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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGCTAACATGGAACGGGCAGAAGGAGATACCAGTGGGCAATTTGACCCGCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaatttttctttcctggtcaactcaaatctaggcctctatggtgatgccgggctgtatccttgattccatctaccggttcttcag

Basic information

species Zea mays
transcript GRMZM2G093359_T02
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G093359_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os02g10310.1 (Oryza sativa), 5'ss of exon 13
GGAGCTAACATGGAACGGGCAGAAGGAGATACCAGTGGGCAATTTGACCCGCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaatttttctttcctggtcaactcaaatctaggcctctat---------------------ggtgatgccgggctgtatccttgat----tccatctaccggttctt-cag
||||||||||||||| ||||||||||||||| |||| || || | |||||||||||| ||||||||||| |||||||||||||||||||  || |||||||||  |  |  |  |   || || ||||  ||||| |||  |||| |                     |  ||| ||  ||| |||| |||||    |||||||||  ||| || |||
GGAGCTAACATGGAATGGGCAGAAGGAGATATCAGTTGGAAACTCGACCCGCAAGTTCCTAGAAGATGGGGATGAGGTCATCTTGACAGCTTGTTGCAAGgtacagcaatctcataagtcttgatcaaaccaaatttagagctcttttcgtctaaaacaaatatctttgaagattccatgctctatc-ttgatgccatccatctacatgtttttacag
















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|9028434|gb|BE238579.1|BE238579
EST:     AGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGC-AG                         GGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
genomic: AGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
EST: gi|19058677|gb|BM737344.1|BM737344
EST:     GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
genomic: GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
EST: gi|5499508|gb|AI855375.1|AI855375
EST:     GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGGCG
genomic: GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
EST: gi|5740120|gb|AI947810.1|AI947810
EST:     GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTCCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
genomic: GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
EST: gi|8516666|gb|BE123391.1|BE123391
EST:     GCAAGTTTTTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAG                         GGTGAAGGCTACACCATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
genomic: GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
EST: gi|149008950|gb|EE153723.2|EE153723
EST:     GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
genomic: GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
EST: gi|89252602|gb|DY624388.1|DY624388
EST:     GCAAGTTTTTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
genomic: GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
EST: gi|149090119|gb|EE179417.2|EE179417
EST:     GCAAGTTTTTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
genomic: GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
EST: gi|148983249|gb|EE029216.2|EE029216
EST:     GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGCCAGGATGCTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG
genomic: GCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaa ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACTTGCACTGGGAAGGTCCTGCCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGCTAACATGGAACGGGCAGAAGGAGATACCAGTGGGCAATTTGACCCGCAAGTTTCTAGAAGATGGAGATGAGGTCATCTTGACAGGATGCTGCAAGgtattgtgaatttttctttcctggtcaactcaaatctaggcctctatggtgatgccgggctgtatccttgattccatctaccggttcttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC