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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtactctattgtcataagtgctaataccatttccagtttccaaacatctgctattcttttgtcaaatcataactcaattccaaatattattacatgaggtattggatatttggatgtcaaatacacatagataaatcatctcatgtaattacatccttttggctcatttctacagGTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAGTCGATAAGAGAAGAATGTGAGAAGTTGCAACCTGAACCATGAGCCTAAC

Basic information

species Oryza sativa
transcript LOC_Os01g74650.1
intron # 9
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|58678120|gb|CK066807.1|CK066807
EST:     CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTG                         GTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
genomic: CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTGgtgagtactc ... atttctacagGTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
EST: gi|86413547|gb|CI019132.1|CI019132
EST:     CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTG                         GTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
genomic: CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTGgtgagtactc ... atttctacagGTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
EST: gi|86886088|gb|CI321124.1|CI321124
EST:     CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTG                         GTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
genomic: CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTGgtgagtactc ... atttctacagGTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
EST: gi|29655936|gb|CB652211.1|CB652211
EST:     CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTG                         GTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
genomic: CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTGgtgagtactc ... atttctacagGTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
EST: gi|58691812|gb|CK080499.1|CK080499
EST:     CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTG                         GTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
genomic: CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTGgtgagtactc ... atttctacagGTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
EST: gi|29616466|gb|CB621478.1|CB621478
EST:     CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTG                         GTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
genomic: CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTGgtgagtactc ... atttctacagGTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
EST: gi|29663371|gb|CB659646.1|CB659646
EST:     CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTG                         GTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
genomic: CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTGgtgagtactc ... atttctacagGTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
EST: gi|29687246|gb|CB683521.1|CB683521
EST:     CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTG                         GTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
genomic: CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTGgtgagtactc ... atttctacagGTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
EST: gi|163927355|gb|EG710663.1|EG710663
EST:     CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTG                         GTTGTGTTTCCAAGCT
genomic: CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTGgtgagtactc ... atttctacagGTTGTGTTTCCAAGCT
EST: gi|84117136|gb|CD150903.1|CD150903
EST:     CTGCCATTAAAGCTGCAAAAAGACCAGAAAATGCTGGAAAGTTGAAAGTG                         GTTGTGTTTCCAAGCTTTGGTGAGAGGTACCT
genomic: CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTGgtgagtactc ... atttctacagGTTGTGTTTCCAAGCTTTGGTGAGAGGTACCT
EST: gi|33801701|gb|CF326722.1|CF326722
EST:     CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTG                         GTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
genomic: CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTGgtgagtactc ... atttctacagGTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
EST: gi|86494722|gb|CI137355.1|CI137355
EST:     CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTG                         GTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
genomic: CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTGgtgagtactc ... atttctacagGTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
EST: gi|29655935|gb|CB652210.1|CB652210
EST:     CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTG                         GTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
genomic: CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTGgtgagtactc ... atttctacagGTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
EST: gi|88847644|gb|CI018335.1|CI018335
EST:     CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTG                         GTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
genomic: CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTGgtgagtactc ... atttctacagGTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
EST: gi|38469869|gb|CF954000.1|CF954000
EST:     CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTG                         GTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
genomic: CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTGgtgagtactc ... atttctacagGTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
EST: gi|29672976|gb|CB669251.1|CB669251
EST:     CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTG                         GTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
genomic: CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTGgtgagtactc ... atttctacagGTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
EST: gi|29677863|gb|CB674138.1|CB674138
EST:     CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTG                         GTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
genomic: CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTGgtgagtactc ... atttctacagGTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
EST: gi|58690422|gb|CK079109.1|CK079109
EST:     CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTG                         GTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
genomic: CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTGgtgagtactc ... atttctacagGTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
EST: gi|88845335|gb|CI084260.1|CI084260
EST:     CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTG                         GTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
genomic: CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTGgtgagtactc ... atttctacagGTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
EST: gi|29616196|gb|CB621208.1|CB621208
EST:     CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTG                         GTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
genomic: CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTGgtgagtactc ... atttctacagGTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
EST: gi|58696201|gb|CK084888.1|CK084888
EST:     CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTG                         GTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
genomic: CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTGgtgagtactc ... atttctacagGTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
EST: gi|86535476|gb|CI175682.1|CI175682
EST:     CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTG                         GTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
genomic: CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTGgtgagtactc ... atttctacagGTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
EST: gi|38471318|gb|CF955449.1|CF955449
EST:     CTGCCATTAAAGTTGCAATAAGACCAGAAAATGCTGGAAAGTTGGTAGTG                         GTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
genomic: CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTGgtgagtactc ... atttctacagGTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
EST: gi|88220621|gb|CI220181.1|CI220181
EST:     CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTG                         GTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
genomic: CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTGgtgagtactc ... atttctacagGTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
EST: gi|29644300|gb|CB649307.1|CB649307
EST:     CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTG                         GTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
genomic: CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTGgtgagtactc ... atttctacagGTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
EST: gi|13420475|gb|AU174565.1|AU174565
EST:     CT-CCATTAAAGTTGCAAAANGACCAGAAAATGCTGGAAAGTTGGNAGTT                         GTTGTNTTTCCAAGCTTT
genomic: CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTGgtgagtactc ... atttctacagGTTGTGTTTCCAAGCTTT
EST: gi|300215770|gb|HO088396.1|HO088396
EST:     CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTG                         GTTGTATTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
genomic: CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTGgtgagtactc ... atttctacagGTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
EST: gi|29684900|gb|CB681175.1|CB681175
EST:     CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTG                         GTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
genomic: CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTGgtgagtactc ... atttctacagGTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
EST: gi|86417511|gb|CI031720.1|CI031720
EST:     CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTG                         GTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
genomic: CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTGgtgagtactc ... atttctacagGTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
EST: gi|88387705|gb|CI585408.1|CI585408
EST:     CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTG                         GTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG
genomic: CTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTGgtgagtactc ... atttctacagGTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAG

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: 67 (upstream exon), 74 (downstream exon)
Score: 64

GTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTGgtgagtactc ... atttctacagGTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAGTCGATAAGAGAAGAATGTGAGAAGTTGCAACCTGAACCATGAGCCTAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacacatagataaatcatctcatgtaattacatccttttggctcatttctacagGTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAGTCGATAAGAGAAGAATGTGAGAAGTTGCAACCTGAACCATGAGCCTAAC
                                          ctcatttct  CT-rich tract
      atagataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtactctattgtcataagtgctaataccatttccagtttccaaacatctgctattcttttgtcaaatcataactcaattccaaatattattacatgaggtattggatatttggatgtcaaatacacatagataaatcatctcatgtaattacatccttttggctcatttctacagGTTGTGTTTCCAAGCTTTGGTGAGAGGTACCTTTCATCTATCCTTTTTCAGTCGATAAGAGAAGAATGTGAGAAGTTGCAACCTGAACCATGAGCCTAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT