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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtccccctaggacccaggctccaggcaccaccgttctctcgatttgaattcgacgttacgcagagttttggtttgatctctgatggcatccgctcccccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCCGAGGTGCCCTCTGAAGACGTCGTCG

Basic information

species Zea mays
transcript GRMZM2G146206_T05
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146206_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g62420.2 (Oryza sativa), 3'ss of exon 1
gtaagt---ccccctaggacccag-gctccaggcaccaccgttctctcgatttgaattcgacgttacgcagagttttggtttgatctct---gatggcatccgct-cccccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCCGAGGTGCCCTCTGAAGACGTCGTCG
||||||   ||||| || ||     |   ||    |||   | |    ||   | |  ||  | |    || | |  || |||   | |   ||||   | ||||    | | |||||||| || || || |||||||||||||||||||||||||| |||||| | |||||||||||||| || ||||||||||
gtaagtattccccccagcactagtcgtctcacaatccagattccggatgagccggagacgctgctgatgagtgatgaggcttgggttttatcgatgcgctgcgctgttgctgcgtgcagAATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCCGAGGTGCCCTCCGAGGACGTCGTCG
















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|34391231|gb|CF384459.1|CF384459
EST:     GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGC                         AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACGAAGCC
genomic: GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGCgtaagtcccc ... ccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
EST: gi|149095398|gb|EE181040.2|EE181040
EST:     GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGC                         AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
genomic: GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGCgtaagtcccc ... ccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
EST: gi|37361179|gb|CF602468.1|CF602468
EST:     GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGC                         AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACGAAGCC
genomic: GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGCgtaagtcccc ... ccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
EST: gi|61118911|gb|DN559872.1|DN559872
EST:     GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGC                         AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACGAAGCC
genomic: GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGCgtaagtcccc ... ccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
EST: gi|6021382|gb|AW066310.1|AW066310
EST:     GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGC                         AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACGAAGCC
genomic: GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGCgtaagtcccc ... ccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
EST: gi|211332034|gb|FL380493.1|FL380493
EST:     GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGC                         AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
genomic: GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGCgtaagtcccc ... ccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
EST: gi|76928137|gb|DV171503.1|DV171503
EST:     GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGC                         AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
genomic: GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGCgtaagtcccc ... ccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
EST: gi|38568995|gb|CF974880.1|CF974880
EST:     GTGGGTGGCAACTGGAAATGC                         AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACGAAGCC
genomic: GTGGGTGGCAACTGGAAATGCgtaagtcccc ... ccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
EST: gi|74242319|gb|DT650233.1|DT650233
EST:     GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGC                         AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
genomic: GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGCgtaagtcccc ... ccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
EST: gi|148995363|gb|EE034577.2|EE034577
EST:     GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGC                         AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
genomic: GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGCgtaagtcccc ... ccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
EST: gi|31351356|gb|CD435713.1|CD435713
EST:     GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGC                         AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
genomic: GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGCgtaagtcccc ... ccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
EST: gi|32915342|gb|CF020154.1|CF020154
EST:     GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATCC                         AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
genomic: GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGCgtaagtcccc ... ccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
EST: gi|37361339|gb|CF602628.1|CF602628
EST:     GACGACCAATGGCTTCCAGGAAGTTCCTCGTGGGTGGCAACTGGAAATGC                         AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACGAAGCC
genomic: GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGCgtaagtcccc ... ccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
EST: gi|211504304|gb|FL391671.1|FL391671
EST:     GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGC                         AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
genomic: GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGCgtaagtcccc ... ccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
EST: gi|31354853|gb|CD439210.1|CD439210
EST:     GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGCAAATGC                         AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
genomic: GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGCgtaagtcccc ... ccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
EST: gi|32851161|gb|CD990842.1|CD990842
EST:     GGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATCC                         AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
genomic: GGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGCgtaagtcccc ... ccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
EST: gi|211405784|gb|FL400096.1|FL400096
EST:     GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGC                         AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
genomic: GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGCgtaagtcccc ... ccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
EST: gi|38229553|gb|CF919866.1|CF919866
EST:     GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGC                         AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACGAAGCC
genomic: GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGCgtaagtcccc ... ccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
EST: gi|211387019|gb|FL373417.1|FL373417
EST:     GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGC                         AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
genomic: GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGCgtaagtcccc ... ccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
EST: gi|28566674|gb|CB278322.1|CB278322
EST:     GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGC                         AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACGAAGCC
genomic: GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGCgtaagtcccc ... ccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
EST: gi|26557616|gb|CA829851.1|CA829851
EST:     GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGC                         AACGGTACTGGCGAGGAC
genomic: GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGCgtaagtcccc ... ccgtgtgcagAACGGTACTGGCGAGGAC
EST: gi|28576049|gb|CB281941.1|CB281941
EST:     GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGC                         AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
genomic: GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGCgtaagtcccc ... ccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
EST: gi|71436570|gb|DR817620.1|DR817620
EST:     CTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGC                         AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
genomic: CTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGCgtaagtcccc ... ccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
EST: gi|211247588|gb|FL403551.1|FL403551
EST:     GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGC                         AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
genomic: GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGCgtaagtcccc ... ccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
EST: gi|33770896|gb|CF273190.1|CF273190
EST:     GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGC                         AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACGAAGCC
genomic: GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGCgtaagtcccc ... ccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
EST: gi|211416108|gb|FL411159.1|FL411159
EST:     GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGC                         AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
genomic: GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGCgtaagtcccc ... ccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
EST: gi|30160504|gb|CB924233.1|CB924233
EST:     GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGC                         AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACGAAGCC
genomic: GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGCgtaagtcccc ... ccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
EST: gi|149097486|gb|EE183358.2|EE183358
EST:     GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGC                         AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
genomic: GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGCgtaagtcccc ... ccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
EST: gi|71330645|gb|DR802096.1|DR802096
EST:     GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGC                         AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
genomic: GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGCgtaagtcccc ... ccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
EST: gi|149005099|gb|EE039628.2|EE039628
EST:     GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGC                         AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC
genomic: GACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGCgtaagtcccc ... ccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgttacgcagagttttggtttgatctctgatggcatccgctcccccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCCGAGGTGCCCTCTGAAGACGTCGTCG
                         ctctgat  putative branch site (score: 4)
                                    tccgctccccc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtccccctaggacccaggctccaggcaccaccgttctctcgatttgaattcgacgttacgcagagttttggtttgatctctgatggcatccgctcccccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCCGAGGTGCCCTCTGAAGACGTCGTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA