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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAGTATGGACACATGTACAGCATGGTTCAGGAAGAAGTTCAAAACAAGACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaatttcttattgttttgtcgtttttcattgcaacttgatcagcacgcatagtatgtgacttttatttactcaaaaaaattgcatgccag

Basic information

species Zea mays
transcript GRMZM2G060870_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060870_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g40890.1 (Oryza sativa), 5'ss of exon 4
CAAAGTATGGACACATGTACAGCATGGTTCAGGAAGAAGTTCAAAACAAGACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaa---tttcttattgttttgtcgtttttca-ttgcaacttgatcagcacgcatagtatgtgacttttatttactcaaaaaaattgcatgccag
|||| ||||  ||  |||||||||||||||||||||| |||||||||||||| || |||||||| ||||||||||||||||| ||||||||||||||||||||||||||   ||  |   |  ||| ||   ||||| ||||| ||| | |||| |  ||    |   | ||||| ||  |||                 
CAAAATATGAGCAATTGTACAGCATGGTTCAGGAAGAGGTTCAAAACAAGACTGCAAAAGGTTCGTCAAGCTGCACAAATGGACTTCTGTGGCTCACGAGgtgcttcaaaccttcttggataatttatcacctttcagttgcagcttaagcagc-cttattaactcaaaattttactt--tcag----------------
















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|32934286|gb|CF039098.1|CF039098
EST:     ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAG                         GGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaat ... tgcatgccagGGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
EST: gi|32932161|gb|CF036973.1|CF036973
EST:     ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAG                         GGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaat ... tgcatgccagGGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
EST: gi|32866744|gb|CF006426.1|CF006426
EST:     ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAG                         GGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaat ... tgcatgccagGGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
EST: gi|32934643|gb|CF039455.1|CF039455
EST:     ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAG                         GGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaat ... tgcatgccagGGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
EST: gi|32930749|gb|CF035561.1|CF035561
EST:     ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAG                         GGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaat ... tgcatgccagGGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
EST: gi|45567822|gb|CK985763.1|CK985763
EST:     ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAG                         GGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaat ... tgcatgccagGGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
EST: gi|60346084|gb|DN213057.1|DN213057
EST:     ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAG                         GGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaat ... tgcatgccagGGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
EST: gi|211296158|gb|FL473352.1|FL473352
EST:     GAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAG                         GGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
genomic: GAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaat ... tgcatgccagGGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
EST: gi|17932440|gb|BM269400.1|BM269400
EST:     ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAG                         GGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaat ... tgcatgccagGGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
EST: gi|6056907|gb|AW091312.1|AW091312
EST:     ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAG                         GGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaat ... tgcatgccagGGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
EST: gi|60401114|gb|DN233921.1|DN233921
EST:     ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAG                         GGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaat ... tgcatgccagGGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
EST: gi|211107785|gb|FL216765.1|FL216765
EST:     ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAG                         GGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaat ... tgcatgccagGGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
EST: gi|6223799|gb|AW154930.1|AW154930
EST:     ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAG                         GGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaat ... tgcatgccagGGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
EST: gi|5686769|gb|AI939862.1|AI939862
EST:     ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAG                         GGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaat ... tgcatgccagGGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
EST: gi|22542222|gb|BU092660.1|BU092660
EST:     ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAG                         GGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaat ... tgcatgccagGGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
EST: gi|60401080|gb|DN233887.1|DN233887
EST:     ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAG                         GGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaat ... tgcatgccagGGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
EST: gi|31359252|gb|CD443609.1|CD443609
EST:     ACCGCGAAAGGGTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAG                         GGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaat ... tgcatgccagGGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
EST: gi|32932571|gb|CF037383.1|CF037383
EST:     ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAG                         GGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaat ... tgcatgccagGGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
EST: gi|6223801|gb|AW154932.1|AW154932
EST:     ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAG                         GGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaat ... tgcatgccagGGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
EST: gi|71770686|gb|DR968623.1|DR968623
EST:     ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAG                         GGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaat ... tgcatgccagGGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
EST: gi|32840612|gb|CD980293.1|CD980293
EST:     ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAG                         GGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaat ... tgcatgccagGGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
EST: gi|26559123|gb|CA831358.1|CA831358
EST:     ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAG                         GGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaat ... tgcatgccagGGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
EST: gi|211107786|gb|FL216766.1|FL216766
EST:     ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAG                         GGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaat ... tgcatgccagGGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
EST: gi|60399775|gb|DN232585.1|DN232585
EST:     ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAG                         GGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaat ... tgcatgccagGGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
EST: gi|211375011|gb|FL430792.1|FL430792
EST:     TCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAG                         GSCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
genomic: TCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaat ... tgcatgccagGGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
EST: gi|6223798|gb|AW154929.1|AW154929
EST:     ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAG                         GGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaat ... tgcatgccagGGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
EST: gi|211296159|gb|FL473353.1|FL473353
EST:     ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAG                         GGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaat ... tgcatgccagGGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
EST: gi|32932100|gb|CF036912.1|CF036912
EST:     ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAG                         GGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaat ... tgcatgccagGGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
EST: gi|211365280|gb|FL463922.1|FL463922
EST:     ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAG                         GGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaat ... tgcatgccagGGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
EST: gi|32867861|gb|CF007543.1|CF007543
EST:     ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAG                         GGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaat ... tgcatgccagGGCCATGGATTTCCTTGTTGAGTTGTTCCGTAACCTGCTTGAGCATCCAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAAGTATGGACACATGTACAGCATGGTTCAGGAAGAAGTTCAAAACAAGACCGCGAAAGGTTCCTCAAGCTGCACAAATGGTCTTCTGTGGCTCACGAGgtgcttcaatttcttattgttttgtcgtttttcattgcaacttgatcagcacgcatagtatgtgacttttatttactcaaaaaaattgcatgccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC