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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGCGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttgtgtttgcgctcggaatggtttcctgtgcttgtttggattgttgatgttgttttcttctgtgatttacag

Basic information

species Zea mays
transcript GRMZM2G140689_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G140689_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os06g06410.1 (Oryza sativa), 5'ss of exon 2
GTACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGCGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttgtgtttgcgctcggaatggtttcctgtgcttgtttg--gattgttgatgttgttttctt--ctgtgatttacag--------------
|||||||||||||||| |||||| ||||||||||||    || |||||||| ||||| |||||||||||||||        |   | |||    |||  |     |||||   |||| |||   |  ||   ||      |  ||   |              
GTACAAGGAGGATGTGTTGAACCCCAAGAAGAAGGATAACGAGAAGGAGAAGCTCGGGCGGAATGTgtgagtgcctaccgcgttttgggatccatttgtttaaagtgtttaacgattattgggatgattggattaatcaagtcttgttggtttattattttag
















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|31352269|gb|CD436626.1|CD436626
EST:     CTGAACCACAAGAAGAAGGACGCGGACAAGGAGAAACTCGGCCGGAATGT                         GCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
genomic: CTGAACCACAAGAAGAAGGACGCGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
EST: gi|71445647|gb|DR826697.1|DR826697
EST:     CGGCCGGAATGT                         GCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
genomic: CGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
EST: gi|88754303|gb|DY538444.1|DY538444
EST:     AACTCGGCCGGAATGT                         GCCGCAGGTTTCGTCGGCG-TGTTCTTCAGCTACAACACAGCATTGGGGCC
genomic: AACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
EST: gi|88746998|gb|DY531139.1|DY531139
EST:     CTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGT                         GCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
genomic: CTGAACCACAAGAAGAAGGACGCGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
EST: gi|74245266|gb|DT653180.1|DT653180
EST:     GGACAAGGAGAAACTCGGCCGGAATGT                         GCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
genomic: GGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
EST: gi|74239821|gb|DT647735.1|DT647735
EST:     GAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGT                         GCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
genomic: GAAGAAGGACGCGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
EST: gi|213173441|gb|FM193835.1|FM193835
EST:     CTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGT                         GCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
genomic: CTGAACCACAAGAAGAAGGACGCGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
EST: gi|78025632|gb|DV494019.1|DV494019
EST:     CTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGT                         GCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
genomic: CTGAACCACAAGAAGAAGGACGCGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
EST: gi|33468200|gb|CF245249.1|CF245249
EST:     CTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGT                         GCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
genomic: CTGAACCACAAGAAGAAGGACGCGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
EST: gi|78077064|gb|DV505498.1|DV505498
EST:     CTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGT                         GCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
genomic: CTGAACCACAAGAAGAAGGACGCGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
EST: gi|76292363|gb|DV031931.1|DV031931
EST:     CAAGGAGAAACTCGGCCGGAATGT                         GCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
genomic: CAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGCGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttgtgtttgcgctcggaatggtttcctgtgcttgtttggattgttgatgttgttttcttctgtgatttacag

- - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - -  GGAGAA