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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATAAATCTTCTGAAGTCCGCAAAGCTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTGgtatgtttcatccacctattactttcattcatctttccatttaatgctgcagcattctcccaacaactgaatttattgtttggcgtag

Basic information

species Zea mays
transcript GRMZM2G009849_T02
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009849_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 29
GATAAATCTTCTGAAGTCCGCAAAGCTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTGgtatgtttcatcc--acctattactttcattcatctttccatttaatgctgcagcattctcccaacaactgaatttattgtttggcgtag
||||||||||||||||| || |||||||||||||||||||||||||||||||||| ||| ||||||||||| |||||||| |  |  |  | || ||| ||| | ||  || || | ||  |   | | | ||  | |    ||||| |   |  ||    ||||
GATAAATCTTCTGAAGTTCGTAAAGCTGCTGAATCCTTTATGAATGAAATTCTCAAGATTTGTGGCCAAGATGTGgtatggtgtaatcttatcttttatttttactcgcctgtctactt--ttaagaaacttttcctctcttactga-tacgtcattgatggtag
















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|17970269|gb|BM277032.1|BM277032
EST:     CTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTG                         GTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCA
genomic: CTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTGgtatgtttca ... tttggcgtagGTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCA
EST: gi|22491327|gb|BU051250.1|BU051250
EST:     CTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTG                         GTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCA
genomic: CTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTGgtatgtttca ... tttggcgtagGTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCA
EST: gi|19351752|gb|BM896284.1|BM896284
EST:     CTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTG                         GTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCA
genomic: CTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTGgtatgtttca ... tttggcgtagGTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCA
EST: gi|32806646|gb|CD958880.1|CD958880
EST:     GATCTGTGGCCAAGAAGTG                         GTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCA
genomic: GATCTGTGGCCAAGAAGTGgtatgtttca ... tttggcgtagGTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCA
EST: gi|87153866|gb|DY398655.1|DY398655
EST:     CTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTG                         GTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCA
genomic: CTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTGgtatgtttca ... tttggcgtagGTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCA
EST: gi|22489504|gb|BU049427.1|BU049427
EST:     CTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTG                         GTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCA
genomic: CTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTGgtatgtttca ... tttggcgtagGTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCA
EST: gi|87153811|gb|DY398600.1|DY398600
EST:     CTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTG                         GTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCA
genomic: CTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTGgtatgtttca ... tttggcgtagGTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATAAATCTTCTGAAGTCCGCAAAGCTGCTGAATCCTTTATGAATGAAATTCTCAGGATCTGTGGCCAAGAAGTGgtatgtttcatccacctattactttcattcatctttccatttaatgctgcagcattctcccaacaactgaatttattgtttggcgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT