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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactgtctttactcacagctagaacgtgatgaatgattaaaaatgtgaaacttttggattagcaaatgaagctaactgtaattttttttcctcatcgcagGAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTTGATGATTTTTAAGGTCATTTCCGGGTGCTTTGTTTTGGTTTTAATTGTA

Basic information

species Oryza sativa
transcript LOC_Os06g07230.1
intron # 6
splice site 3'
intron type U2

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|88450344|gb|CI544466.1|CI544466
EST:     TAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTG                         GAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
genomic: TAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTGgtgagttatc ... ctcatcgcagGAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
EST: gi|87015767|gb|CI277725.1|CI277725
EST:     CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTG                         GAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
genomic: CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTGgtgagttatc ... ctcatcgcagGAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
EST: gi|88968606|gb|CI098832.1|CI098832
EST:     CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTG                         GAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
genomic: CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTGgtgagttatc ... ctcatcgcagGAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
EST: gi|29671625|gb|CB667900.1|CB667900
EST:     CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTG                         GAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
genomic: CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTGgtgagttatc ... ctcatcgcagGAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
EST: gi|66914151|gb|CX100999.1|CX100999
EST:     CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTG                         GAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAACTT
genomic: CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTGgtgagttatc ... ctcatcgcagGAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
EST: gi|88384275|gb|CI551201.1|CI551201
EST:     CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTG                         GAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
genomic: CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTGgtgagttatc ... ctcatcgcagGAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
EST: gi|29677838|gb|CB674113.1|CB674113
EST:     CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTG                         GAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
genomic: CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTGgtgagttatc ... ctcatcgcagGAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
EST: gi|87040215|gb|CI194837.1|CI194837
EST:     CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTG                         GAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
genomic: CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTGgtgagttatc ... ctcatcgcagGAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
EST: gi|86547057|gb|CI187263.1|CI187263
EST:     CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTG                         GAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
genomic: CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTGgtgagttatc ... ctcatcgcagGAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
EST: gi|29666887|gb|CB663162.1|CB663162
EST:     CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTG                         GAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
genomic: CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTGgtgagttatc ... ctcatcgcagGAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
EST: gi|88983304|gb|CI028541.1|CI028541
EST:     CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTG                         GAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
genomic: CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTGgtgagttatc ... ctcatcgcagGAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
EST: gi|86541132|gb|CI181338.1|CI181338
EST:     CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTG                         GAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
genomic: CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTGgtgagttatc ... ctcatcgcagGAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
EST: gi|88206223|gb|CI206072.1|CI206072
EST:     CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTG                         GAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
genomic: CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTGgtgagttatc ... ctcatcgcagGAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
EST: gi|88226394|gb|CI226310.1|CI226310
EST:     CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTG                         GAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
genomic: CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTGgtgagttatc ... ctcatcgcagGAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
EST: gi|86494937|gb|CI137570.1|CI137570
EST:     CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTG                         GAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
genomic: CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTGgtgagttatc ... ctcatcgcagGAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
EST: gi|29642958|gb|CB647965.1|CB647965
EST:     CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTG                         GAAAGGCACGTCAGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
genomic: CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTGgtgagttatc ... ctcatcgcagGAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
EST: gi|86418593|gb|CI032802.1|CI032802
EST:     CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTG                         GAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
genomic: CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTGgtgagttatc ... ctcatcgcagGAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
EST: gi|29671665|gb|CB667940.1|CB667940
EST:     CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTG                         GAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
genomic: CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTGgtgagttatc ... ctcatcgcagGAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
EST: gi|87033523|gb|CI188147.1|CI188147
EST:     CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTG                         GAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
genomic: CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTGgtgagttatc ... ctcatcgcagGAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
EST: gi|88973033|gb|CI019652.1|CI019652
EST:     CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTG                         GAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT
genomic: CCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTGgtgagttatc ... ctcatcgcagGAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTT

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: 65 (upstream exon), 45 (downstream exon)
Score: 4

TCTCGTCCGACAATGGATGAAGTTGTCAAGCACCTGACGCCGTTGCAGGACCTAAATGACATGGCGTCTGCATCATATAGACCTCGATCATCTCAGCGTGgtgagttatc ... ctcatcgcagGAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTTGATGATTTTTAAGGTCATTTCCGGGTGCTTTGTTTTGGTTTTAATTGTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaacttttggattagcaaatgaagctaactgtaattttttttcctcatcgcagGAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTTGATGATTTTTAAGGTCATTTCCGGGTGCTTTGTTTTGGTTTTAATTGTA
                        agctaac  putative branch site (score: 4)
                                    ttttttttcctcatcg  putative PPT
                           taactgtaattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactgtctttactcacagctagaacgtgatgaatgattaaaaatgtgaaacttttggattagcaaatgaagctaactgtaattttttttcctcatcgcagGAAAGGCACGTCGGTGATGGCCGGATCCACTGCTAAAAAGCAGCGAAATTTGATGATTTTTAAGGTCATTTCCGGGTGCTTTGTTTTGGTTTTAATTGTA

- - - - - - - - - - - - - tgatgaa
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