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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaagctgttatgtgttttccattctgttgtgtatttgcgctaaactataaccttatttatgtttggccttgaagtttgttcattacaagtccctttttgctacagTTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAAATTCTGTGTTCTATTTCTCATCAACTGTGTTCAGAAGTGTGGGTGTGCC

Basic information

species Oryza sativa
transcript LOC_Os02g17500.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g17500.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G412899_T05 (Zea mays), 3'ss of exon 9
gtacaagctgttatgtgttttccattctgttgtgtatttgcgctaaactataaccttatttatgtttggccttgaagtttgttcattacaagtcccttttt-gctacagTTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAAATTCTGTGTTCTATTTCTCATCAACTGTGTTCAGAAGTGTGGGTGTGCC
|||||||||||| | | |  |   || |||||||| | ||  ||     ||||||| | ||  || || |  ||||||||||||||||||||| ||||||| | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||| |||||
gtacaagctgttctatatcct---ttttgttgtgtttatggacttc-taataacctgagttcagtctgtctgtgaagtttgttcattacaagttccttttttggtacagTTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAAATTCTGTGTTCTATTTCTCATCAACTGTATTCAGAAGTGTGGGGGTGCC

upper sequence: LOC_Os02g17500.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA07G09270.3 (Glycine max), 3'ss of exon 9
---------------gtacaagctgttatgtgttttccattctgttgtgtatttgc----gctaaactataacc-ttatttatgtttggcctt-gaagtttgttcattacaagtccctttttgctacagTTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAAATTCTGTGTTCTATTTCTCATCAACTGTGTTCAGAAGTGTGGGTGTGCC
               |      || |    |  ||   | |     ||||||||||    | |    | |   |  |  ||   || ||  |   ||  || ||  |||        ||  |  | ||||||||||||||||  |||| || ||||||||||||||| |||| || |||||| ||||||| |||||||| |||||||| || | |||||  || |||||
gtatgcatttttcctggtttgtctctgggatagttgtgacttgtgagtgtatttgccattgttgttatctggtcactggtttccttaggtttccaaaagttattttttattcacaagttcgttttgcagTTGTTTTTATTGGATCAACCCTATTTGCTTTACAACAGCTATCTGGTATAAATGCTGTGTTTTATTTCTCTTCAACTGTTTTTAAAAGTGCTGGAGTGCC

upper sequence: LOC_Os02g17500.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA09G32510.1 (Glycine max), 3'ss of exon 9
gtacaagctgttatgtgttttccattctgttgtgtatttgcgctaaactataaccttatttatgtttggccttgaagtttgttcattacaagtccctttttgctacagTTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAAATTCTGTGTTCTATTTCTCATCAACTGTGTTCAGAAGTGTGGGTGTGCC--------------------------------------------
                                                                                                                 ||||||||  |||| || ||||||||||||||| |||| || |||||| ||||||| |||||||| |||||||| || | |||||  || || ||                                            
-----------------------------------------------------------------------------------------------------------------tttattggatcaaccctatttgctttacaacagctatctggtataaatgctgtgttttatttctcttcaactgtttttaaaagtgctggagtcccatcagACATTGCAAATGTCTGCATAGGAATCGCTAATTTGGCAG

upper sequence: LOC_Os02g17500.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT1G67300.1 (Arabidopsis thaliana), 3'ss of exon 9
----gtacaagctgttatgtgttttccattctg----ttgtg--tatttgcgctaaactataaccttatttatgtttggccttgaagtttgttcattacaagtccctttttgctacagTTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAAATTCTGTGTTCTATTTCTCATCAACTGTGTTCAGAAGTGTGGGTGTGCC
    ||| ||    ||   | | | ||           ||     || |  | | |    |     ||||| | |   |  | | | ||||||  | ||  || ||||||     ||||||||||||||||  |||| || |||||||| |||||| |||| || |||||| |||| || |||||||| || || || |||| |||||  || || ||
gtatgtagaactctttgcttttgtcccgcggaaggaactgcaaacatgtatgttgattgttgtgtctatttgtttcctgtatagtactttgttattcacttgttcctttt----gcagTTGTTTTTATTGGATCAACCCTGTTTGCTTTGCAACAGCTATCTGGTATAAATGCTGTTTTTTATTTCTCTTCTACCGTATTCAAAAGTGCTGGAGTACC

upper sequence: LOC_Os02g17500.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT1G79820.4 (Arabidopsis thaliana), 3'ss of exon 9
gtacaagctgttatgtgttttccattctgttgtgtatttgcgctaaactataaccttatttatgtttggccttgaagtttgttcattacaagtccctttttgctacagTTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAAATTCTGTGTTCTATTTCTCATCAACTGTGTTCAGAAGTGTGGGTGTGCC
   |||      |||   ||| |||| ||      |  | |    |  |      |    | |   |  |||| |  ||| | | ||  || |    |     | |||| ||||| |||||  | || || ||||||||||||||||| || || |||||| ||||||||||||||||||||||||| ||||  |  |  ||||| ||
--ccaaa--aaaatgacattttcatt-tgccaaaaacatacatatagatgatgtgtagcctcttaattaccttca--tttttacgtt-taaattttctccgattgcagTGGTTTTCATTGGATCTACCCTTTTTGCTTTACAACAGTTGTCTGGGATAAATGCTGTGTTCTATTTCTCATCAACTGTCTTCAAGAAAGCTGGTGTACC

upper sequence: LOC_Os02g17500.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv09s0002g04380.t01 (Vitis vinifera), 3'ss of exon 8
gtacaagctgttatgtgttttccattctgttgtgtatttgcgctaaactataaccttatttatgtttggccttgaagtttgttcattacaagtccctttttgctacagTTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAAATTCTGTGTTCTATTTCTCATCAACTGTGTTCAGAAGTGTGGGTGTGCC
                                 ||| |   |||||| ||| |   | |||||        || |  ||   |   |  |  |   ||| |   ||||| ||||| |||||  |||  || ||||||||||||||| | || ||||||||| |||||||||||||||| |||||||| |||| | | |  || || ||
---------------------------------gtaat-atgctaaattattagtgt-tttatccactatgtttattttgagttgatttatctgaatttatttcacagTGGTTTTCATTGGATCAAGCCTATTTGCTTTACAACAGCTTTCTGGCATAAATGCTGTGTTCTATTTCTCTTCAACTGTCTTCAAAGGAGCTGGAGTACC

upper sequence: LOC_Os02g17500.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv11s0016g03660.t01 (Vitis vinifera), 3'ss of exon 9
----------------------------------------gtacaagctgttatgtgttttccattctgttgtgtatttgcgctaa-actataac-----cttatttatgtttggccttgaagtttgttcattacaagtccctttttgctacagTTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAAATTCTGTGTTCTATTTCTCATCAACTGTGTTCAGAAGTGTGGGTGTGCC
                                        |   | | | |  | || |||    | |  || ||  |   |||    |    ||     ||||||    ||| ||||  |||  || |   ||        ||  |  | ||||||||||||||||  |||| || ||||||||||||||| |||| || |||||  |||| || |||||||| || ||||| || | ||| | ||| |||||
gtagatatgatacttctttggtatgcacctatgagtttgtgagtatgttctcgtctgctttgagatttactgagtgctgctgctgttgccggcacttcttcttattctccttttgcctccaagaatgctttgtattcactgattccttttgcagTTGTTTTTATTGGATCAACCCTATTTGCTTTACAACAGCTATCTGGTATAAACGCTGTTTTTTATTTCTCTTCCACTGTATTTAAAAGCGCGGGAGTGCC

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|29643521|gb|CB648528.1|CB648528
EST:     TGGAGAAAATGTGAAGTATTCGGAATTGTTTTATGGTCGCAACTTTAATG                         TTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAA
genomic: TGGAGAAAATGTGAAGTATTCGGAATTGTTTTATGGTCGCAACTTTAATGgtacaagctg ... tttgctacagTTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAA
EST: gi|218501803|gb|FG948060.1|FG948060
EST:     TGGAGAAAATGTGAAGTATTCGGAATTGTTTTATGGTCGCAACTTTAATG                         TTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAA
genomic: TGGAGAAAATGTGAAGTATTCGGAATTGTTTTATGGTCGCAACTTTAATGgtacaagctg ... tttgctacagTTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAA
EST: gi|88362011|gb|CI607011.1|CI607011
EST:     TGGAGAAAATGTGAAGTATTCGGAATTGTTTTATGGTCGGAACTTTAATG                         TTGTTTTTATTGGGACAACGCTCTTTGCTTTACAACAGTTATCC
genomic: TGGAGAAAATGTGAAGTATTCGGAATTGTTTTATGGTCGCAACTTTAATGgtacaagctg ... tttgctacagTTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCC
EST: gi|218499348|gb|FG943597.1|FG943597
EST:     TGGAGAAAATGTGAAGTATTCGGAATTGTTTTATGGTCGCAACTTTAATG                         TTGTTCCTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATA
genomic: TGGAGAAAATGTGAAGTATTCGGAATTGTTTTATGGTCGCAACTTTAATGgtacaagctg ... tttgctacagTTGTTT-TTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATA
EST: gi|88827907|gb|CI778472.1|CI778472
EST:     TGGAGAAAATGTGAAGTATTCGGAATTGTTTTATGGTCGCAACTTTAATG                         TTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAA
genomic: TGGAGAAAATGTGAAGTATTCGGAATTGTTTTATGGTCGCAACTTTAATGgtacaagctg ... tttgctacagTTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAA
EST: gi|218496023|gb|FG951379.1|FG951379
EST:     TGGAGAAAATGTGAAGTATTCGGAATTGTTTTATGGTCGCAACTTTAATG                         TTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAA
genomic: TGGAGAAAATGTGAAGTATTCGGAATTGTTTTATGGTCGCAACTTTAATGgtacaagctg ... tttgctacagTTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAA
EST: gi|88732502|gb|CI755679.1|CI755679
EST:     TGGAGAAAATGTGAAGTATTCGGAATTGTTTTATGGTCGCAACTTTAATG                         TTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAA
genomic: TGGAGAAAATGTGAAGTATTCGGAATTGTTTTATGGTCGCAACTTTAATGgtacaagctg ... tttgctacagTTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAA
EST: gi|66922886|gb|CX109734.1|CX109734
EST:     TGGAGAAAATGTGAAGTATTCGGAATTGTTTTATGGTCGCAACTTTAATG                         TTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAA
genomic: TGGAGAAAATGTGAAGTATTCGGAATTGTTTTATGGTCGCAACTTTAATGgtacaagctg ... tttgctacagTTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAA
EST: gi|218498315|gb|FG958350.1|FG958350
EST:     TGGAGAAAATGTGAAGTATTCAGAATTGTTTTATGGTCGCAACTTTAATG                         TCGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAA
genomic: TGGAGAAAATGTGAAGTATTCGGAATTGTTTTATGGTCGCAACTTTAATGgtacaagctg ... tttgctacagTTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAA
EST: gi|88827571|gb|CI778136.1|CI778136
EST:     TGGAGAAAATGTGAAGTATTCGGAATTGTTTTATGGTCGCAACTTTAATG                         TTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAA
genomic: TGGAGAAAATGTGAAGTATTCGGAATTGTTTTATGGTCGCAACTTTAATGgtacaagctg ... tttgctacagTTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAA

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: 73 (upstream exon), 70 (downstream exon)
Score: 101

CATGTTAAGTCTGCTATGGCAGAACTCTCCCGATCTGAAAGAGGCGATGATGGAGAAAATGTGAAGTATTCGGAATTGTTTTATGGTCGCAACTTTAATGgtacaagctg ... tttgctacagTTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAAATTCTGTGTTCTATTTCTCATCAACTGTGTTCAGAAGTGTGGGTGTGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttatttatgtttggccttgaagtttgttcattacaagtccctttttgctacagTTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAAATTCTGTGTTCTATTTCTCATCAACTGTGTTCAGAAGTGTGGGTGTGCC
                                       tccctttttgctac  CT-rich tract
     tttatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaagctgttatgtgttttccattctgttgtgtatttgcgctaaactataaccttatttatgtttggccttgaagtttgttcattacaagtccctttttgctacagTTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAAATTCTGTGTTCTATTTCTCATCAACTGTGTTCAGAAGTGTGGGTGTGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT