Skip to another splice site:
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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_Os06g43860.3
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|58695270|gb|CK083957.1|CK083957
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAGCAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|87008402|gb|CI301160.1|CI301160
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29659496|gb|CB655771.1|CB655771
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29667364|gb|CB663639.1|CB663639
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCTAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29657257|gb|CB653532.1|CB653532
EST:     CTACTTTGAAAGCAGGGTGGCAGGCTCACTCTAAATGGCCATACCCAGCT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29640636|gb|CB645645.1|CB645645
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|58692037|gb|CK080724.1|CK080724
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|58693265|gb|CK081952.1|CK081952
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|58695467|gb|CK084154.1|CK084154
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAGCAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29645298|gb|CB650305.1|CB650305
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29615078|gb|CB620091.1|CB620091
EST:     TTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAGCAG
genomic: TTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29678380|gb|CB674655.1|CB674655
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29667393|gb|CB663668.1|CB663668
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCTATCT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29660832|gb|CB657107.1|CB657107
EST:     GAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: GAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29667392|gb|CB663667.1|CB663667
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCTAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29645255|gb|CB650262.1|CB650262
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29645297|gb|CB650304.1|CB650304
EST:     ATACTTTGAAAGCATGGTGGCAGGCTCACTTTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29657258|gb|CB653533.1|CB653533
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|14571398|gb|BI118766.1|BI118766
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAGCAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29645222|gb|CB650229.1|CB650229
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29659495|gb|CB655770.1|CB655770
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29618507|gb|CB623519.1|CB623519
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAGCAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29679811|gb|CB676086.1|CB676086
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|87011013|gb|CI286088.1|CI286088
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|14571386|gb|BI118754.1|BI118754
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAGCAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29637144|gb|CB642153.1|CB642153
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29640635|gb|CB645644.1|CB645644
EST:     ATATTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGGTGCAGGAAACAGGGTTGCAACTAAAACA
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTT-GGTGCAGGAAACAGGGTTGCAACTAAAACA
EST: gi|29663219|gb|CB659494.1|CB659494
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29667365|gb|CB663640.1|CB663640
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCTAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29640783|gb|CB645790.1|CB645790
EST:     TTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|58689485|gb|CK078172.1|CK078172
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAGCAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29669194|gb|CB665469.1|CB665469
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29657867|gb|CB654142.1|CB654142
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 73 (downstream exon)
Score: 39

AGAGATACTCCGAAAGCGAAGAGCTGGAAAACTCCCAGGAGATACAGCGTCTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAGATCAATAATTGGTTTATCAACCAACGTAAACGGAACTGGCACAGCAATC




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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