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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGCTGGTGGCCCTGGAGGAGGCCGGCGCCGAGTACGAGGTCGTTCCGATGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagcctctcataattctcgcactatatcttcttcgcatgttacgcaaattagtccaaagggtcagagcgacctacagtgcaggctgattcatgg...

Basic information

species Oryza sativa
transcript LOC_Os01g27210.1
intron # 1
splice site 5'
intron type U2

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|88335790|gb|CI647146.1|CI647146
EST:     TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|88290470|gb|CI665259.1|CI665259
EST:     TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|88570430|gb|CI661803.1|CI661803
EST:     TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|86517182|gb|CI157388.1|CI157388
EST:     ACCACCGCCGGCCGGAGCACCTCGCCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
genomic: ACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|86831146|gb|CI295623.1|CI295623
EST:     TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|454518|gb|D28287.1|D28287
EST:     TGAGCAGGTCCGNCGGCGACCACCGNCGGCCGGAGCACCTCGCCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGNTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|88336380|gb|CI648967.1|CI648967
EST:     TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|88742546|gb|CI766054.1|CI766054
EST:     TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|55414863|gb|CV727239.1|CV727239
EST:     TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|88574439|gb|CI666208.1|CI666208
EST:     TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|55414167|gb|CV726543.1|CV726543
EST:     TGAGCAGGTCCGGCGGCGACCACCGCCGGCCTTTGTATTTCGCCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|33796153|gb|CF323942.1|CF323942
EST:     TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|88305839|gb|CI633419.1|CI633419
EST:     TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGAACTGACGCTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|29667780|gb|CB664055.1|CB664055
EST:     TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|25799620|gb|CA755581.1|CA755581
EST:     TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|287276|gb|D16078.1|D16078
EST:     TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGNCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGNTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|88348212|gb|CI637673.1|CI637673
EST:     TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|86906390|gb|CI294513.1|CI294513
EST:     TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|88306238|gb|CI636623.1|CI636623
EST:     TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|88826284|gb|CI776849.1|CI776849
EST:     TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGACCACCTCGCCACAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|88764479|gb|CI773597.1|CI773597
EST:     TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|32948407|gb|BP184979.1|BP184979
EST:     TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|88828083|gb|CI778648.1|CI778648
EST:     TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|88350933|gb|CI620593.1|CI620593
EST:     TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|3090514|gb|C93501.1|C93501
EST:     TGAGCAGGNCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|88742188|gb|CI765696.1|CI765696
EST:     TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|88363216|gb|CI643074.1|CI643074
EST:     TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|51946184|gb|CV152525.1|CV152525
EST:     CAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
genomic: CAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|32948287|gb|BP184859.1|BP184859
EST:     TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|88353725|gb|CI633116.1|CI633116
EST:     TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|88347219|gb|CI631299.1|CI631299
EST:     TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|88362614|gb|CI608763.1|CI608763
EST:     TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|88575573|gb|CI669718.1|CI669718
EST:     TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|55414769|gb|CV727145.1|CV727145
EST:     TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGGAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
EST: gi|88326634|gb|CI658354.1|CI658354
EST:     TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAAC                         CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC
genomic: TGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC

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: 61 (upstream exon), 49 (downstream exon)
Score: 30

GGTGCTGGTGGCCCTGGAGGAGGCCGGCGCCGAGTACGAGGTCGTTCCGATGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagc ... aattatgcagCCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGCTGGTGGCCCTGGAGGAGGCCGGCGCCGAGTACGAGGTCGTTCCGATGAGCAGGTCCGGCGGCGACCACCGCCGGCCGGAGCACCTCGCCAGAAACgtacgtgagcctctcataattctcgcactatatcttcttcgcatgttacgcaaattagtccaaagggtcagagcgacctacagtgcaggctgattcatgg

- - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA