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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcctctgggatgaatatccacagcagtcctgtaagttgaagtgaaatgtatgcacgagacatctttctcatactttgatgctgtgcattttcttttcagAGGAGCTTAGTGAAGTCCCTGTTAAGAAGGCTGAAGATGGAGCAGCTGCCCCCTCTGTTGCTTCTTTTGTTGAGGAAAAGGATGATGCTGCAAACATGGA

Basic information

species Oryza sativa
transcript LOC_Os01g43540.1
intron # 3
splice site 3'
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|29661448|gb|CB657723.1|CB657723
EST:     TGACTCAAGGTTTACTCGCCTAATGAAGGAGTGTGATGAGCGCATTGCTG                         AGGAGCTTAGTGAAGTCCCTGTTAAGAAGGCTGAAGATGGAGCAGCTGCCC
genomic: TGACTCAAGGTTTACTCGCCTAATGAAGGAGTGTGATGAGCGCATTGCTGgtaagctgtc ... ttcttttcagAGGAGCTTAGTGAAGTCCCTGTTAAGAAGGCTGAAGATGGAGCAGCTGCCC
EST: gi|58586137|gb|CF984445.1|CF984445
EST:     TGACTCAAGGTTTACTCGCCTAATGAAGGAGTGTGATGAGCGCATTGCTG                         AGGAGCTTAGTGAAGTCCCTGTTAAGAAGGCTGAAGATGGAGCAGCTGCGC
genomic: TGACTCAAGGTTTACTCGCCTAATGAAGGAGTGTGATGAGCGCATTGCTGgtaagctgtc ... ttcttttcagAGGAGCTTAGTGAAGTCCCTGTTAAGAAGGCTGAAGATGGAGCAGCTGCCC
EST: gi|29625917|gb|CB630928.1|CB630928
EST:     TGACTCAAGGTTTACTCGCCTAATGAAGGAGTGTGATGAGCGCATTGCTG                         AGGAGCTTAGTGAAGTCCCTGTTAAGAAGGCTGAAGATGGAGCAGCTGCGC
genomic: TGACTCAAGGTTTACTCGCCTAATGAAGGAGTGTGATGAGCGCATTGCTGgtaagctgtc ... ttcttttcagAGGAGCTTAGTGAAGTCCCTGTTAAGAAGGCTGAAGATGGAGCAGCTGCCC
EST: gi|33797195|gb|CF324461.1|CF324461
EST:     TGACTCAAGGTTTACTCGCCTAATGAAGGAGTGTGATGAGCGCATTGCTG                         AGGAGCTTAGTGAAGTCCCTGTTAAGAAGGCTGAAGATGGAGCAGCTGCCC
genomic: TGACTCAAGGTTTACTCGCCTAATGAAGGAGTGTGATGAGCGCATTGCTGgtaagctgtc ... ttcttttcagAGGAGCTTAGTGAAGTCCCTGTTAAGAAGGCTGAAGATGGAGCAGCTGCCC
EST: gi|29660561|gb|CB656836.1|CB656836
EST:     TGACTCAAGGTTTACTCGCCTAATGAAGGAGTGTGATGAGCGCATTGCTG                         AGGAGCTTAGTGAAGTCCCTGTTAAGAAGGCTGAAGATGGAGCAGCTGCCC
genomic: TGACTCAAGGTTTACTCGCCTAATGAAGGAGTGTGATGAGCGCATTGCTGgtaagctgtc ... ttcttttcagAGGAGCTTAGTGAAGTCCCTGTTAAGAAGGCTGAAGATGGAGCAGCTGCCC
EST: gi|163920381|gb|EG714468.1|EG714468
EST:     TGACTCAAGGTTTACTCACCTAATGAAGGAGTGTGATGAGCGCATTGCTG                         AGGAGCTTAGTGAAGTCCCTGTTAAGAAGGCTGAAGATGGAGCAGCTGCCC
genomic: TGACTCAAGGTTTACTCGCCTAATGAAGGAGTGTGATGAGCGCATTGCTGgtaagctgtc ... ttcttttcagAGGAGCTTAGTGAAGTCCCTGTTAAGAAGGCTGAAGATGGAGCAGCTGCCC
EST: gi|2312755|gb|C28910.1|C28910
EST:     TGACTCAAGGTTTACTCGCCTAATGAAGGAGTGTGATGAGCGCATTGCTG                         AGGGAGCTTTAGTNAAGTCCCTGTTAA
genomic: TGACTCAAGGTTTACTCGCCTAATGAAGGAGTGTGATGAGCGCATTGCTGgtaagctgtc ... ttcttttcagAGG-AGCTT-AGTGAAGTCCCTGTTAA
EST: gi|58594119|gb|CF992427.1|CF992427
EST:     TGACTCAAGGTTTACTCGCCTAATGAGGGAGTGTGATGAGCGCATTGCTG                         AGGAGCTTAGTGAAGTCCCTGTTAAGAAGGCTGAAGATGGAGCAGCTGCGC
genomic: TGACTCAAGGTTTACTCGCCTAATGAAGGAGTGTGATGAGCGCATTGCTGgtaagctgtc ... ttcttttcagAGGAGCTTAGTGAAGTCCCTGTTAAGAAGGCTGAAGATGGAGCAGCTGCCC
EST: gi|218487981|gb|FG959844.1|FG959844
EST:     TGACTC-AGG-TTACTCGCCTAATGAAGGAGTGTGATGAGCGCATTGCTG                         AGGAGCTTAGTGAAGTCCCTGTTAAGAAGGCTGAAGATGGAGCAGCTGCGC
genomic: TGACTCAAGGTTTACTCGCCTAATGAAGGAGTGTGATGAGCGCATTGCTGgtaagctgtc ... ttcttttcagAGGAGCTTAGTGAAGTCCCTGTTAAGAAGGCTGAAGATGGAGCAGCTGCCC
EST: gi|286480|gb|D15287.1|D15287
EST:     TGACTCAAGGTTTACTCGCCTAATGAAGGAGTGTGATGAGCGCATTGCTG                         AGGAGCTTAGTGAAGTCCCTGTTAAGAAGGCTGAAGATGGAGCAGCTGNCC
genomic: TGACTCAAGGTTTACTCGCCTAATGAAGGAGTGTGATGAGCGCATTGCTGgtaagctgtc ... ttcttttcagAGGAGCTTAGTGAAGTCCCTGTTAAGAAGGCTGAAGATGGAGCAGCTGCCC
EST: gi|88364728|gb|CI612543.1|CI612543
EST:     TGACTCAAGGTTTACTCGCCTAATGAAGGAGTGTGATGAGCGCATTGCTG                         AGGAGCTTAGTGAAGTCCCTGTTAAGAAGGCTTGAAGATGGAGCAGCTG
genomic: TGACTCAAGGTTTACTCGCCTAATGAAGGAGTGTGATGAGCGCATTGCTGgtaagctgtc ... ttcttttcagAGGAGCTTAGTGAAGTCCCTGTTAAGAAGGCT-GAAGATGGAGCAGCTG
EST: gi|29659289|gb|CB655564.1|CB655564
EST:     TGACTCAAGGTTTACTCGCCTAATGAAGGAGTGTGATGAGCGCATTGCTG                         AGGAGCTTAGTGAAGTCCCTGTTAAGAAGGCTGAAGATGGAGCAGCTGCCC
genomic: TGACTCAAGGTTTACTCGCCTAATGAAGGAGTGTGATGAGCGCATTGCTGgtaagctgtc ... ttcttttcagAGGAGCTTAGTGAAGTCCCTGTTAAGAAGGCTGAAGATGGAGCAGCTGCCC
EST: gi|29669129|gb|CB665404.1|CB665404
EST:     TGACTCAAGGTTTACTCGCCTAATGAAGGAGTGTGATGAGCGCATTGCTG                         AGGAGCTTAGTGAAGTCCCTGTTAAGAAGGCTGAAGATGGAGCAGCTGCCC
genomic: TGACTCAAGGTTTACTCGCCTAATGAAGGAGTGTGATGAGCGCATTGCTGgtaagctgtc ... ttcttttcagAGGAGCTTAGTGAAGTCCCTGTTAAGAAGGCTGAAGATGGAGCAGCTGCCC
EST: gi|29658976|gb|CB655251.1|CB655251
EST:     TGACTCAAGGTTTACTCGCCTAATGAAGGAGTGTGATGAGCGCATTGCTG                         AGGAGCTTAGTGAAGTCCCTGTTAAGAAGGCTGAAGATGGAGCAGCTGCCC
genomic: TGACTCAAGGTTTACTCGCCTAATGAAGGAGTGTGATGAGCGCATTGCTGgtaagctgtc ... ttcttttcagAGGAGCTTAGTGAAGTCCCTGTTAAGAAGGCTGAAGATGGAGCAGCTGCCC
EST: gi|33678214|gb|CF306453.1|CF306453
EST:     TGACTCAAGGTTTACTCGCCTAATGAAGGAGTGTGATGAGCGCATTGCTG                         AGGAGCTTAGTGAAGTCCCTGTTAAGAAGGCTGAAGATGGAGCAGCTGCCC
genomic: TGACTCAAGGTTTACTCGCCTAATGAAGGAGTGTGATGAGCGCATTGCTGgtaagctgtc ... ttcttttcagAGGAGCTTAGTGAAGTCCCTGTTAAGAAGGCTGAAGATGGAGCAGCTGCCC

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: 74 (upstream exon), 73 (downstream exon)
Score: 108

TATCAAACTGCAAAAGCAGCTCTTGAATTGGGTTACTCGTTCGCATCTGGTGACTCAAGGTTTACTCGCCTAATGAAGGAGTGTGATGAGCGCATTGCTGgtaagctgtc ... ttcttttcagAGGAGCTTAGTGAAGTCCCTGTTAAGAAGGCTGAAGATGGAGCAGCTGCCCCCTCTGTTGCTTCTTTTGTTGAGGAAAAGGATGATGCTGCAAACATGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgtatgcacgagacatctttctcatactttgatgctgtgcattttcttttcagAGGAGCTTAGTGAAGTCCCTGTTAAGAAGGCTGAAGATGGAGCAGCTGCCCCCTCTGTTGCTTCTTTTGTTGAGGAAAAGGATGATGCTGCAAACATGGA
                            ctttgat  putative branch site (score: 108)
                                       tgcattttcttttc  putative PPT
                                          attttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcctctgggatgaatatccacagcagtcctgtaagttgaagtgaaatgtatgcacgagacatctttctcatactttgatgctgtgcattttcttttcagAGGAGCTTAGTGAAGTCCCTGTTAAGAAGGCTGAAGATGGAGCAGCTGCCCCCTCTGTTGCTTCTTTTGTTGAGGAAAAGGATGATGCTGCAAACATGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - tgggatg
- - - - - - - - - - -cagcagt
- - - - - - - - - - - - - - - - - - - -aagtgaaa
- - - - - - - - - - - - - - - - - - - - - - - -tgtatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgctg