891
EST:     GAGCCGGAGAGCATGAAGGAGCTGCGCGAGATCACCGCCAAGCACCCATG                         GAACCTGATGACCACCTCCGCCGACGAGGGCCAGTTCCTCAACATGCTCAT
genomic: GAGCCGGAGAGCATGAAGGAGCTGCGCGAGATCACCGCCAAGCACCCATGgtatgtcccg ... tggcgtgcagGAACCTGATGACCACCTCCGCCGACGAGGGCCAGTTCCTCAACATGCTCAT
EST: gi|37379818|gb|CF626673.1|CF626673
EST:     GAGCCGGAGAGCATGAAGGAGCTGCGCGAGATCACCGCCAAGCACCCATG                         GAACCTGATGACCACCTCCGCCGACGAGGGCCAGTTCCTCAACATGCTCAT
genomic: GAGCCGGAGAGCATGAAGGAGCTGCGCGAGATCACCGCCAAGCACCCATGgtatgtcccg ... tggcgtgcagGAACCTGATGACCACCTCCGCCGACGAGGGCCAGTTCCTCAACATGCTCAT
EST: gi|91879069|gb|EB409026.1|EB409026
EST:     GAGCCGGAGAGCATGAAGGAGCTGCGCGAGATCACCGGCAAGCACCCATG                         GAACCTGATGACCACCTCCGCCGACGAGGGCCAGTTCCTCAACATGGTCAT
genomic: GAGCCGGAGAGCATGAAGGAGCTGCGCGAGATCACCGCCAAGCACCCATGgtatgtcccg ... tggcgtgcagGAACCTGATGACCACCTCCGCCGACGAGGGCCAGTTCCTCAACATGCTCAT
EST: gi|50337681|gb|CO532807.1|CO532807
EST:     GAGCCGGAGAGCATGAAGGAGCTGCGCGAGATCACCGCCAAGCACCCATG                         GAACCTGATGACCACCTCCGCCGACGAGGGCCAGTTCCTCAACATGCTCAT
genomic: GAGCCGGAGAGCATGAAGGAGCTGCGCGAGATCACCGCCAAGCACCCATGgtatgtcccg ... tggcgtgcagGAACCTGATGACCACCTCCGCCGACGAGGGCCAGTTCCTCAACATGCTCAT
EST: gi|211091281|gb|FL220529.1|FL220529
EST:     ATCACCGCCAAGCACCCATG                         GAACCTGATGACCACCTCCGCCGACGAGGGCCAGTTCCTCAACATGCTCAT
genomic: ATCACCGCCAAGCACCCATGgtatgtcccg ... tggcgtgcagGAACCTGATGACCACCTCCGCCGACGAGGGCCAGTTCCTCAACATGCTCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGGGAAGAATGATCCGCAGTACATCCTGGACACGAGCGTGTACCCGCGGGAGCCGGAGAGCATGAAGGAGCTGCGCGAGATCACCGCCAAGCACCCATGgtatgtcccgctagcttttcgccctgtcgtacgtggtggattcgagtgtgtgggcctgctggacgtggacagaccgagatctgagaacgaacgtggcgtggcgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA