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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCATCGGGCTGCTTTTGTTCTGCCAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAGgtaggttacttactgcctgttgctatttcttttcttttctgtctgcgaactgcgatgctatttcggattgttgtaatggaattattgctgatatacataatcttgatgccataacaggataaatcag

Basic information

species Oryza sativa
transcript LOC_Os06g33710.4
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g33710.4 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G047867_T02 (Zea mays), 5'ss of exon 10
GTTCATCGGGCTGCTTTTGTTCTGCCAACATTTGTAAGGAGAGAACTGGAATCACACAATACT---------TGTGCTGAAAAGgtaggttacttactgcctgttgctatttcttttcttttctgtctgcgaa-ctgcg-atgctatttcg--gattgttgtaatggaattattgctgatatacataa-tcttgatgccataacag--gataaatcag---------------------------------------
 | ||| ||||||||||||||||||||||||||||||| |||||||||||| || | |  |||         | ||||||||| ||  |||  ||  |   |  | |||||  |  | |  |  ||||      |   | ||  | ||  |   |   || |||    |  | ||   | ||| |  | ||    |    |  ||   | ||   |||                                       
ATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGCTGAAAACgtgagttgtttgttagttact-ctattgatggtgtggttagtctttatgtccatgcattttgttctgccaacatttataagaagagaactggaaacatataccactccctttttttttgcaattgctactgcagtgctaacctttgcctctattttcatatgcatcatgacag

upper sequence: LOC_Os06g33710.4 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G047867_T02 (Zea mays), 5'ss of exon 10
GTTCATCGGGCTGCTTTTGTTCTGCCAACATTTGTAAGGAGAGAACTGGAATCACACAATACT---------TGTGCTGAAAAGgtaggttacttactgcctgttgctatttcttttcttttctgtctgcgaa-ctgcg-atgctatttcg--gattgttgtaatggaattattgctgatatacataa-tcttgatgccataacag--gataaatcag---------------------------------------
 | ||| ||||||||||||||||||||||||||||||| |||||||||||| || | |  |||         | ||||||||| ||  |||  ||  |   |  | |||||  |  | |  |  ||||      |   | ||  | ||  |   |   || |||    |  | ||   | ||| |  | ||    |    |  ||   | ||   |||                                       
ATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGCTGAAAACgtgagttgtttgttagttact-ctattgatggtgtggttagtctttatgtccatgcattttgttctgccaacatttataagaagagaactggaaacatataccactccctttttttttgcaattgctactgcagtgctaacctttgcctctattttcatatgcatcatgacag
















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|29681921|gb|CB678196.1|CB678196
EST:     CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAG                         G
genomic: CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAGgtaggttact ... gataaatcag-
EST: gi|29681921|gb|CB678196.1|CB678196
EST:     CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAG                         G
genomic: CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAGgtaggttact ... gataaatcag-
EST: gi|29639075|gb|CB644084.1|CB644084
EST:     CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAG                         G
genomic: CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAGgtaggttact ... gataaatcag-
EST: gi|29639075|gb|CB644084.1|CB644084
EST:     CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAG                         G
genomic: CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAGgtaggttact ... gataaatcag-
EST: gi|88848995|gb|CI087517.1|CI087517
EST:     CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAGGATAAATCAG                
genomic: CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCT------G--AAA--AGgtaggttact ... g
EST: gi|8527728|gb|AU092543.1|AU092543
EST:     CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAGGATAAATCAG                
genomic: CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCT------G--AAA--AGgtaggttact ... g
EST: gi|29660328|gb|CB656603.1|CB656603
EST:     CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAG                         G
genomic: CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAGgtaggttact ... gataaatcag-
EST: gi|29660328|gb|CB656603.1|CB656603
EST:     CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAG                         G
genomic: CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAGgtaggttact ... gataaatcag-
EST: gi|29681268|gb|CB677543.1|CB677543
EST:     CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAG                         G
genomic: CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAGgtaggttact ... gataaatcag-
EST: gi|29681268|gb|CB677543.1|CB677543
EST:     CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAG                         G
genomic: CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAGgtaggttact ... gataaatcag-
EST: gi|86419330|gb|CI054131.1|CI054131
EST:     CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAGGATAAATCAG                
genomic: CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCT------G--AAA--AGgtaggttact ... g
EST: gi|88258477|gb|CI361063.1|CI361063
EST:     TTGTAAGGAGAGAACTGGAATCACACAATACTTGTTCTGAAAAG                         AAACCAAGCCACTCGCGAAACCAAAGAAGATGAAAATAATGCCGAATAGTG
genomic: TTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAGgtaggttact ... gataaatcagAAACCAAGCCAGTCGCGAAACCAAAGAAGATGAAAATAATGCCGAATAGTG
EST: gi|29674258|gb|CB670533.1|CB670533
EST:     CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAG                         G
genomic: CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAGgtaggttact ... gataaatcag-
EST: gi|29674258|gb|CB670533.1|CB670533
EST:     CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAG                         G
genomic: CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAGgtaggttact ... gataaatcag-
EST: gi|9865343|gb|AU101093.1|AU101093
EST:     CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAGGATAAATCAG                
genomic: CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCT------G--AAA--AGgtaggttact ... g
EST: gi|29657895|gb|CB654170.1|CB654170
EST:     CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAG                         G
genomic: CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAGgtaggttact ... gataaatcag-
EST: gi|29657895|gb|CB654170.1|CB654170
EST:     CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAG                         G
genomic: CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAGgtaggttact ... gataaatcag-
EST: gi|29677613|gb|CB673888.1|CB673888
EST:     CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAGGATAAATCAG                
genomic: CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCT------G--AAA--AGgtaggttact ... g
EST: gi|86862613|gb|CI345627.1|CI345627
EST:     CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAGGATAAATCAG                
genomic: CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCT------G--AAA--AGgtaggttact ... g
EST: gi|86494920|gb|CI137553.1|CI137553
EST:     CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAGGATAAATCAG                
genomic: CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCT------G--AAA--AGgtaggttact ... g
EST: gi|29661774|gb|CB658049.1|CB658049
EST:     CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAG                         G
genomic: CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAGgtaggttact ... gataaatcag-
EST: gi|29661774|gb|CB658049.1|CB658049
EST:     CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAG                         G
genomic: CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAGgtaggttact ... gataaatcag-
EST: gi|29665561|gb|CB661836.1|CB661836
EST:     CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAG                         G
genomic: CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAGgtaggttact ... gataaatcag-
EST: gi|29665561|gb|CB661836.1|CB661836
EST:     CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAG                         G
genomic: CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAGgtaggttact ... gataaatcag-
EST: gi|86492595|gb|CI135228.1|CI135228
EST:     CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAGGATAAATCAG                
genomic: CAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCT------G--AAA--AGgtaggttact ... g

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), 74 (downstream exon)
Score: 4

GTTCATCGGGCTGCTTTTGTTCTGCCAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAGgtaggttact ... gataaatcagAAACCAAGCCAGTCGCGAAACCAAAGAAGATGAAAATAATGCCGAATAGTGCCATTCCGACTGCTTCCTAGATTCGGGCGGCCATATGCGACAACCATGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCATCGGGCTGCTTTTGTTCTGCCAACATTTGTAAGGAGAGAACTGGAATCACACAATACTTGTGCTGAAAAGgtaggttacttactgcctgttgctatttcttttcttttctgtctgcgaactgcgatgctatttcggattgttgtaatggaattattgctgatatacataatcttgatgccataacaggataaatcag

- - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - AGGAGA