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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataacttttatgaagggaaggttctgcatttaggaatgctttccattgtggtacatctatatctattgttgatttttagttcataatatgtattctgttgttactatgtgtattccatagGTTGCGGACTTTGGTGTTTCTGCACAGCTGACTAAAACAATGTCTAGGAGGAAG

Basic information

species Zea mays
transcript GRMZM2G027756_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027756_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g32400.2 (Oryza sativa), 3'ss of exon 6
gtataacttttatgaagggaaggttctgcatttaggaatgctttccattgtggtacatctatatctattgttgatttttagttcataatatgtattctgttgttactatgtgtattccatagGTTGCGGACTTTGGTGTTTCTGCACAGCTGACTAAAACAATGTCTAGGAGGAAG
||||||| ||| | | |         ||  |||| |     ||  ||   |||| |    |  ||| || || ||| |||| | | ||||| ||| |    |||  ||| | ||||||||||||||| ||||||||||||||||| |||||||||||||||||||| ||||| |||
gtataacctttct-acgatttctcaatgattttatgttccattgtcaggatggtcc--tgagttctgttattaattcttagcttacaatatctatgcaaacgtttatatttttattccatagGTTGCAGACTTTGGTGTTTCTGCGCAGCTGACTAAAACAATGTCAAGGAGAAAG

upper sequence: GRMZM2G027756_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT1G53165.2 (Arabidopsis thaliana), 3'ss of exon 7
gtataacttttatgaagggaaggttctgcatttaggaatgctttccattgtggtacatctatatctattgttgatttttagttcataata-tgtattctgttgttactatgtgtattccatagGTTGCGGACTTTGGTGTTTCTGCACAGCTGACTAAAACAATGTCTAGGAGGAAG
                           | ||||   | | |||    || |  |  ||  || |||    ||   |||||  ||  | |  | || |  |   ||  |    | ||    |||||||| ||||||||||||||||||||  | ||    || || || ||| | |||
---------------------------gtattttctacttcttaaacttat--ttgattaatttcttaaattttcttttatatccgagtggtttagttggaacttctttcacgcatat--tagGTTGCAGACTTTGGTGTTTCTGCACAATTAACCCGGACTATATCAAGGCGAAAG
















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|86473445|gb|DY239815.1|DY239815
EST:     CGGCAAATATCCTCCTCACTGAAAGTGGAGACGTGAAG                         GTTGCGGACTTTGGTGTTTCTGCACAGCTGACTAAAACAATGTCTAGGAGG
genomic: CGGCAAATATCCTCCTCACTGAAAGTGGAGACGTGAAGgtataacttt ... tattccatagGTTGCGGACTTTGGTGTTTCTGCACAGCTGACTAAAACAATGTCTAGGAGG
EST: gi|38502591|gb|CF972451.1|CF972451
EST:     CGGCAAATATCCTCCTCACTGAAAGTGGAGATGTGAAG                         GTTGCGGACTTTGGTGTTTCTGCACAGCTGACTAAAACAATGTCTAGGAGA
genomic: CGGCAAATATCCTCCTCACTGAAAGTGGAGACGTGAAGgtataacttt ... tattccatagGTTGCGGACTTTGGTGTTTCTGCACAGCTGACTAAAACAATGTCTAGGAGG
EST: gi|76282537|gb|DV022105.1|DV022105
EST:     GGAGACGTGAAG                         GTTGCGGACTTTGGTGTTTCTGCACAGCTGACTAAAACAATGTCTAGGAGG
genomic: GGAGACGTGAAGgtataacttt ... tattccatagGTTGCGGACTTTGGTGTTTCTGCACAGCTGACTAAAACAATGTCTAGGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttgatttttagttcataatatgtattctgttgttactatgtgtattccatagGTTGCGGACTTTGGTGTTTCTGCACAGCTGACTAAAACAATGTCTAGGAGGAAG
 tgttgat  putative branch site (score: 4)
      atttttagttcataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataacttttatgaagggaaggttctgcatttaggaatgctttccattgtggtacatctatatctattgttgatttttagttcataatatgtattctgttgttactatgtgtattccatagGTTGCGGACTTTGGTGTTTCTGCACAGCTGACTAAAACAATGTCTAGGAGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA