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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtcctggttcctccccttgcctggccgaggttttcctttttcaggacttggatgtgttttgcgctaacactggagtgtgcttttgtgctgatgtgatgcagATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACG

Basic information

species Zea mays
transcript GRMZM2G065757_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G065757_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g49200.2 (Oryza sativa), 3'ss of exon 1
gtgcgtcctggttcctccccttgcctggccgaggttttcctttt--tcaggacttggatgtgttttgcgctaacactggagtgtgcttttgtgctgatg--tgatgcagATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACG
||| ||||  ||||    |  ||       |   || |||      ||  |    |  || |   || |||||   |||| | |  |||  |  ||  |  |||||||||| || |||| ||||||||| ||||||||||| || ||||| ||||||||  ||||||| |
gtgagtccctgttcgatgcactggtcaaggggaattctcccaagagtcttgttgcgattgcgacctgtgctaatggtggatttttttttccttgtggcgattgatgcagATTGCGTGCTTCTTCCACTCTCGCTACAAGTCCGGACAGTCGAGCACTTATCAGAAGAATG
















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|31440937|gb|CD510368.1|CD510368
EST:     ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCG                         ATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
genomic: ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCGgtgcgtcctg ... tgtgatgcagATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
EST: gi|29576941|gb|CB617053.1|CB617053
EST:     ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCG                         ATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
genomic: ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCGgtgcgtcctg ... tgtgatgcagATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
EST: gi|149095835|gb|EE181486.2|EE181486
EST:     ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCG                         ATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
genomic: ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCGgtgcgtcctg ... tgtgatgcagATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
EST: gi|149078470|gb|EE167250.2|EE167250
EST:     ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCG                         ATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
genomic: ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCGgtgcgtcctg ... tgtgatgcagATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
EST: gi|32830382|gb|CD970060.1|CD970060
EST:     ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCG                         ATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
genomic: ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCGgtgcgtcctg ... tgtgatgcagATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
EST: gi|32840007|gb|CD979688.1|CD979688
EST:     ACACCGGCAGGTCCAACCTCTGGGTGCCGGCCTCCAAGTGCTACTTCTCG                         ATCGCTTGCTACTTCCACTCGCGCTACAAGGCAGGGCAGTCAAGCACTTAC
genomic: ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCGgtgcgtcctg ... tgtgatgcagATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
EST: gi|32850768|gb|CD990449.1|CD990449
EST:     ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCG                         ATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
genomic: ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCGgtgcgtcctg ... tgtgatgcagATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
EST: gi|211063419|gb|FL406486.1|FL406486
EST:     ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCG                         ATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
genomic: ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCGgtgcgtcctg ... tgtgatgcagATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
EST: gi|211314123|gb|FL216094.1|FL216094
EST:     ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCG                         ATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
genomic: ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCGgtgcgtcctg ... tgtgatgcagATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
EST: gi|50338072|gb|CO533198.1|CO533198
EST:     ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCG                         ATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
genomic: ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCGgtgcgtcctg ... tgtgatgcagATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
EST: gi|32839505|gb|CD979186.1|CD979186
EST:     ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCG                         ATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
genomic: ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCGgtgcgtcctg ... tgtgatgcagATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
EST: gi|211514658|gb|FK981816.1|FK981816
EST:     GGGTGCCGTCCTCCAAGTGCTACTTCTCG                         ATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
genomic: GGGTGCCGTCCTCCAAGTGCTACTTCTCGgtgcgtcctg ... tgtgatgcagATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
EST: gi|32839962|gb|CD979643.1|CD979643
EST:     ACACCGGCAGGTCCAACCTCTGGGTGCCGGCCTCCAAGTGCTACTTCTCG                         ATCGCTTGCTACTTCCACTCGCGCTACAAGGCAGGGCAGTCAAGCACTTAC
genomic: ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCGgtgcgtcctg ... tgtgatgcagATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
EST: gi|32839693|gb|CD979374.1|CD979374
EST:     ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCG                         ATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
genomic: ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCGgtgcgtcctg ... tgtgatgcagATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
EST: gi|148956524|gb|EC902364.2|EC902364
EST:     ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCG                         ATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
genomic: ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCGgtgcgtcctg ... tgtgatgcagATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
EST: gi|211092714|gb|FK945554.1|FK945554
EST:     ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCG                         ATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
genomic: ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCGgtgcgtcctg ... tgtgatgcagATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
EST: gi|211312095|gb|FL216082.1|FL216082
EST:     ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCG                         ATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
genomic: ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCGgtgcgtcctg ... tgtgatgcagATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
EST: gi|148931369|gb|EC874278.2|EC874278
EST:     ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCG                         ATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
genomic: ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCGgtgcgtcctg ... tgtgatgcagATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
EST: gi|33099258|gb|CF059218.1|CF059218
EST:     ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCG                         ATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
genomic: ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCGgtgcgtcctg ... tgtgatgcagATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
EST: gi|211314127|gb|FL216098.1|FL216098
EST:     ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCG                         ATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC
genomic: ACACCGGCAGTTCCAACCTCTGGGTGCCGTCCTCCAAGTGCTACTTCTCGgtgcgtcctg ... tgtgatgcagATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgtcctggttcctccccttgcctggccgaggttttcctttttcaggacttggatgtgttttgcgctaacactggagtgtgcttttgtgctgatgtgatgcagATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC