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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgaggtttatcttgtgatttgtgaatatattttctgccttaattttcttttggattgtttacctgtgtatcattgttcttgtggtgtcggctcttgcagATTGTGAATCCAGGTGCTTCATCCAACCCTCAATTGAATCAATCTCAGCCAAGCACCAGCACCAGCATTGCTTCTGGTCCTCCACTCCCTCAGCATCTCA

Basic information

species Oryza sativa
transcript LOC_Os05g50480.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g50480.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G163888_T01 (Zea mays), 3'ss of exon 8
--ttgaggtttatc--ttgtgatttgtgaatatattttctgccttaattttcttttggattgtttacctgtgtatcattgttcttgtggtgtcggctcttgcagATTGTGAATCCAGGTGCTTCATCCAACCCTCAATTGAATCAATCTCAGCCAAGCACCAGCACCAGCATTGCTTCTGGTCCTCCACTCCCTCAGCATCTCA------
  | ||| |  | |   |   ||||  |||   |     |   ||  | ||   |  |||  | ||| || | |  ||| || |||||   | |  ||| ||||| ||  ||||||| || || | ||||||||||||||| ||||||||||| ||||||      |||||||||||| || ||||||||||||||||||||        
tctagagctaaaacgactactattttggaacggaaggagtatttt--tcttggatctgat-atatacatg-gcacaattcttattgtgtgtttgattctcgcagAATGCCAATCCAGTTGGTTTACCCAACCCTCAATTGACTCAATCTCAGCAAAGCAC------CAGCATTGCTTCAGGGCCTCCACTCCCTCAGCATCTTCTTCATC

upper sequence: LOC_Os05g50480.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G150484_T01 (Zea mays), 3'ss of exon 8
ttgaggtttatcttgtg-atttgtgaatata--ttttctgccttaattttcttttggattgtttacctgtgtatcattgttcttgtggtgt---cggctcttgcagATTGTGAATCCAGGTGCTTCATCCAACCCTCAATTGAATCAATCTCAGCCAAGCACCAGCACCAGCATTGCTTCTGGTCCTCCACTCCCTCAGCATCTCA------
      |||  ||  || |  | |  || ||  ||| ||   |||  ||| | ||||||    |   |   |  ||   ||||||| ||||    |  ||| ||||| ||  ||||||| || || | ||||||||||||||| ||||||||||||||||||      |||||||||| | || ||||||||||||||||||||        
------tttgcctaatggacatattcatgtagttttcctagtttatatttttcttggatctgatgtatacatggcacaattcttgttgtgtgtttgattctcgcagAATGCCAATCCAGTTGGTTTACCCAACCCTCAATTGACTCAATCTCAGCCAAGCAC------CAGCATTGCTCCAGGGCCTCCACTCCCTCAGCATCTTCTTCATC
















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|33795709|gb|CF323724.1|CF323724
EST:     CATCATCGTCCATGGGCAATGCAACTACTGTTTCTACACAACCACAAGAG                         ATTGTGAATCCAGGTGCTTCATCCAACCCTCAATTGAATCAATCTCAGCCA
genomic: CATCATCGTCCATGGGCAATGCAACTACTGTTTCTACACAACCACAAGAGgtgtggaaca ... gctcttgcagATTGTGAATCCAGGTGCTTCATCCAACCCTCAATTGAATCAATCTCAGCCA
EST: gi|58665344|gb|CK054030.1|CK054030
EST:     CATCATCGTCCATGGGCAATGCAACTACTGTTTCTACACAACCACAAGAG                         ATTGTGAATCCAGGTGCTTCATCCAACCCTCAATTGAATCAATCTCAGCCA
genomic: CATCATCGTCCATGGGCAATGCAACTACTGTTTCTACACAACCACAAGAGgtgtggaaca ... gctcttgcagATTGTGAATCCAGGTGCTTCATCCAACCCTCAATTGAATCAATCTCAGCCA
EST: gi|84117320|gb|CD151087.1|CD151087
EST:     CATCATCGTCCATGGGCAATGCAACTACTGTTTCTACACAACCACAAGAG                         ATTGTGAATCCAGGTGCTTCATCCAACCCTCAATTGAATCAATCTCAGCCA
genomic: CATCATCGTCCATGGGCAATGCAACTACTGTTTCTACACAACCACAAGAGgtgtggaaca ... gctcttgcagATTGTGAATCCAGGTGCTTCATCCAACCCTCAATTGAATCAATCTCAGCCA
EST: gi|58660206|gb|CK048886.1|CK048886
EST:     CATCATCGTCCATGGGCAATGCAACTACTGTTTCTACACAACCACAAGAG                         ATTGTGAATCCAGGTGCTTCATCCAACCCTCAATTGAATCAATCTCAGCCA
genomic: CATCATCGTCCATGGGCAATGCAACTACTGTTTCTACACAACCACAAGAGgtgtggaaca ... gctcttgcagATTGTGAATCCAGGTGCTTCATCCAACCCTCAATTGAATCAATCTCAGCCA
EST: gi|58691641|gb|CK080328.1|CK080328
EST:     CATCATCGTCCATGGGCAATGCAACTACTGTTTCTACACAACCACAAGAG                         ATTGTGAATCCAGGTGCTTCATCCAACCCTCAATTGAATCAATCTCAGCCA
genomic: CATCATCGTCCATGGGCAATGCAACTACTGTTTCTACACAACCACAAGAGgtgtggaaca ... gctcttgcagATTGTGAATCCAGGTGCTTCATCCAACCCTCAATTGAATCAATCTCAGCCA
EST: gi|58590928|gb|CF989236.1|CF989236
EST:     CATCATCGTCCATGGGCAATGCAACTACTGTTTCTACACAACCACAAGAG                         ATTGTGAATCCAGGTGCTGGGGTCCAACCCTCAATTGAATCAATCTCAGCC
genomic: CATCATCGTCCATGGGCAATGCAACTACTGTTTCTACACAACCACAAGAGgtgtggaaca ... gctcttgcagATTGTGAATCCAGGTGCT-TCATCCAACCCTCAATTGAATCAATCTCAGCC
EST: gi|58676022|gb|CK064709.1|CK064709
EST:     CATCATCGTCCATGGGCAATGCAACTACTGTTTCTACACAACCACAAGAG                         ATTGTGAATCCAGGTGCTTCATCCAACCCTCAATTGAATCAATCTCAGCCA
genomic: CATCATCGTCCATGGGCAATGCAACTACTGTTTCTACACAACCACAAGAGgtgtggaaca ... gctcttgcagATTGTGAATCCAGGTGCTTCATCCAACCCTCAATTGAATCAATCTCAGCCA
EST: gi|33801990|gb|CF326868.1|CF326868
EST:     CTACACAACCACAAGAG                         ATTGTGAATCCAGGTGCTTCATCCAACCCTCAATTGAATCAATCTCAGCCA
genomic: CTACACAACCACAAGAGgtgtggaaca ... gctcttgcagATTGTGAATCCAGGTGCTTCATCCAACCCTCAATTGAATCAATCTCAGCCA

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: 62 (upstream exon), 73 (downstream exon)
Score: 26

CTCATTATTACTTACTAACCCACCATTGGCTACGATGGTTCATGGCACAACATCATCGTCCATGGGCAATGCAACTACTGTTTCTACACAACCACAAGAGgtgtggaaca ... gctcttgcagATTGTGAATCCAGGTGCTTCATCCAACCCTCAATTGAATCAATCTCAGCCAAGCACCAGCACCAGCATTGCTTCTGGTCCTCCACTCCCTCAGCATCTCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttttggattgtttacctgtgtatcattgttcttgtggtgtcggctcttgcagATTGTGAATCCAGGTGCTTCATCCAACCCTCAATTGAATCAATCTCAGCCAAGCACCAGCACCAGCATTGCTTCTGGTCCTCCACTCCCTCAGCATCTCA
                                              ctcttgc  CT-rich tract
         attgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgaggtttatcttgtgatttgtgaatatattttctgccttaattttcttttggattgtttacctgtgtatcattgttcttgtggtgtcggctcttgcagATTGTGAATCCAGGTGCTTCATCCAACCCTCAATTGAATCAATCTCAGCCAAGCACCAGCACCAGCATTGCTTCTGGTCCTCCACTCCCTCAGCATCTCA

- - - - - - ttgtgat
- - - - - - - - - - - - - - - - ttctgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtggtg