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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaattttctctacttgaaaagttgaatttctattataacccttgtcttatccctcatccaaccattggaatggtggtctacagAATTGGAAGGCCTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACATATGAGGAAGTGAAACGGAATGGCAGGAAAACACAATTTCGCTGTTAGAAC

Basic information

species Oryza sativa
transcript LOC_Os10g37740.1
intron # 12
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|89183237|gb|CI045802.1|CI045802
EST:     CTTGTCAAATGGACGATCATTACCACCCTTGTTCGACTTCTCAGCTGCTG                         AATTGGAA-GCACTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACAT
genomic: CTTGTCAAATGGACGATCATTACCACCCTTGTTCGACTTCTCAGCTGCTGgtaagaattt ... tggtctacagAATTGGAAGGC-CTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACAT
EST: gi|86413065|gb|CI067470.1|CI067470
EST:     CGATCATTACCACCCTTGTTCGACTTCTCAGCTGCTG                         AATTGGAAGGCCTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACATA
genomic: CGATCATTACCACCCTTGTTCGACTTCTCAGCTGCTGgtaagaattt ... tggtctacagAATTGGAAGGCCTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACATA
EST: gi|86500213|gb|CI142846.1|CI142846
EST:     CTTGTCAAATGGACGATCATTACCACCCTTGTTCGACTTCTCAGCTGCTG                         AATTGGAAGGCCTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACATA
genomic: CTTGTCAAATGGACGATCATTACCACCCTTGTTCGACTTCTCAGCTGCTGgtaagaattt ... tggtctacagAATTGGAAGGCCTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACATA
EST: gi|86481063|gb|CI123696.1|CI123696
EST:     CTTGTCAAATGGACGATCATTACCACCCTTGTTCGACTTCTCAGCTGCTG                         AATTGGAAGGCCTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACATA
genomic: CTTGTCAAATGGACGATCATTACCACCCTTGTTCGACTTCTCAGCTGCTGgtaagaattt ... tggtctacagAATTGGAAGGCCTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACATA
EST: gi|88216344|gb|CI216193.1|CI216193
EST:     TACCACCCTTGTTCGACTTCTCAGCTGCTG                         AATTGGAAGGCCTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACATA
genomic: TACCACCCTTGTTCGACTTCTCAGCTGCTGgtaagaattt ... tggtctacagAATTGGAAGGCCTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACATA
EST: gi|89185453|gb|CI051781.1|CI051781
EST:     CTTGTCAAATGGACGATCATTACCACCCTTGTTCGACTTCTCAGCTGCTG                         AATTGGAAGGCCTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACATA
genomic: CTTGTCAAATGGACGATCATTACCACCCTTGTTCGACTTCTCAGCTGCTGgtaagaattt ... tggtctacagAATTGGAAGGCCTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACATA
EST: gi|29666991|gb|CB663266.1|CB663266
EST:     CTTGTCAAATGGACGATCATTACCACCCTTGTTCGACTTCTCAGCTGCTG                         AATTGGAAGGCCTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACATA
genomic: CTTGTCAAATGGACGATCATTACCACCCTTGTTCGACTTCTCAGCTGCTGgtaagaattt ... tggtctacagAATTGGAAGGCCTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACATA
EST: gi|86255608|gb|CI065285.1|CI065285
EST:     CTTGTCAAATGGACGATCATTACCACCCTTGTTCGACTTCTCAGCTGCTG                         AATTGGAAGGCCTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACATA
genomic: CTTGTCAAATGGACGATCATTACCACCCTTGTTCGACTTCTCAGCTGCTGgtaagaattt ... tggtctacagAATTGGAAGGCCTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACATA
EST: gi|33681320|gb|CF309559.1|CF309559
EST:     CTTGTCAAATGGACGATCATTACCACCCTTGTTCGACTTCTCAGCTGCTG                         AATTGGAAGGCCTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACATA
genomic: CTTGTCAAATGGACGATCATTACCACCCTTGTTCGACTTCTCAGCTGCTGgtaagaattt ... tggtctacagAATTGGAAGGCCTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACATA
EST: gi|86834816|gb|CI345900.1|CI345900
EST:     TTCTCAGCTGCTG                         AATTGGAAGGCCTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACATA
genomic: TTCTCAGCTGCTGgtaagaattt ... tggtctacagAATTGGAAGGCCTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACATA
EST: gi|29680415|gb|CB676690.1|CB676690
EST:     CTTGTCAAATGGACGATCATTACCACCCTTGTTCGACTTCTCAGCTGCTG                         AATTGGAAGGCCTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACATA
genomic: CTTGTCAAATGGACGATCATTACCACCCTTGTTCGACTTCTCAGCTGCTGgtaagaattt ... tggtctacagAATTGGAAGGCCTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACATA
EST: gi|86834815|gb|CI345899.1|CI345899
EST:     CGACTTCTCAGCTGCTG                         AATTGGAAGGCCTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACATA
genomic: CGACTTCTCAGCTGCTGgtaagaattt ... tggtctacagAATTGGAAGGCCTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACATA
EST: gi|218488407|gb|FG957568.1|FG957568
EST:     CTTGTCAAATGGACGATCATTACCACCCTTGTTCGACTTCTCAGCTGCTG                         AATTGGAAGGCCTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACATA
genomic: CTTGTCAAATGGACGATCATTACCACCCTTGTTCGACTTCTCAGCTGCTGgtaagaattt ... tggtctacagAATTGGAAGGCCTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACATA
EST: gi|89173539|gb|CI041432.1|CI041432
EST:     CTTGTCAAATGGACGATCATTACCACCCTTGTTCGACTTCTCAGCTGCTG                         AATTGGAAGGCCTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACATA
genomic: CTTGTCAAATGGACGATCATTACCACCCTTGTTCGACTTCTCAGCTGCTGgtaagaattt ... tggtctacagAATTGGAAGGCCTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACATA
EST: gi|86431262|gb|CI083685.1|CI083685
EST:     CTTGTCAAATGGACGATCATTACCACCCTTGTTCGACTTCTCAGCTGCTG                         AATCGGAAGGCCTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACATA
genomic: CTTGTCAAATGGACGATCATTACCACCCTTGTTCGACTTCTCAGCTGCTGgtaagaattt ... tggtctacagAATTGGAAGGCCTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACATA

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: 70 (upstream exon), 75 (downstream exon)
Score: 19

GATGCTTGTGCTCATCCATTCTTTGATGAACTGCGGGATCCCAAGACCTGCTTGTCAAATGGACGATCATTACCACCCTTGTTCGACTTCTCAGCTGCTGgtaagaattt ... tggtctacagAATTGGAAGGCCTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACATATGAGGAAGTGAAACGGAATGGCAGGAAAACACAATTTCGCTGTTAGAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctattataacccttgtcttatccctcatccaaccattggaatggtggtctacagAATTGGAAGGCCTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACATATGAGGAAGTGAAACGGAATGGCAGGAAAACACAATTTCGCTGTTAGAAC
    ttataac  putative branch site (score: 19)
     tataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaattttctctacttgaaaagttgaatttctattataacccttgtcttatccctcatccaaccattggaatggtggtctacagAATTGGAAGGCCTTCCTGTTGAGCTAGTCCACCGAATCATTCCTGAACATATGAGGAAGTGAAACGGAATGGCAGGAAAACACAATTTCGCTGTTAGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT