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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGCATTGCTTGAGACTTCATCGGTTGATGATGACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCGgtatgtattaatgctcaaactatgagacgatgtcaagtttcatttaacacacaagacaatacatctgatatttatgtgaacagagccagacccactgata...

Basic information

species Oryza sativa
transcript LOC_Os01g67000.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g67000.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G017077_T01 (Zea mays), 5'ss of exon 10
TTTGCATTGCTTGAGACTTCATCGGTTGATGATGACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCGgtatgtattaatgctcaaactatgagacgatgtcaagtttcatttaacacacaagacaatacatctgatatttatgtgaacagagccagacccactgata----
|||||| |||||||||||||||| ||||||||||| ||| ||||| ||||||||||| | ||||||||||||| ||||||||||  |        ||| | |  |     | ||  |   |    |    |  | | | ||| | | ||| |          |    || |        
TTTGCACTGCTTGAGACTTCATCTGTTGATGATGATCTTTCACAACTGAAAAAGGAATTGTCTGGAAGCTCTTTGgtatgtattcttatctgggttatcaaatta----gaattctaacgattgaagctaatgagatacctgctgtctatttatttcagtaaatgttcattctagctgc
















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|11564773|gb|AU165409.1|AU165409
EST:     TTGATGATGACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCG                         AAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCG
genomic: TTGATGATGACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCGgtatgtatta ... ttatctacagAAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCG
EST: gi|88987357|gb|CI034321.1|CI034321
EST:     TTGATGATGACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCG                         AAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCG
genomic: TTGATGATGACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCGgtatgtatta ... ttatctacagAAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCG
EST: gi|87007164|gb|CI277239.1|CI277239
EST:     TTGATGATGACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCG                         AAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCG
genomic: TTGATGATGACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCGgtatgtatta ... ttatctacagAAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCG
EST: gi|33797534|gb|CF324627.1|CF324627
EST:     TTGATGATGACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCG                         AAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCG
genomic: TTGATGATGACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCGgtatgtatta ... ttatctacagAAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCG
EST: gi|88995507|gb|CI022830.1|CI022830
EST:     TTGATGATGACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCG                         AAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCG
genomic: TTGATGATGACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCGgtatgtatta ... ttatctacagAAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCG
EST: gi|88988016|gb|CI018059.1|CI018059
EST:     TTGATGATGACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCG                         AAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCG
genomic: TTGATGATGACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCGgtatgtatta ... ttatctacagAAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCG
EST: gi|86836488|gb|CI348366.1|CI348366
EST:     ACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCG                         AAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCG
genomic: ACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCGgtatgtatta ... ttatctacagAAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCG
EST: gi|86594857|gb|CI258111.1|CI258111
EST:     TTGATGATGACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCG                         AAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCG
genomic: TTGATGATGACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCGgtatgtatta ... ttatctacagAAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCG
EST: gi|88252713|gb|CI351141.1|CI351141
EST:     GAAATTTCTGGAAGCTCTTCG                         AAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCG
genomic: GAAATTTCTGGAAGCTCTTCGgtatgtatta ... ttatctacagAAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCG
EST: gi|88200513|gb|CI200363.1|CI200363
EST:     TTGATGATGACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCG                         AAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCG
genomic: TTGATGATGACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCGgtatgtatta ... ttatctacagAAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCG
EST: gi|86486380|gb|CI129013.1|CI129013
EST:     TTGATGATGACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCG                         AAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCG
genomic: TTGATGATGACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCGgtatgtatta ... ttatctacagAAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCG
EST: gi|86497463|gb|CI140096.1|CI140096
EST:     TTAATGATGACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCG                         AAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCG
genomic: TTGATGATGACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCGgtatgtatta ... ttatctacagAAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCG
EST: gi|86593881|gb|CI260110.1|CI260110
EST:     TTGATGATGACCTTGCACAAATGAAAAAGGAAATTTTTGGAAGCTCTTCG                         AAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCG
genomic: TTGATGATGACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCGgtatgtatta ... ttatctacagAAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCG
EST: gi|88228435|gb|CI227915.1|CI227915
EST:     TTGATGATGACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCG                         AAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCG
genomic: TTGATGATGACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCGgtatgtatta ... ttatctacagAAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCG
EST: gi|86493106|gb|CI135739.1|CI135739
EST:     TTGATGATGACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCG                         AAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCG
genomic: TTGATGATGACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCGgtatgtatta ... ttatctacagAAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCG
EST: gi|86432017|gb|CI085628.1|CI085628
EST:     TTGATGATGACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCG                         AAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCG
genomic: TTGATGATGACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCGgtatgtatta ... ttatctacagAAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCG

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: 71 (upstream exon), 51 (downstream exon)
Score: 27

TTTGCATTGCTTGAGACTTCATCGGTTGATGATGACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCGgtatgtatta ... ttatctacagAAAGGAGAACTTCCTCCAGGTAGAACGGCAGTCAGCAATTCAGGAGCAGCGCGCCCTTTCCGAGACATCGAGATTGAGAATGAGCTAAATGAGCTGCGGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGCATTGCTTGAGACTTCATCGGTTGATGATGACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCGgtatgtattaatgctcaaactatgagacgatgtcaagtttcatttaacacacaagacaatacatctgatatttatgtgaacagagccagacccactgata

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG