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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtcatttgtgttattatagggcgacatttactttcaggcactgcctctttcaagttttaactctgagaaatacagGATGAATTGGAACTCTCACAGTGGAAACAGCTATTAGACCGTGATGTTGAAATTCTGAAGGCAAAAGCTAACACGTCAAAGATCCAGTCG

Basic information

species Oryza sativa
transcript LOC_Os07g47530.2
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g47530.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G157621_T02 (Zea mays), 3'ss of exon 15
gtgtgtcatt-tgt--gttattatagggcgacatt-tactt---tcaggcactgcctctttcaagttttaactctgagaaa----tacagGATGAATTGGAACTCTCACAGTGGAAACAGCTATTAGACCGTGATGTTGAAATTCTGAAGGCAAAAGCTAACACGTCAAAGATCCAGTCG
|||||||||| |||  ||| | |   ||  | ||  ||  |   ||  | | || || || |||||||||||||| | ||     |||||||||||  ||||||||| ||||||||||||||||| |  |||||  |||||||||| |||||||| |||||    |  || || || || 
gtgtgtcattatgttagttctcaagagggtatataatatatagatctagaattggcttttgcaagttttaactcttaaaatatgctacagGATGAAACGGAACTCTCCCAGTGGAAACAGCTATTGGGTCGTGACATTGAAATTCTTAAGGCAAAGGCTAATTTTTTGAAAATACAATCT
















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|33797016|gb|CF324371.1|CF324371
EST:     AGCATCTGACTAAACTCTTCCCAAATAAAGTGACAATACAAACACCGCAG                         GATGAATTGGAACTCTCACAGTGGAAACAGCTATTAGACCGTGATGTTGAA
genomic: AGCATCTGACTAAACTCTTCCCAAATAAAGTGACAATACAAACACCGCAGgtgtgtcatt ... agaaatacagGATGAATTGGAACTCTCACAGTGGAAACAGCTATTAGACCGTGATGTTGAA
EST: gi|58692536|gb|CK081223.1|CK081223
EST:     AGCATCTGACTAAACTCTTCCCAAATAAAGTGACAATACAAACACCGCAG                         GATGAATTGGAACTCTCACAGTGGAAACAGCTATTAGACCGTGATGTTGAA
genomic: AGCATCTGACTAAACTCTTCCCAAATAAAGTGACAATACAAACACCGCAGgtgtgtcatt ... agaaatacagGATGAATTGGAACTCTCACAGTGGAAACAGCTATTAGACCGTGATGTTGAA
EST: gi|58690470|gb|CK079157.1|CK079157
EST:     AGCATCTGACTAAACTCTTCCCAAATAAAGTGACAATACAAACACCGCAG                         GATGAATTGGAACTCTCACAGTGGAAACAGCTATTAGACCGTGATGTTGAA
genomic: AGCATCTGACTAAACTCTTCCCAAATAAAGTGACAATACAAACACCGCAGgtgtgtcatt ... agaaatacagGATGAATTGGAACTCTCACAGTGGAAACAGCTATTAGACCGTGATGTTGAA
EST: gi|58652949|gb|CK041629.1|CK041629
EST:     AGCATCTGACTAAACTCTTCCCAAATAAAGTGACAATACAAACACCGCAG                         GATGAATTGGAACTCTCACAGTGGAAACAGCTATTAGACCGTGATGTTGAA
genomic: AGCATCTGACTAAACTCTTCCCAAATAAAGTGACAATACAAACACCGCAGgtgtgtcatt ... agaaatacagGATGAATTGGAACTCTCACAGTGGAAACAGCTATTAGACCGTGATGTTGAA
EST: gi|58690512|gb|CK079199.1|CK079199
EST:     AGCATCTGACTAAACTCTTCCCAAATAAAGTGACAATACAAACACCGCAG                         GATGAATTGGAACTCTCACAGTGGAAACAGCTATTAGACCGTGATGTTGAA
genomic: AGCATCTGACTAAACTCTTCCCAAATAAAGTGACAATACAAACACCGCAGgtgtgtcatt ... agaaatacagGATGAATTGGAACTCTCACAGTGGAAACAGCTATTAGACCGTGATGTTGAA
EST: gi|33675839|gb|CF304078.1|CF304078
EST:     AGCATCTGACTAAACTCTTCCCAAATAAAGTGACAATACAAACACCGCAG                         GATGAATTGGAACTCTCACAGTGGAAACAGCTATTAGACCGTGATGTTGAA
genomic: AGCATCTGACTAAACTCTTCCCAAATAAAGTGACAATACAAACACCGCAGgtgtgtcatt ... agaaatacagGATGAATTGGAACTCTCACAGTGGAAACAGCTATTAGACCGTGATGTTGAA
EST: gi|58658063|gb|CK046743.1|CK046743
EST:     AGCATCTGACTAAACTCTTCCCAAATAAAGTGACAATACAAACACCGCAG                         GATGAATTGGAACTCTCACAGTGGAAACAGCTATTAGACCGTGATGTTGAA
genomic: AGCATCTGACTAAACTCTTCCCAAATAAAGTGACAATACAAACACCGCAGgtgtgtcatt ... agaaatacagGATGAATTGGAACTCTCACAGTGGAAACAGCTATTAGACCGTGATGTTGAA
EST: gi|33675419|gb|CF303658.1|CF303658
EST:     AGCATCTGACTAAACTCTTCCCAAATAAAGTGACAATACAAACACCGCAG                         GATGAATTGGAACTCTCACAGTGGAAACAGCTATTAGACCGTGATGTTGAA
genomic: AGCATCTGACTAAACTCTTCCCAAATAAAGTGACAATACAAACACCGCAGgtgtgtcatt ... agaaatacagGATGAATTGGAACTCTCACAGTGGAAACAGCTATTAGACCGTGATGTTGAA
EST: gi|29685521|gb|CB681796.1|CB681796
EST:     AGCATCTGACTAGACTCTTCCCAAATAAAGTGACAATACAAACACCGCAG                         GATGAATTGGAACTCTC
genomic: AGCATCTGACTAAACTCTTCCCAAATAAAGTGACAATACAAACACCGCAGgtgtgtcatt ... agaaatacagGATGAATTGGAACTCTC
EST: gi|58660377|gb|CK049057.1|CK049057
EST:     AGCATCTGACTAAACTCTTCCCAAATAAAGTGACAATACAAACACCGCAG                         GATGAATTGGAACTCTCACAGTGGAAACAGCTATTAGACCGTGATGTTGAA
genomic: AGCATCTGACTAAACTCTTCCCAAATAAAGTGACAATACAAACACCGCAGgtgtgtcatt ... agaaatacagGATGAATTGGAACTCTCACAGTGGAAACAGCTATTAGACCGTGATGTTGAA
EST: gi|33676430|gb|CF304669.1|CF304669
EST:     AGCATCTGACTAAACTCTTCCCAAATAAAGTGACAATACAAACACCGCAG                         GATGAATTGGAACTCTCACAGTGGAAACAGCTATTAGACCGTGATGTTGAA
genomic: AGCATCTGACTAAACTCTTCCCAAATAAAGTGACAATACAAACACCGCAGgtgtgtcatt ... agaaatacagGATGAATTGGAACTCTCACAGTGGAAACAGCTATTAGACCGTGATGTTGAA

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), 72 (downstream exon)
Score: 44

TAGCTTTGGTCGGGTGAATGATAAAAACAAAGAGGCTCTGAAGATAGCGAAGCATCTGACTAAACTCTTCCCAAATAAAGTGACAATACAAACACCGCAGgtgtgtcatt ... agaaatacagGATGAATTGGAACTCTCACAGTGGAAACAGCTATTAGACCGTGATGTTGAAATTCTGAAGGCAAAAGCTAACACGTCAAAGATCCAGTCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgacatttactttcaggcactgcctctttcaagttttaactctgagaaatacagGATGAATTGGAACTCTCACAGTGGAAACAGCTATTAGACCGTGATGTTGAAATTCTGAAGGCAAAAGCTAACACGTCAAAGATCCAGTCG
                                  ttttaac  putative branch site (score: 44)
     atttacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtcatttgtgttattatagggcgacatttactttcaggcactgcctctttcaagttttaactctgagaaatacagGATGAATTGGAACTCTCACAGTGGAAACAGCTATTAGACCGTGATGTTGAAATTCTGAAGGCAAAAGCTAACACGTCAAAGATCCAGTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG