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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgacatagtgagaacagagaaaactgcattggattcaattgtagaagaaagattttcctccctattgccactgcctactaactgaattttaattgcagATGACATACCATTTTTTTCACTGGAAGAAGGGAACTCCGTTTGCTGATGACCAGGGGATGTATAATAGATTGACTTGGTGGGAGCAAATGGACAATGGGA

Basic information

species Oryza sativa
transcript LOC_Os04g47970.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g47970.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA16G02540.1 (Glycine max), 3'ss of exon 1
-cttgacatagtgagaacagagaaaactgcattggattcaattgtagaagaaagattttcctccctattgccactgcctactaactgaattttaattg-cagATGACATACCATTTTTTTCACTGGAAGAAGGGAACTCCGTTTGCTGATGACCAGGGGATGTATAATAGATTGACTTGGTGGGAGCAAATGGACAATGGGA
   | | | | | | |              ||||  || |    |   | ||  ||||  || |         |     | | | |   || |      ||| | ||||| || ||||||||||||||||| |||||||| ||||| || ||||| ||||| || |||||||||||||||||||||||  | |||||||| |
aggttataaattaatattttgtttgtaaatattg--ttaatggatgttaaaataatttaacttctctacatggcgcttaattgattatgttgtgtccatcagGTAACATATCACTTTTTTCACTGGAAGAAAGGAACTCCATTTGCGGAGGACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAA

upper sequence: LOC_Os04g47970.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA07G05940.1 (Glycine max), 3'ss of exon 1
cttgacatagtgagaacagagaaaactgcattggattcaattgtagaagaaagattttcctccctattgccactgccta-ctaactgaattttaattg-cagATGACATACCATTTTTTTCACTGGAAGAAGGGAACTCCGTTTGCTGATGACCAGGGGATGTATAATAGATTGACTTGGTGGGAGCAAATGGACAATGGGA
|  |  |||     | | |       |  |||    | ||| |  |   ||| | |||     || |    |  |||||  | | |   || |      ||| | ||||| || ||||||||||||||||| |||||||| ||||| || ||||| ||||| || |||||||||||||||||||||||  | |||||||| |
caggttataaattaatctgttgtttgtaaattattgttaatggatgctaaaacaatttaacttctctaa--atggcctaattgattatgttgtgtccatcagGTAACATATCACTTTTTTCACTGGAAGAAAGGAACTCCATTTGCAGAGGACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAA

upper sequence: LOC_Os04g47970.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA16G01830.1 (Glycine max), 3'ss of exon 1
cttgacatagtgagaacagagaaaactgcat-tggattcaattgtagaaga--aagattttcctccctattgccactgccta-ctaactgaattttaattg-cagATGACATACCATTTTTTTCACTGGAAGAAGGGAACTCCGTTTGCTGATGACCAGGGGATGTATAATAGATTGACTTGGTGGGAGCAAATGGACAATGGGA
         || | ||   |  |   ||  | |  ||    ||   | |    || ||  |    | | |   ||  || ||  | | |   || |      ||| | |||||  | ||||||||||||||||| |||||||||||||| || ||||| ||||| || |||||||||||||||||||||||  | |||||||| |
-----tcaggttataaattaatattttgtttgtaaatattgttaatggatgttaaaataatttaacttctctacatggcttaattgattatgttgtgtccatcagGTAACATATGACTTTTTTCACTGGAAGAAAGGAACTCCGTTTGCAGAGGACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAA

upper sequence: LOC_Os04g47970.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT5G42000.2 (Arabidopsis thaliana), 3'ss of exon 1
cttgacatagtgagaacagagaaaactgcattggattcaattgtagaagaaagattttcctccctattgccactgcctactaactgaattttaattgcagATGACATACCATTTTTTTCACTGGAAGAAGGGAACTCCGTTTGCTGATGACCAGGGGATGTATAATAGATTGACTTGGTGGGAGCAAATGGACAATGGGA
              |  |      |   | |  ||| |||||        ||  | ||  |  |||  |        |  | | |   |||   ||  || | || || ||||  || || |||||||||||||| || ||||  ||||| || ||  | ||||||||||||||||||||||| || || || ||||| |
------------gtattattcccgatctcctccgatccaatttcg-----aaattgttggtttcta--gatttgaatttttgagtttttttgttttctagGTCACGTATCATTCCTTCCATTGGAAGAAGGGAACACCATTTGGAGATGATCAAGGAGTCTATAATAGATTGACTTGGTGGGAACAGATTGATAATGGCA

upper sequence: LOC_Os04g47970.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT1G01230.1 (Arabidopsis thaliana), 3'ss of exon 1
cttgacatagtgagaacagagaaaactgcattggattcaattgtagaagaaagattttcctccctattgccactgcctactaact---gaattttaattg-cagATGACATACCATTTTTTTCACTGGAAGAAGGGAACTCCGTTTGCTGATGACCAGGGGATGTATAATAGATTGACTTGGTGGGAGCAAATGGACAATGGGA
  || ||| |   ||   |  |||||   |||  ||  |||| |  ||  |   |||       | |     |||  ||  || |   | || ||  ||| ||| | || || ||    || ||||||| ||| |||||||| ||||| |||||||| || || || ||| | || ||||||||||| ||||||||||||||  
--tggcattgcttga-ttgtcaaaaccaaatttaatctaatt-tctaattactctttaggaaaatgtgatgtctgagtagaaatttgtggatatttgttgtcagGTAACGTATCACAGCTTCCACTGGATGAAAGGAACTCCTTTTGCAGATGACCAAGGAATCTACAATGGTTTAACTTGGTGGGAACAAATGGACAATGGTC

upper sequence: LOC_Os04g47970.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv15s0046g00140.t01 (Vitis vinifera), 3'ss of exon 1
-cttgacatagtgagaacagagaaaactgcattggattcaattgtagaagaaagattttcctccctattgccactgcctactaactgaatttta-attgcagATGACATACCATTTTTTTCACTGGAAGAAGGGAACTCCGTTTGCTGATGACCAGGGGATGTATAATAGATTGACTTGGTGGGAGCAAATGGACAATGGGA
  |||      |         | | ||       ||| | |   ||||  |     | ||||| ||||  ||  ||  |    |      || | | |  || | || || || || || || |||||||| |||||||| |||||||| |||||||| || || ||||| ||||| ||||||||||| || |||||||| |
gtttgtttatcttctttgtctgtatacccttcctgatgctacattagattactttatatcctctctatgacc--tgattgaggagcatgcttcacactttagGTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGACCAGGGAATCTACAATAGGTTGACGTGGTGGGAGCAGATAGACAATGGAA

upper sequence: LOC_Os04g47970.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv02s0025g02260.t01 (Vitis vinifera), 3'ss of exon 1
cttgacatagtgagaacagagaaaactgcattggattcaattgtagaagaaagattttcctccctatt---gccactgcctactaactgaattttaat-----tgcagATGACATACCATTTTTTTCACTGGAAGAAGGGAACTCCGTTTGCTGATGACCAGGGGATGTATAATAGATTGACTTGGTGGGAGCAAATGGACAATGGGA
    |   | |||   |     |   | ||| |    | ||| |   |      |||| ||     ||   |  |||   ||| |  ||  ||||  |     ||||| | || || || |  |||||||||||||||||||| || || || ||||||||||| || || |||||  | || |||||||||||||| |||| |||||
----aagaaatgaattcttgtcatcttccatcg----cgattctgatatgtcatttttgcttgtagttcatgttacttaatacaatttgggtttttgtcgtcctgcagGTTACTTATCACTGCTTTCACTGGAAGAAGGGAACACCATTCGCGGATGACCAGGGTATCTACAATAGGCTAACCTGGTGGGAGCAAATAGACAGTGGGA

upper sequence: LOC_Os04g47970.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ31295 (Selaginella moellendorffii), 3'ss of exon 1
cttgacatagtgagaacagagaaaactgcattggattcaattgtagaagaaagattttcctccctattgccactgcctactaactgaattttaattgcagATGACATACCATTTTTTTCACTGGAAGAAGGGAACTCCGTTTGCTGATGACCAGGGGATGTATAATAGATTGACTTGGTGGGAGCAAATGGACAATGGGA
           |  | |    ||   |   ||    ||  | ||          || |        ||    ||     |      || |      | || |||||||| | || || |||||||||||||| || |||||||| || ||||| ||  | ||||  | |||||| |||||||||||||||||  | ||| 
-----------gtaagccttcaattttttgttcccctctttggttttttttttcttgtttctatggttttttctaagatcacgagaaaatgcgtgcgtagGTGACATACAACTTCTTCCACTGGAAGAAGGGGACGCCGTTTGCCGAGGACCAAGGCCTATATAGCAAATTGACGTGGTGGGAGCAAATGGATCACGGGC

upper sequence: LOC_Os04g47970.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ34305 (Selaginella moellendorffii), 3'ss of exon 1
cttgacatagtgagaacagagaaaactgca----ttggattcaattgtagaagaaagattttcctccctattgccactgcctac-taactgaattttaattgc--agATGACATACCATTTTTTTCACTGGAAGAAGGGAACTCCGTTTGCTGATGACCAGGGGATGTATAATAGATTGACTTGGTGGGAGCAAATGGACAATGGGA
                     ||  || |     || | | |  |  | |        || |  |  |||| |    | |  |  | || | |   |   |||  || |||| ||| |||| || |||||||||||||| || |||||||| || ||||| ||  ||||||  | |||||| |||||||||||||||||  | ||| 
-------------------gtaagccttcgattttttgttcccctctttggtttttttttcttgtttctatggttttttctaagatcacgggaaaatgcgtgcgtagGTGACGTACAATTTCTTCCACTGGAAGAAGGGGACGCCGTTTGCCGAGGACCAAGGCCTGTATAGCAAATTGACGTGGTGGGAGCAAATGGATCACGGGC

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|86542403|gb|CI182609.1|CI182609
EST:     CTGCACCCCCGGCATGGCGTGGACGTTCGTCAACCTCGCTCACTTCGCG                         ATGACATACCANNNNNNNCACTGGAAGAAGGGAACTCCGTTTGCTGATGAC
genomic: CTGCACCCCCGGCATGGCGTGGACGTTCGTCAACCTCGCCCACTTCGCGgtaaggaccc ... ttaattgcagATGACATACCATTTTTTTCACTGGAAGAAGGGAACTCCGTTTGCTGATGAC
EST: gi|86902849|gb|CI312226.1|CI312226
EST:     ATGGCGTGGACGTTCGTCAACCTCGCCCACTTCGCG                         ATGACATACCANNNNNNNCACTGGAAGAAGGGAACTCCGTTTGCTGATGAC
genomic: ATGGCGTGGACGTTCGTCAACCTCGCCCACTTCGCGgtaaggaccc ... ttaattgcagATGACATACCATTTTTTTCACTGGAAGAAGGGAACTCCGTTTGCTGATGAC
EST: gi|88575156|gb|CI669301.1|CI669301
EST:     GCTGCACCCCCGGCATGGCGTGGACGTTCGTCAACCTCGCCCACTTCGCG                         ATGACATACCANNNNNNNCACTGGAAGAAGGGAACTCCGTTTGCTGATGAC
genomic: GCTGCACCCCCGGCATGGCGTGGACGTTCGTCAACCTCGCCCACTTCGCGgtaaggaccc ... ttaattgcagATGACATACCATTTTTTTCACTGGAAGAAGGGAACTCCGTTTGCTGATGAC
EST: gi|88241938|gb|CI241787.1|CI241787
EST:     GGCATGGCGTGGACGTTCGTCAACCTCGCCCACTTCGCG                         ATGACATACCANNNNNNNCACTGGAAGAAGGGAACTCCGTTTGCTGATGAC
genomic: GGCATGGCGTGGACGTTCGTCAACCTCGCCCACTTCGCGgtaaggaccc ... ttaattgcagATGACATACCATTTTTTTCACTGGAAGAAGGGAACTCCGTTTGCTGATGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagaaagattttcctccctattgccactgcctactaactgaattttaattgcagATGACATACCATTTTTTTCACTGGAAGAAGGGAACTCCGTTTGCTGATGACCAGGGGATGTATAATAGATTGACTTGGTGGGAGCAAATGGACAATGGGA
                                   taactgaattttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgacatagtgagaacagagaaaactgcattggattcaattgtagaagaaagattttcctccctattgccactgcctactaactgaattttaattgcagATGACATACCATTTTTTTCACTGGAAGAAGGGAACTCCGTTTGCTGATGACCAGGGGATGTATAATAGATTGACTTGGTGGGAGCAAATGGACAATGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA