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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCACTTCAAGGAAATAGACTGATTGGCAAAATTCCTGAAGTGATTGGCCTCATGCAGGCTCTTGCTGTCCTgtgagtacaaaaaaatgacacttcaatccatgcttattgatttctttatctttactagcctataatgagttcttttgtcaaacattgtttctcag

Basic information

species Zea mays
transcript GRMZM2G082855_T05
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082855_T04 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os06g03970.1 (Oryza sativa), 5'ss of exon 10
GTCACTTCAAGGAAATAGACTGATTGGCAAAATTCCTGAAGTGATTGGCCTCATGCAGGCTCTTGCTGTCCTgtgagtacaaaaaaatgacacttcaatccatg---cttattgatttcttta-tctttactagcctataatgagttcttttgtcaaacattgtttctcag-----------------------------
||||||||||||||||||||||| ||| |||||||| || ||||||||||| ||||| ||||||||||| |||||||||    |  | |||| ||||||||||     ||| |  ||||| || | |||  | | ||  |||    |  ||| |  || ||||  |                                  
GTCACTTCAAGGAAATAGACTGACTGGGAAAATTCCAGATGTGATTGGCCTGATGCAAGCTCTTGCTGTTCTgtgagta---gagcacgacatttcaatccataggttttagtagtttctgtaatatttttttgactgaaattcagtagtttctgtaatattggataatgaattcttatattcattttttttattctcag

upper sequence: GRMZM2G082855_T04 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA10G38730.1 (Glycine max), 5'ss of exon 11
GTCACTTCAAGGAAATAGACTGATTGGCAAAATTCCTGAAGTGATTGGCCTCATGCAGGCTCTTGCTGTCCTgtgagtacaaaaaaatgacacttcaatccatgcttattgatttctttatctttactagcctataatgagttcttttgtcaaacattgtttctcag-----------
||||||||||||||||||||| | ||| || ||||| |||||||||||  | ||||| || |||||  |  ||| || | |    |       | |||         | |  |  || | |  || ||  | | | |||   |    | |      ||||||||              
GTCACTTCAAGGAAATAGACTAACTGGGAAGATTCCAGAAGTGATTGGTTTAATGCAAGCCCTTGCAATATTgtaagcataccttatcatttttccaagatgaagaaaatattagctatttaattgct--catttgatgcaattcaatatatttttttgtttcttgacattgtggtag

upper sequence: GRMZM2G082855_T04 (Zea mays), 5'ss of exon 10
lower sequence: AT5G62230.1 (Arabidopsis thaliana), 5'ss of exon 11
GTCACTTCAAGGAAATAGACTGATTGGCAAAATTCCTGAAGTGATTGGCCTCATGCAGGCTCTTGCTGTCCTgtgagtacaaaaaa-atgacacttcaatccatgcttattgatttctttatctttactagcctataatgagttcttttgtcaaacattgtttctcag
||||||||||||||| ||| |||  || | |||||| ||||| ||||| || |||||||||||||||||  ||| ||| |||   | |||  |    ||      |  | |   ||||| |  ||  || | ||     || ||  |   ||  |  |   ||| |||
GTCACTTCAAGGAAACAGATTGACGGGTAGAATTCCAGAAGTTATTGGTCTAATGCAGGCTCTTGCTGTTTTgtaagttcaattcatatggaaaagtaacg---acaaagtacattcttgaatttggctcgtct-----gactttgtgaatcctat-tcaattcacag

upper sequence: GRMZM2G082855_T04 (Zea mays), 5'ss of exon 10
lower sequence: AT5G07180.1 (Arabidopsis thaliana), 5'ss of exon 11
GTCACTTCAAGGAAATAGACTGATTGGCAAAATTCCTGAAGTGATTGGCCTCATGCAGGCTCTTGCTGTCCTgtgagtacaaaaaaatgacacttcaatccatgcttattgatttctttatctttactagcctataa-tgagttcttttgtcaaacattgtttctcag
||||||||||||||| |   ||| ||||| |||||| ||||||||||| || |||||||||||||||||  |||  ||     |   | | | |  ||| | ||||| ||   | || |   ||      | | | | ||| |    |   |  |      | | |||
GTCACTTCAAGGAAACAAGTTGACTGGCAGAATTCCGGAAGTGATTGGTCTGATGCAGGCTCTTGCTGTATTgtatgtc----attttcatattcaaatgcttgcttttttcctactctcgtttcttgctcttctgactgaatgaaataaacttat-ccaatgcgcag

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|148940443|gb|EC885241.2|EC885241
EST:     ATTGGCAAAATTCCTGAAGTGATTGGCCTCATGCAGGCTCTTGCTGTCCT                         AGACCTTAGTGAGAATGAACTGGTGGGGCCTATTCCTCCTATACTTGGCAA
genomic: ATTGGCAAAATTCCTGAAGTGATTGGCCTCATGCAGGCTCTTGCTGTCCTgtgagtacaa ... tgtttctcagAGACCTTAGTGAGAATGAACTGGTGGGGCCTATTCCTCCTATACTTGGCAA
EST: gi|149079906|gb|EE168912.2|EE168912
EST:     ATTGGCAAAATTCCTGAAGTGATTGGCCTCATGCAGGCTCTTGCTGTCCT                         AGACCTTAGTGAGAATGAACTGGTGGGGCCTATTCCTCCTATACTTGGCAA
genomic: ATTGGCAAAATTCCTGAAGTGATTGGCCTCATGCAGGCTCTTGCTGTCCTgtgagtacaa ... tgtttctcagAGACCTTAGTGAGAATGAACTGGTGGGGCCTATTCCTCCTATACTTGGCAA
EST: gi|148964982|gb|EC906062.2|EC906062
EST:     ATTGGCAAAATTCCTGAAGTGATTGGCCTCATGCAGGCTCTTGCTGTCCT                         AGACCTTAGTGAGAATGAACTGGTGGGGCCTATTCCTCCTATACTTGGCAA
genomic: ATTGGCAAAATTCCTGAAGTGATTGGCCTCATGCAGGCTCTTGCTGTCCTgtgagtacaa ... tgtttctcagAGACCTTAGTGAGAATGAACTGGTGGGGCCTATTCCTCCTATACTTGGCAA
EST: gi|101383199|gb|EB813654.1|EB813654
EST:     ATTGGCAAAATTCCTGAAGTGATTGGCCTCATGCAGGCTCTTGCTGTCCT                         AGACCTTAGTGAGAATGAACTGGTGGGGCCTATTCCTCCTATACTTGGCAA
genomic: ATTGGCAAAATTCCTGAAGTGATTGGCCTCATGCAGGCTCTTGCTGTCCTgtgagtacaa ... tgtttctcagAGACCTTAGTGAGAATGAACTGGTGGGGCCTATTCCTCCTATACTTGGCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCACTTCAAGGAAATAGACTGATTGGCAAAATTCCTGAAGTGATTGGCCTCATGCAGGCTCTTGCTGTCCTgtgagtacaaaaaaatgacacttcaatccatgcttattgatttctttatctttactagcctataatgagttcttttgtcaaacattgtttctcag

- - - - - - - - - - - - - - - - -  CTGAAG