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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaactattttgttgagtgcttatagattcatttgtgtattgggcatgcatacattgtaataactggatgacgtatttgctctgcataatacagGATGATGCAGATTGGTCTACTTTGGGAGTGAAAGAT

Basic information

species Zea mays
transcript GRMZM2G028733_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028733_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g36930.1 (Oryza sativa), 3'ss of exon 2
gtaaactattttgttgagtgcttatagattcatttgtgtattgggcatgcatacattgta---------ataactggatgacgtatttgctctgc--ataatacagGATGATGCAGATTGGTCTACTTTGGGAGTGAAAGAT
||||  ||  |  |   |||||||| ||  ||  ||  | |   | |    || |||  |          ||||    ||    |||| || |     |||| |||||||||||||||||||||||||||||||||||||||
gtaa--tacatgctcacgtgcttatggacacaactgattttcatgtacttctatatttaatctttctttgtaacaacgtggtcaattttctgtatttgtaatgcagGATGATGCAGATTGGTCTACTTTGGGAGTGAAAGAT

upper sequence: GRMZM2G028733_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT3G21280.1 (Arabidopsis thaliana), 3'ss of exon 2
---------gtaaactattttgttgagtgcttatagattcatttgtgtattgggc-atgcatacattg-taataactggatgacgtatttgctctgcataatacagGATGATGCAGATTGGTCTACTTTGGGAGTGAAAGAT
          |  |||    || || ||| || ||| || | |  ||| ||   | ||   |   ||| | || | |  | ||    |||  | |   |    ||||||||||||||||||||||| |||||| ||||| ||
gtaatttggattcacttgcctgctgcgtgtttgtagttttactgctgtgttcctctatttgtttgttgatgatgattt-acgataggtttcttttaattttcgcagGATGATGCAGATTGGTCTACGTTGGGACTGAAAAAT

upper sequence: GRMZM2G028733_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv09s0002g02500.t01 (Vitis vinifera), 3'ss of exon 2
----------------------------------------------------------------------gtaaactattttgttgagtgcttatagattcatttgtgtattgggcatgcatacattg--taataactggatgacgtatttgctctgcataatacagGATGATGCAGATTGGTCTACTTTGGGAGTGAAAGAT
                                                                      || ||  ||     | | |||| |    |||   ||||  |||    ||   | |  |  |  ||  |   | |  | | | || |  |||||||||||||||||||||||||| || || ||||| ||||| 
gtaattggatagttctgtatgatatggaaaagtagaattgattcataacttacttgattgaatatagtttgtgaatgataaacctcactgctcaagagttc---tgtggtttgcatttgttaagagcggctgttagatttcttagctgtgttcttttgataatacagGATGATGCAGATTGGTCAACCTTAGGAGTAAAAGAG

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|211181945|gb|FL254908.1|FL254908
EST:     GTGTGCCACCTGAACGCCAAAAAATTATGGTGAAGGGTGGATTATTGAAG                         GATGATGCAGATTGGTCTACTTTGGGAGTGAAAGAT
genomic: GTGTGCCACCTGAACGCCAAAAAATTATGGTGAAGGGTGGATTATTGAAGgtaaactatt ... cataatacagGATGATGCAGATTGGTCTACTTTGGGAGTGAAAGAT
EST: gi|211181944|gb|FL254907.1|FL254907
EST:     GTGTGCCACCTGAACGCCAAAAAATTATGGTGAAGGGTGGATTATTGAAG                         GATGATGCAGATTGGTCTACTTTGGGAGTGAAAGAT
genomic: GTGTGCCACCTGAACGCCAAAAAATTATGGTGAAGGGTGGATTATTGAAGgtaaactatt ... cataatacagGATGATGCAGATTGGTCTACTTTGGGAGTGAAAGAT
EST: gi|211181946|gb|FL254909.1|FL254909
EST:     GTGTGCCACCTGAACGCCAAAAAATTATGGTGAAGGGTGGATTATTGAAG                         GATGATGCAGATTGGTCTACTTTGGGAGTGAAAGAT
genomic: GTGTGCCACCTGAACGCCAAAAAATTATGGTGAAGGGTGGATTATTGAAGgtaaactatt ... cataatacagGATGATGCAGATTGGTCTACTTTGGGAGTGAAAGAT
EST: gi|211181947|gb|FL254910.1|FL254910
EST:     GTGTGCCACCTGAACGCCAAAAAATTATGGTGAAGGGTGGATTATTGAAG                         GATGATGCAGATTGGTCTACTTTGGGAGTGAAAGAT
genomic: GTGTGCCACCTGAACGCCAAAAAATTATGGTGAAGGGTGGATTATTGAAGgtaaactatt ... cataatacagGATGATGCAGATTGGTCTACTTTGGGAGTGAAAGAT
EST: gi|211181949|gb|FL254912.1|FL254912
EST:     GTGTGCCACCTGAACGCCAAAAAATTATGGTGAAGGGTGGATTATTGAAG                         GATGATGCAGATTGGTCTACTTTGGGAGTGAAAGAT
genomic: GTGTGCCACCTGAACGCCAAAAAATTATGGTGAAGGGTGGATTATTGAAGgtaaactatt ... cataatacagGATGATGCAGATTGGTCTACTTTGGGAGTGAAAGAT
EST: gi|211181948|gb|FL254911.1|FL254911
EST:     GTGTGCCACCTGAACGCCAAAAAATTATGGTGAAGGGTGGATTATTGAAG                         GATGATGCAGATTGGTCTACTTTGGGAGTGAAAGAT
genomic: GTGTGCCACCTGAACGCCAAAAAATTATGGTGAAGGGTGGATTATTGAAGgtaaactatt ... cataatacagGATGATGCAGATTGGTCTACTTTGGGAGTGAAAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgggcatgcatacattgtaataactggatgacgtatttgctctgcataatacagGATGATGCAGATTGGTCTACTTTGGGAGTGAAAGAT
                  taataac  putative branch site (score: 1)
          atacattgtaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaactattttgttgagtgcttatagattcatttgtgtattgggcatgcatacattgtaataactggatgacgtatttgctctgcataatacagGATGATGCAGATTGGTCTACTTTGGGAGTGAAAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT