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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcattccatcatctgtacagattacaaaatgcagaaaactggtcaatgcgtaaattcaaaatagacctggggcctcctataattcgttttttcatctcatgcagGGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAG

Basic information

species Oryza sativa
transcript LOC_Os03g57130.1
intron # 7
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|87026215|gb|CI252365.1|CI252365
EST:     CTGCTGAAGCACATAATTCGCTGCTACCTCAGGCTGTCAGAAAATTCCAG                         GGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAAC
genomic: CTGCTGAAGCACATAATTCGCTGCTACCTCAGGCTGTCAGAAAATTCCAGgttcattcca ... tctcatgcagGGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAAC
EST: gi|87010056|gb|CI279153.1|CI279153
EST:     CTGCTGAAGCACATAATTCGCTGCTACCTCAGGCTGTCAGAAAATTCCAG                         GGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAAC
genomic: CTGCTGAAGCACATAATTCGCTGCTACCTCAGGCTGTCAGAAAATTCCAGgttcattcca ... tctcatgcagGGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAAC
EST: gi|89198053|gb|CI117531.1|CI117531
EST:     CTACCTCAGGCTGTCAGAAAATTCCAG                         GGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAAC
genomic: CTACCTCAGGCTGTCAGAAAATTCCAGgttcattcca ... tctcatgcagGGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAAC
EST: gi|218481822|gb|FG963644.1|FG963644
EST:     CTGCTGAAGCACATAATTCGCTGCTACCTCAGGCTGTCAGAAAATTCCAG                         GGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAAC
genomic: CTGCTGAAGCACATAATTCGCTGCTACCTCAGGCTGTCAGAAAATTCCAGgttcattcca ... tctcatgcagGGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAAC
EST: gi|89198745|gb|CI003482.1|CI003482
EST:     AGCACATAATTCGCTGCTACCTCAGGCTGTCAGAAAATTCCAG                         GGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAAC
genomic: AGCACATAATTCGCTGCTACCTCAGGCTGTCAGAAAATTCCAGgttcattcca ... tctcatgcagGGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAAC
EST: gi|86504776|gb|CI147409.1|CI147409
EST:     CTGCTGAAGCACATAATTCGCTGCTACCTCAGGCTGTCAGAAAATTCCAG                         GGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAAC
genomic: CTGCTGAAGCACATAATTCGCTGCTACCTCAGGCTGTCAGAAAATTCCAGgttcattcca ... tctcatgcagGGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAAC
EST: gi|44678276|gb|CR291710.1|CR291710
EST:     CTGCTGAAGCACATAATTCGCTGCTACCTCAGGCTGTCCGACAATTCCAG                         GGCATGTAACGCGCTGAACAGCTG
genomic: CTGCTGAAGCACATAATTCGCTGCTACCTCAGGCTGTCAGAAAATTCCAGgttcattcca ... tctcatgcagGGCATGTACCGCGCTGAACAGCTG
EST: gi|87029166|gb|CI276434.1|CI276434
EST:     CTGCTGAAGCACATAATTCGCTGCTACCTCAGGCTGTCAGAAAATTCCAG                         GGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAAC
genomic: CTGCTGAAGCACATAATTCGCTGCTACCTCAGGCTGTCAGAAAATTCCAGgttcattcca ... tctcatgcagGGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAAC
EST: gi|86504154|gb|CI146787.1|CI146787
EST:     CTGCTGAAGCACATAATTCGCTGCTACCTCAGGCTGTCAGAAAATTCCAG                         GGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAAC
genomic: CTGCTGAAGCACATAATTCGCTGCTACCTCAGGCTGTCAGAAAATTCCAGgttcattcca ... tctcatgcagGGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAAC
EST: gi|88227912|gb|CI227392.1|CI227392
EST:     CTGCTGAAGCACATAATTCGCTGCTACCTCAGGCTGTCAGAAAATTCCAG                         GGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAAC
genomic: CTGCTGAAGCACATAATTCGCTGCTACCTCAGGCTGTCAGAAAATTCCAGgttcattcca ... tctcatgcagGGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAAC
EST: gi|88239243|gb|CI240405.1|CI240405
EST:     CTGCTGAAGCACATAATTCGCTGCTACCTCAGGCTGTCAGAAAATTCCAG                         GGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAAC
genomic: CTGCTGAAGCACATAATTCGCTGCTACCTCAGGCTGTCAGAAAATTCCAGgttcattcca ... tctcatgcagGGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAAC
EST: gi|86494403|gb|CI137036.1|CI137036
EST:     CTGCTGAAGCACATAATTCGCTGCTACCTCAGGCTGTCAGAAAATTCCAG                         GGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAAC
genomic: CTGCTGAAGCACATAATTCGCTGCTACCTCAGGCTGTCAGAAAATTCCAGgttcattcca ... tctcatgcagGGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAAC
EST: gi|87011439|gb|CI279348.1|CI279348
EST:     CTGCTGAAGCACATAATTCGCTGCTACCTCAGGCTGTCAGAAAATTCCAG                         GGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAAC
genomic: CTGCTGAAGCACATAATTCGCTGCTACCTCAGGCTGTCAGAAAATTCCAGgttcattcca ... tctcatgcagGGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAAC
EST: gi|86501806|gb|CI144439.1|CI144439
EST:     CTGCTGAAGCACATAATTCGCTGCTACCTCAGGCTGTCAGAAAATTCCAG                         GGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAAC
genomic: CTGCTGAAGCACATAATTCGCTGCTACCTCAGGCTGTCAGAAAATTCCAGgttcattcca ... tctcatgcagGGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAAC
EST: gi|86598079|gb|CI278469.1|CI278469
EST:     CTGCTGAAGCACATAATTCGCTGCTACCTCAGGCTGTCAGAAAATTCCAG                         GGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAAC
genomic: CTGCTGAAGCACATAATTCGCTGCTACCTCAGGCTGTCAGAAAATTCCAGgttcattcca ... tctcatgcagGGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAAC

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), 62 (downstream exon)
Score: 22

GTGTTCTATCACAGATGGTTCAGGCACTTGCTGATCAACCTTCTCCAAGACTGCTGAAGCACATAATTCGCTGCTACCTCAGGCTGTCAGAAAATTCCAGgttcattcca ... tctcatgcagGGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaattcaaaatagacctggggcctcctataattcgttttttcatctcatgcagGGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAG
                                 ttcgttttttcatctc  CT-rich tract
                            tataattcgtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcattccatcatctgtacagattacaaaatgcagaaaactggtcaatgcgtaaattcaaaatagacctggggcctcctataattcgttttttcatctcatgcagGGCATGTACCGCGCTGAACAGCTGCCTCCCCAACGCGCTGAAAGATGGAACCCTCAACAACTTCCTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA