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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCAGATTGCACCCATTGTGGCGAAAACTCCGTTTTCACAGAAGAAGACTTTCAGAAGTTTGACTATGAGAGCTTCACACAGTCACCAATGTCTGATAAGgtaatgtgaatggatgtcgcagtgcagatcacattaaagaatgatcttgaaacctgtggccttatctactgttacatctactgcag

Basic information

species Zea mays
transcript GRMZM2G157836_T03
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157836_T04 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os02g32460.1 (Oryza sativa), 5'ss of exon 10
TCCAGATTGCACCCATTGTGGCGAAAACTCCGTTTTCACAGAAGAAGACTTTCAGAAGTTTGACTATGAGAGCTTCACACAGTCACCAATGTCTGATAAGgtaatgtgaatggatg--tcgcagtgcagatcacattaaagaatgatcttgaaacctgtg-gccttatctactgttacatctactgcag--------------
  | | ||||||   |||||| ||||| || | ||| ||  |||| || |||||||||||||| ||||||| |||||| ||||| |||||||||||||||||| |||     |||   |  |    ||  | | ||||   |      | | |  ||||  |  | |   | |   | |   | ||| |              
GACTGTTTGCACGGTTTGTGGAGAAAATTCAGCTTTTACTCAAGATGATTTTCAGAAGTTTGATTATGAGAACTTCACGCAGTCTCCAATGTCTGATAAGgta-tgtctccagatcattgacttcacaatttatattatttatca--ttagcattctgtatgtatcactgaattgaaaaaggaatgctgtctgtctaatctga
















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|149085669|gb|EE175184.2|EE175184
EST:     TTCAGAAGTTTGACTATGAGAGCTTCACACAGTCACCAATGTCTGATAAG                         GCAGCAGCAAGCGTGAACGTACTCCCAGAGAGCGCGCGTATCACTTGCAGA
genomic: TTCAGAAGTTTGACTATGAGAGCTTCACACAGTCACCAATGTCTGATAAGgtaatgtgaa ... tctactgcagGCAGCAGCAAGCGTGAACGTACTCCCAGAGAGCGCGCGTATCACTTGCAGA
EST: gi|71442271|gb|DR823321.1|DR823321
EST:     TTCAGAAGTTTGACTATGAGAGCTTCACACAGTCACCAATGTCTGATAAG                         GCAGCAGCAAGCGTGAACGTACTCCCAGAGAGCGCGCGTATCACTTGCAGA
genomic: TTCAGAAGTTTGACTATGAGAGCTTCACACAGTCACCAATGTCTGATAAGgtaatgtgaa ... tctactgcagGCAGCAGCAAGCGTGAACGTACTCCCAGAGAGCGCGCGTATCACTTGCAGA
EST: gi|71445495|gb|DR826545.1|DR826545
EST:     TTCAGAAGTTTGACTATGAGAGCTTCACACAGTCACCAATGTCTGATAAG                         GCAGCAGCAAGCGTGAACGTACTCCCAGAGAGCGCGCGTATCACTTGCAGA
genomic: TTCAGAAGTTTGACTATGAGAGCTTCACACAGTCACCAATGTCTGATAAGgtaatgtgaa ... tctactgcagGCAGCAGCAAGCGTGAACGTACTCCCAGAGAGCGCGCGTATCACTTGCAGA
EST: gi|78092058|gb|DV520432.1|DV520432
EST:     TTCAGAAGTTTGACTATGAGAGCTTCACACAGTCACCAATGTCTGATAAG                         GCAGCAGCAAGCGTGAACGTACTCCCAGAGAGCGCGCGTATCACTTGCAGA
genomic: TTCAGAAGTTTGACTATGAGAGCTTCACACAGTCACCAATGTCTGATAAGgtaatgtgaa ... tctactgcagGCAGCAGCAAGCGTGAACGTACTCCCAGAGAGCGCGCGTATCACTTGCAGA
EST: gi|30705123|gb|CD058666.1|CD058666
EST:     ACACAGTCACCAATGTCTGATAAG                         GCAGCAGCAAGCGTGAACGTACTCCCAGAGAGCGCGCGTATCACTTGCAGA
genomic: ACACAGTCACCAATGTCTGATAAGgtaatgtgaa ... tctactgcagGCAGCAGCAAGCGTGAACGTACTCCCAGAGAGCGCGCGTATCACTTGCAGA
EST: gi|30705125|gb|CD058667.1|CD058667
EST:     TTCAGAAGTTTGACTATGAGAGCTTCACACAGTCACCAATGTCTGATAAG                         GCAGCAGCAAGCGTGAACGTACTCCCAGAGAGCGCGCGTATCACTTGCAGA
genomic: TTCAGAAGTTTGACTATGAGAGCTTCACACAGTCACCAATGTCTGATAAGgtaatgtgaa ... tctactgcagGCAGCAGCAAGCGTGAACGTACTCCCAGAGAGCGCGCGTATCACTTGCAGA
EST: gi|71758127|gb|DR956064.1|DR956064
EST:     TTCAGAAGTTTGACTATGAGAGCTTCACACAGTCACCAATGTCTGATAAG                         GCAGCAGCAAGCGTGAACGTACTCCCAGAGAGCGCGCGTATCACTTGCAGA
genomic: TTCAGAAGTTTGACTATGAGAGCTTCACACAGTCACCAATGTCTGATAAGgtaatgtgaa ... tctactgcagGCAGCAGCAAGCGTGAACGTACTCCCAGAGAGCGCGCGTATCACTTGCAGA
EST: gi|78088795|gb|DV517188.1|DV517188
EST:     TTCAGAAGTTTGACTATGAGAGCTTCACACAGTCACCAATGTCTGATAAG                         GCAGCAGCAAGCGTGAACGTACTTCCAGAGAGCGCGCGTATCACTTGCAGA
genomic: TTCAGAAGTTTGACTATGAGAGCTTCACACAGTCACCAATGTCTGATAAGgtaatgtgaa ... tctactgcagGCAGCAGCAAGCGTGAACGTACTCCCAGAGAGCGCGCGTATCACTTGCAGA
EST: gi|50332337|gb|CO527463.1|CO527463
EST:     TTCAGAAGTTTGACTATGAGAGCTTCACACAGTCACCAATGTCTGATAAG                         GCAGCAGCAAGCGTGAACGTACTCCCAGAGAGCGCGCGTATCACTTGCAGA
genomic: TTCAGAAGTTTGACTATGAGAGCTTCACACAGTCACCAATGTCTGATAAGgtaatgtgaa ... tctactgcagGCAGCAGCAAGCGTGAACGTACTCCCAGAGAGCGCGCGTATCACTTGCAGA
EST: gi|148964307|gb|EE015497.2|EE015497
EST:     TTCAGAAGTTTGACTATGAGAGCTTCACACAGTCACCAATGTCTGATAAG                         GCAGCAGCAAGCGTGAACGTACTCCCAGAGAGCGCGCGTATCACTTGCAGA
genomic: TTCAGAAGTTTGACTATGAGAGCTTCACACAGTCACCAATGTCTGATAAGgtaatgtgaa ... tctactgcagGCAGCAGCAAGCGTGAACGTACTCCCAGAGAGCGCGCGTATCACTTGCAGA
EST: gi|71756834|gb|DR954771.1|DR954771
EST:     TTCAGAAGTTTGACTATGAGAGCTTCACACAGTCACCAATGTCTGATAAG                         GCAGCAGCAAGCGTGAACGTACTCCCAGAGAGCGCGCGTATCACTTGCAGA
genomic: TTCAGAAGTTTGACTATGAGAGCTTCACACAGTCACCAATGTCTGATAAGgtaatgtgaa ... tctactgcagGCAGCAGCAAGCGTGAACGTACTCCCAGAGAGCGCGCGTATCACTTGCAGA
EST: gi|18164079|gb|BM333918.1|BM333918
EST:     TTCAGAAGTTTGACTATGAGAGCTTCACACAGTCACCAATGTCTGATAAG                         GCAGCAGCAAGCGTGAACGTACTCCCAGAGAGCGCGCGTATCACTTGCAGA
genomic: TTCAGAAGTTTGACTATGAGAGCTTCACACAGTCACCAATGTCTGATAAGgtaatgtgaa ... tctactgcagGCAGCAGCAAGCGTGAACGTACTCCCAGAGAGCGCGCGTATCACTTGCAGA
EST: gi|67015106|gb|CO443855.1|CO443855
EST:     TGACTATTTGAGCTTCACACAGTCACCAATGTCTGATAAG                         GCAGCACCAAGCGTGAACGTACTCCCAGAGAGCGCGCGTATCACTTGCAGA
genomic: TGACTATGAGAGCTTCACACAGTCACCAATGTCTGATAAGgtaatgtgaa ... tctactgcagGCAGCAGCAAGCGTGAACGTACTCCCAGAGAGCGCGCGTATCACTTGCAGA
EST: gi|78087901|gb|DV516294.1|DV516294
EST:     TTCAGAAGTTGGACTATGAGAGCTTCACACAGTCACCAATGTCTGATAAG                         GCAGCAGCAAGCGTGAACGTACTCCCAGAGAGCGCGCGTATCACTTGCAGA
genomic: TTCAGAAGTTTGACTATGAGAGCTTCACACAGTCACCAATGTCTGATAAGgtaatgtgaa ... tctactgcagGCAGCAGCAAGCGTGAACGTACTCCCAGAGAGCGCGCGTATCACTTGCAGA
EST: gi|148945732|gb|EC891011.2|EC891011
EST:     TTCAGAAGTTTGACTATGAGAGCTTCACACAGTCACCAATGTCTGATAAG                         GCAGCAGCAAGCGTGAACGTACTCCCAGAGAGCGCGCGTATCACTTGCAGA
genomic: TTCAGAAGTTTGACTATGAGAGCTTCACACAGTCACCAATGTCTGATAAGgtaatgtgaa ... tctactgcagGCAGCAGCAAGCGTGAACGTACTCCCAGAGAGCGCGCGTATCACTTGCAGA
EST: gi|101400845|gb|EB822120.1|EB822120
EST:     TTCAGAAGTTTGACTATGAGAGCTTCACACAGTCACCAATGTCTGATAAG                         GCAGCAGCAAGCGTGAACGTACTCCCAGAGAGCGCGCGTATCACTTGCAGA
genomic: TTCAGAAGTTTGACTATGAGAGCTTCACACAGTCACCAATGTCTGATAAGgtaatgtgaa ... tctactgcagGCAGCAGCAAGCGTGAACGTACTCCCAGAGAGCGCGCGTATCACTTGCAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCAGATTGCACCCATTGTGGCGAAAACTCCGTTTTCACAGAAGAAGACTTTCAGAAGTTTGACTATGAGAGCTTCACACAGTCACCAATGTCTGATAAGgtaatgtgaatggatgtcgcagtgcagatcacattaaagaatgatcttgaaacctgtggccttatctactgttacatctactgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT