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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcggttttggccttgtgtcgtttattttttgcacaagatgtagatgtttcaggggttcggaatcgcaaggtgctgatatatatagctttatttgctttgtgcgcagGGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGGCTGGAAGTGTCAGGACACGGACTAATCGCTCGGGTGGTGTGCAG

Basic information

species Zea mays
transcript GRMZM2G036861_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G036861_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g14990.1 (Oryza sativa), 3'ss of exon 9
--gtgcggttttggccttgtgtcgtttattttttgcacaagatgtagatgtttcaggggttcggaatcgcaaggtgctgatatatatagctttatttgctttgtgcgcagGGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGGCTGGAAGTGTCAGGACACGGACTAATCGCTCGGGTGGTGTGCAG
      |  ||   |      |  ||  ||  ||  |     || | ||   |   |  | |  | |     | | |||   |  |||        |   |||||| |||| || ||||  || ||||||||||||||||||||||| ||||||||| ||||||||| ||| || ||| | |||||||| || || |||||||||
gtaattgaattaatctgcacataattagttgatt-tattttttgcaaatagct-gtgcatgccaactactttgctactggcctcaatactaactaataacttgtgcccagGTACTGACTACACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGGCTGGAAATGTGAGAACAAGAACTAATCGTTCAGGCGGTGTGCAG
















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|148951093|gb|EC896758.2|EC896758
EST:     GCTTTCTATTCCTGCGAGCAACGGGTTCGAGATTGGCAGCGGATTCGCCG                         GGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGG
genomic: GCTTTCTATTCCTGCGAGCAACGGGTTCGAGATTGGCAGCGGATTCGCCGgtgcggtttt ... ttgtgcgcagGGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGG
EST: gi|78109643|gb|DV528059.1|DV528059
EST:     GCTTTCTATTCCTGCGAGCAACGGGTTCGAGATTGGCAGCGGATTCGCCG                         GGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGG
genomic: GCTTTCTATTCCTGCGAGCAACGGGTTCGAGATTGGCAGCGGATTCGCCGgtgcggtttt ... ttgtgcgcagGGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGG
EST: gi|211012763|gb|FL448392.1|FL448392
EST:     GCTTTCTATTCCTGCGAGCAACGGGTTCGAGATTGGCAGCGGATTCGCCG                         GGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGG
genomic: GCTTTCTATTCCTGCGAGCAACGGGTTCGAGATTGGCAGCGGATTCGCCGgtgcggtttt ... ttgtgcgcagGGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGG
EST: gi|76281789|gb|DV021357.1|DV021357
EST:     GCTTTCTATTCCTGCGAGCAACGGGTTCGAGATTGGCAGCGGATTCGCCG                         GGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGG
genomic: GCTTTCTATTCCTGCGAGCAACGGGTTCGAGATTGGCAGCGGATTCGCCGgtgcggtttt ... ttgtgcgcagGGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGG
EST: gi|148940355|gb|EC885142.2|EC885142
EST:     GAGCAACGGGTTCGAGATTGGCAGCGGATTCGCCG                         GGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGG
genomic: GAGCAACGGGTTCGAGATTGGCAGCGGATTCGCCGgtgcggtttt ... ttgtgcgcagGGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGG
EST: gi|76934910|gb|DV174082.1|DV174082
EST:     ATTGGCAGCGGATTCGCCG                         GGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGG
genomic: ATTGGCAGCGGATTCGCCGgtgcggtttt ... ttgtgcgcagGGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGG
EST: gi|149098824|gb|EE184837.2|EE184837
EST:     GCTTTCTATTCCTGCGAGCAACGGGTTCGAGATTGGCAGCGGATTCGCCG                         GGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGG
genomic: GCTTTCTATTCCTGCGAGCAACGGGTTCGAGATTGGCAGCGGATTCGCCGgtgcggtttt ... ttgtgcgcagGGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGG
EST: gi|78109644|gb|DV528060.1|DV528060
EST:     GCTTTCTATTCCTGCGAGCAACGGGTTCGAGATTGGCAGCGGATTCGCCG                         GGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGG
genomic: GCTTTCTATTCCTGCGAGCAACGGGTTCGAGATTGGCAGCGGATTCGCCGgtgcggtttt ... ttgtgcgcagGGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggggttcggaatcgcaaggtgctgatatatatagctttatttgctttgtgcgcagGGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGGCTGGAAGTGTCAGGACACGGACTAATCGCTCGGGTGGTGTGCAG
                   tgctgat  putative branch site (score: 3)
                                       tttgcttt  putative PPT
                        atatatatagctttat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcggttttggccttgtgtcgtttattttttgcacaagatgtagatgtttcaggggttcggaatcgcaaggtgctgatatatatagctttatttgctttgtgcgcagGGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGGCTGGAAGTGTCAGGACACGGACTAATCGCTCGGGTGGTGTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG