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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGATACTCCGAAAGCGAAGAGCTGGAAAACTCCCAGGAGATACAGCGTCTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagctcacagataccattatcaggccttcctgcatttccttttctaccactgatgctcatgtttcttaacctttatag

Basic information

species Oryza sativa
transcript LOC_Os06g43860.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g43860.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G055243_T01 (Zea mays), 5'ss of exon 4
AGAGATACTCCGAAAGCGAAGAGCTGGAAAACTCCCAGGAGATACAGCGTCTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagctcacagataccattat---caggccttcctgcatttcctttt-------ctaccac-tgatgctcatgtttcttaacctttatag-------------------------------------------------
||||||| | || |||||||||||||| |||||||| || || || || ||||| || |||||||||||||||||||| ||||| ||||| |||||||| ||| || | | ||  ||| | || |    |||  |       | || ||  |        ||  || |    | ||||  || || |  |   ||                                                 
AGAGATATTGCGGAAGCGAAGAGCTGGGAAACTCCCTGGCGACACTGCTTCTACCTTAAAAGCATGGTGGCAGGCTCATTCTAAGTGGCCGTACCCAACCgtaagtgaacacattgatcctatcactcccagcaccattcctagttactcatgagcatattattacgttgaacacatggatcctatcactcccagcaccattcctatttactcatgagtatattatcgtggaccacttgtttag
















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|87008402|gb|CI301160.1|CI301160
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29638818|gb|CB643827.1|CB643827
EST:     TTACTTTGAAAGCATGGTGGCAGGCTCACTTTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|23514961|gb|BU673870.1|BU673870
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAGCAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29679811|gb|CB676086.1|CB676086
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|38565817|gb|CK085270.1|CK085270
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29663219|gb|CB659494.1|CB659494
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|38475492|gb|CF959625.1|CF959625
EST:     GGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAGCAG
genomic: GGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29645298|gb|CB650305.1|CB650305
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|38565678|gb|CK085131.1|CK085131
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29657867|gb|CB654142.1|CB654142
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29659496|gb|CB655771.1|CB655771
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|58693265|gb|CK081952.1|CK081952
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29645222|gb|CB650229.1|CB650229
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29637144|gb|CB642153.1|CB642153
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29657258|gb|CB653533.1|CB653533
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|31818558|gb|CD645554.1|CD645554
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAGCAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29669194|gb|CB665469.1|CB665469
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29645255|gb|CB650262.1|CB650262
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|87011013|gb|CI286088.1|CI286088
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29667364|gb|CB663639.1|CB663639
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCTAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29667365|gb|CB663640.1|CB663640
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCTAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|109974476|gb|DT806929.1|DT806929
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAGCAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|58695467|gb|CK084154.1|CK084154
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAGCAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGATACTCCGAAAGCGAAGAGCTGGAAAACTCCCAGGAGATACAGCGTCTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagctcacagataccattatcaggccttcctgcatttccttttctaccactgatgctcatgtttcttaacctttatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG