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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatctcacatgcacattggacctcatatatttagtcttaatgttgtggtccaatttgcatggccaactgactgagtttttttgcattggataattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCACAACTTTGCGACCACCTGTGTTTGCAGGGTTCCTAAGCACCTAAGGGAAG

Basic information

species Oryza sativa
transcript LOC_Os12g05410.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g05410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA07G15700.1 (Glycine max), 3'ss of exon 3
aaatctcacatgcacattggacctcatatatttagtcttaatgt-tgtggtccaatttgcatggccaactgactgagtttttttgcattggat--aattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCACAACTTTGCGACCACCTGTGTTTGCAGGGTTCCTAAGCACCTAAGGGAAG
  |||||  |      ||  |    |||   ||  |  || |   |||| |    |     ||   |  | | | |   |||||   |||| |  |||||||||  || ||||| ||||| |||||| || | ||||| ||| ||||  | ||||| ||||| ||||| ||||||||||| ||||| ||| |||| ||||| |
--atctctgagaactgttaaaatatata-gcttgtttatagtacatgtgctttcttggatttgagtacttaaatcatgattttttttttggtttgaattgcagCCTGGTTATGAACGTCTATGCTGCTTGGGGTGTATGCAGCCACGCAATCACAATTTTGCCACCACTTGTGTTTGCAGAGTTCCCAAGAACCTTAGGGAGG

upper sequence: LOC_Os12g05410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G11450.1 (Glycine max), 3'ss of exon 4
aaatctcacatgcac----attggacctcatatatttagtcttaatgttgtggtcc---aatttgcatggccaactgactgagtttttttgcattggataattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCACAACTTTGCGACCACCTGTGTTTGCAGGGTTCCTAAGCACCTAAGGGAAG
   | | || | |||    |||  |  |||| | |  | |||   ||| ||  ||    | ||||  |    || | | |   | ||||||   ||   |||||||||  || ||||| ||||| ||||||||| | || || ||| |||| || ||||| ||||| ||||| ||||||||||| || || ||||| || ||||| |
--gttttactttcaccaagattttatttcatttgtgcattctatgtgtagttttcttggattttgagtacttaaatcatt--atgtttttggtctg---aattgcagCCTGGTTATGAACGTCTTTGCTGCCTGAGGTGCATGCAGCCACGTGATCACAATTTTGCCACCACTTGTGTTTGCAGAGTACCCAAGCAACTTAGGGAGG

upper sequence: LOC_Os12g05410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA05G28440.2 (Glycine max), 3'ss of exon 5
---aaatctcacatgcacattggacctcatatatttagt---cttaatgttgtggtccaatttgcatggccaactgactgagtttttttgcattggataattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCACAACTTTGCGACCACCTGTGTTTGCAGGGTTCCTAAGCACCTAAGGGAAG
      | | ||   ||| |  ||  | || |  || ||    |   |||| |  |  | ||||  |    || | |     | ||||||   ||   |||||||||  || ||||| ||||| ||||||||| | || || ||| |||| || ||||| ||||| ||||| ||||||||||| ||||| ||||| || ||||| |
gtattgttttactgtcac-taagattttatttgatttgtgcattctgtgttttcttggattttgagtaattaaatcatc--atgtttttggtctg---aattgcagCCTGGTTATGAACGTCTTTGCTGCCTGAGGTGCATGCAGCCACGTGATCACAATTTTGCCACCACTTGTGTTTGCAGAGTTCCCAAGCAACTTAGGGAGG

upper sequence: LOC_Os12g05410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv05s0020g01520.t01 (Vitis vinifera), 3'ss of exon 3
aaatctcacatgcacattggacctcatatatttagtcttaatgttgtggtccaatttgcatggccaactgactgagtttttttgcattggat-------aattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCACAACTTTGCGACCACCTGTGTTTGCAGGGTTCCTAAGCACCTAAGGGAAG
       | |  ||   ||    |    || ||  ||| || | |     | ||  || ||   || ||     |   |||||  ||   ||       ||||||||| ||| ||||| |||||||||||| || | || || ||  |||| || ||||||||||| ||||| ||||| ||| |||| || |||||||||||||| |
-------aaaaacaggctgatatttgcttaatttctctaaaagataaaagcaaagatgaatttacatctccaaaatccttttttaatgatatgcttttgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCACAACTTTGCCACCACATGTGTGTGCCGGGTCCCCAAGCACCTAAGGGAGG

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|55411448|gb|CV723824.1|CV723824
EST:     GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAG                         CAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
genomic: GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAGgtatgcactt ... ataattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
EST: gi|58677898|gb|CK066585.1|CK066585
EST:     GCCTTGACCANGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAG                         CAAGGCTATGAGCGTCTCTGCTGCCT
genomic: GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAGgtatgcactt ... ataattgcagCAAGGCTATGAGCGTCTCTGCTGCCT
EST: gi|25801397|gb|CA757358.1|CA757358
EST:     GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCNAATGGAAGAAG                         CAAGGCTATGAGCGTCTCTTCTGCCTGCGCTGTATCCAGACACGAGACCAC
genomic: GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAGgtatgcactt ... ataattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
EST: gi|29626505|gb|CB631516.1|CB631516
EST:     GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAG                         CAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
genomic: GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAGgtatgcactt ... ataattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
EST: gi|88570606|gb|CI661979.1|CI661979
EST:     GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAG                         CAAGGCTATGAGCGTCTCTGCTGCCTGCGCTG
genomic: GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAGgtatgcactt ... ataattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTG
EST: gi|88510397|gb|CI437903.1|CI437903
EST:     GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAG                         CAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
genomic: GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAGgtatgcactt ... ataattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
EST: gi|88587103|gb|CI704831.1|CI704831
EST:     GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAG                         CAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCC
genomic: GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAGgtatgcactt ... ataattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCC
EST: gi|88404303|gb|CI578180.1|CI578180
EST:     GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAG                         CAAGGCTATGAGCGTCTCTGCTGCCTGCGC
genomic: GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAGgtatgcactt ... ataattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGC
EST: gi|88554417|gb|CI484597.1|CI484597
EST:     GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAG                         CAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
genomic: GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAGgtatgcactt ... ataattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
EST: gi|88449544|gb|CI538901.1|CI538901
EST:     ACCGTAACCTCATCGCCAAATGGAAGAAG                         CAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
genomic: ACCGTAACCTCATCGCCAAATGGAAGAAGgtatgcactt ... ataattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
EST: gi|29626506|gb|CB631517.1|CB631517
EST:     GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCCAATGGAAGAAG                         CAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
genomic: GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAGgtatgcactt ... ataattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
EST: gi|58590796|gb|CF989104.1|CF989104
EST:     GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAG                         CAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
genomic: GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAGgtatgcactt ... ataattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
EST: gi|88450395|gb|CI544517.1|CI544517
EST:     CAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAG                         CAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
genomic: CAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAGgtatgcactt ... ataattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
EST: gi|88283255|gb|CI404701.1|CI404701
EST:     GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAG                         CAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
genomic: GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAGgtatgcactt ... ataattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
EST: gi|15851433|gb|BI799709.1|BI799709
EST:     GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAG                         CAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
genomic: GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAGgtatgcactt ... ataattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
EST: gi|218483294|gb|FG957299.1|FG957299
EST:     GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAG                         CAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
genomic: GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAGgtatgcactt ... ataattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
EST: gi|88261793|gb|CI365369.1|CI365369
EST:     GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAG                         CAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
genomic: GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAGgtatgcactt ... ataattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
EST: gi|88365136|gb|CI540448.1|CI540448
EST:     CTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAG                         CAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
genomic: CTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAGgtatgcactt ... ataattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
EST: gi|88343583|gb|CI622958.1|CI622958
EST:     GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAG                         CAAGGCTATGAG
genomic: GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAGgtatgcactt ... ataattgcagCAAGGCTATGAG
EST: gi|88514914|gb|CI442568.1|CI442568
EST:     GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAG                         CAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
genomic: GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAGgtatgcactt ... ataattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
EST: gi|33811912|gb|CF331845.1|CF331845
EST:     GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAG                         CAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
genomic: GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAGgtatgcactt ... ataattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
EST: gi|88297717|gb|CI553346.1|CI553346
EST:     GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAG                         CAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
genomic: GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAGgtatgcactt ... ataattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
EST: gi|87007984|gb|CI296962.1|CI296962
EST:     GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAG                         CAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATC
genomic: GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAGgtatgcactt ... ataattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATC
EST: gi|88271145|gb|CI387000.1|CI387000
EST:     GCCTTGACCAGGGACATGCTGACCGTAACCTCATCCCCAAATGGAAGAAG                         CAAGGCTATGAGCGTCTCTTCTGCCTGCGCTGTATCCAGACACGAGACCAC
genomic: GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAGgtatgcactt ... ataattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
EST: gi|33659786|gb|CF282399.1|CF282399
EST:     GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAG                         CAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
genomic: GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAGgtatgcactt ... ataattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
EST: gi|86417352|gb|CI031561.1|CI031561
EST:     GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAG                         CAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
genomic: GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAGgtatgcactt ... ataattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
EST: gi|88573909|gb|CI665678.1|CI665678
EST:     GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAG                         CAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGA
genomic: GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAGgtatgcactt ... ataattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGA
EST: gi|88347614|gb|CI634299.1|CI634299
EST:     GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAG                         CAAGGGTATGAGCGTCTCTGCTGCCTGCGCTG
genomic: GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAGgtatgcactt ... ataattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTG
EST: gi|88420526|gb|CI562160.1|CI562160
EST:     GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAG                         CAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC
genomic: GCCTTGACCAGGGACATGCTGACCGTAACCTCATCGCCAAATGGAAGAAGgtatgcactt ... ataattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggtccaatttgcatggccaactgactgagtttttttgcattggataattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCACAACTTTGCGACCACCTGTGTTTGCAGGGTTCCTAAGCACCTAAGGGAAG
                    aactgac  putative branch site (score: 2)
                             agttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatctcacatgcacattggacctcatatatttagtcttaatgttgtggtccaatttgcatggccaactgactgagtttttttgcattggataattgcagCAAGGCTATGAGCGTCTCTGCTGCCTGCGCTGTATCCAGACACGAGACCACAACTTTGCGACCACCTGTGTTTGCAGGGTTCCTAAGCACCTAAGGGAAG

- - - -acatgca
- - - - - - - - - - - - - - - - - - - - atgttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgactg