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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtactgttgagcctagccctagatgtacataccacaacttgctatactgcttacagtttctttattttgcatccttttaagcatattgcaaccttccagATAATCAATGCCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCTGGTGGAGGGAAGAGCCTCTGCTATCAACTACCTGCTGTACTTCATGATG

Basic information

species Oryza sativa
transcript LOC_Os11g48090.4
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g48090.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G451856_T02 (Zea mays), 3'ss of exon 3
------ggtactgttgagcctagccctagatgtacataccacaacttgctatactgcttacagtttcttt--attttgcatccttttaagcatattgcaaccttccagATAATCAATGCCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCTGGTGGAGGGAAGAGCCTCTGCTATCAACTACCTGCTGTACTTCATGATG
       || | |  || || | | |    |    ||   |||  || || |      ||||||||| |   |||||||| || || || ||||||     |||  ||||||| |||||  ||||||||||||||||||| |||||||||||||| ||||||||||||||||| || || || || || || |||||||||| |||||
aactttagt-caggggaaccaaacacccccttcgtattgtacagtttcctct----tgtacagtttcctctcattttgcacccatt-aaacatattctg--cttatagATAATTAATGCAGTCATGAGTGGAAGAGATGTTCTGGTCATAATGGCAGCTGGTGGAGGGAAGAGTCTATGTTACCAGCTCCCAGCTGTACTTCGTGATG

upper sequence: LOC_Os11g48090.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G34860.1 (Glycine max), 3'ss of exon 2
ggtactgttgagcctagccctagatgtacataccacaacttgctatac-tgcttacagtttctttattttgcatccttttaagcatattgcaaccttc----cagATAATCAATGCCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCTGGTGGAGGGAAGAGCCTCTGCTATCAACTACCTGCTGTACTTCATGATG
     |  | | |   | | |   | ||   |       ||| ||||  |    |  ||  ||||    |  | | || | | ||  | | ||  |      |||||||| |||||||| ||||||||||||||||| ||||| || |||||||| ||||| || |||||||||||||| || || |||||||| |||| |||||
----atcataatcaagggctttagtttatg-atttttttttggtatatatagggattgtgacttttgggtaaaactttgttaacaagtagtaatgtcgatgacagATAATTAATGCCATTATGAGTGGAAGAGATGTTCTGGTGATTATGGCTGCAGGTGGTGGCAAGAGCCTCTGCTACCAGCTTCCTGCTGTTCTTCGTGATG

upper sequence: LOC_Os11g48090.3 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G31360.1 (Arabidopsis thaliana), 3'ss of exon 2
--------ggtactgttgagcctagccctagatgtacataccacaacttgctatactgcttacagtttcttt-attttgcatccttttaagcatattgcaacct-tccagATAATCAATGCCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCTGGTGGAGGGAAGAGCCTCTGCTATCAACTACCTGCTGTACTTCATGATG
          | ||||     ||   |||| || |  || |        ||  |  ||||   | ||  ||| || || |||   || |  | |      |  | || |||| || || || || ||||  ||||||||||| ||||| || ||||| || ||||| |||||||| || ||||||||||| || ||| | |||| || ||
gtaagtgactttctgtattttctgatcctaaatatg-attcttgtgtccgcgtt--tgctagaaattcgtttgatgttccatttgttgattctttgaatgatatgtcaagATTATTAACGCTATAATGACGGGAAGAGATGTCCTGGTGATCATGGCAGCAGGTGGTGGGAAGAGTCTTTGCTATCAACTTCCAGCTATGCTTCGTGGTG

upper sequence: LOC_Os11g48090.3 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G31360.2 (Arabidopsis thaliana), 3'ss of exon 2
--------ggtactgttgagcctagccctagatgtacataccacaacttgctatactgcttacagtttcttt-attttgcatccttttaagcatattgcaacct-tccagATAATCAATGCCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCTGGTGGAGGGAAGAGCCTCTGCTATCAACTACCTGCTGTACTTCATGATG-----------------------------------------------
          | ||||     ||   |||| || |  || |        ||  |  ||||   | ||  ||| || || |||   || |  | |      |  | || |||| || || || || ||||  ||||||||||| ||||| || ||||| || ||||| |||||||| || ||||||||||| || ||| | |||| || ||                                               
gtaagtgactttctgtattttctgatcctaaatatg-attcttgtgtccgcgtt--tgctagaaattcgtttgatgttccatttgttgattctttgaatgatatgtcaagattattaacgctataatgacgggaagagatgtcctggtgatcatggcagCAGGTGGTGGGAAGAGTCTTTGCTATCAACTTCCAGCTATGCTTCGTGGTGGGACAACTCTTGTTGTCAGTCCTCTACTTTCACTGATTCAGGATCAG

upper sequence: LOC_Os11g48090.3 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv02s0087g00070.t01 (Vitis vinifera), 3'ss of exon 2
ggtactgttgagcctagccctagat-gtacatacca---caacttgctatactgcttacagt-ttctttattttgcatccttttaagcatattgcaaccttccagATAATCAATGCCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCTGGTGGAGGGAAGAGCCTCTGCTATCAACTACCTGCTGTACTTCATGATG
  |  | |  |   ||    ||  | | ||| ||     |||  |  | | |     ||| | ||| ||  ||| ||  |  | |  ||  ||      | |||||| || |||||  ||||||||||||| ||||| ||||| || |||||||| ||||| || |||||||| || || || || || ||| |||||| |||||
attgttataaaatttatgtttaatttgaacacactgtttcaaaattttgttccctacacaatgttcattgatttacaaacaatcattcaattt-----ttaccagATTATAAATGCAGTCATGAGTGGAAGGGATGTTCTGGTGATCATGGCTGCAGGTGGTGGTAAGAGCCTTTGTTACCAGCTTCCAGCTATACTTCGTGATG

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|29673292|gb|CB669567.1|CB669567
EST:     TTCGTTTTAATGTATTTGGGATTTCTTCATACCGGCAGAATCAAAGAGAG                         ATAATCAATGCCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCT
genomic: TTCGTTTTAATGTATTTGGGATTTCTTCATACCGGCAGAATCAAAGAGAGgtaaggttag ... aaccttccagATAATCAATGCCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCT
EST: gi|58671155|gb|CK059841.1|CK059841
EST:     TTCATACCGGCAGAATCAAAGAGAG                         ATAATCAATGCCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCT
genomic: TTCATACCGGCAGAATCAAAGAGAGgtaaggttag ... aaccttccagATAATCAATGCCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCT
EST: gi|58672003|gb|CK060689.1|CK060689
EST:     TTCGTTTTAATGTATTTGGGATTTCTTCATACCGGCAGAATCAAAGAGAG                         ATAATCAATGGCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCT
genomic: TTCGTTTTAATGTATTTGGGATTTCTTCATACCGGCAGAATCAAAGAGAGgtaaggttag ... aaccttccagATAATCAATGCCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCT
EST: gi|29626858|gb|CB631869.1|CB631869
EST:     TTCGTTTTAATGTATTTGGGATTTCTTCATACCGGCAGAATCAAAGAGAG                         ATAATCAATGCCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCT
genomic: TTCGTTTTAATGTATTTGGGATTTCTTCATACCGGCAGAATCAAAGAGAGgtaaggttag ... aaccttccagATAATCAATGCCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactgcttacagtttctttattttgcatccttttaagcatattgcaaccttccagATAATCAATGCCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCTGGTGGAGGGAAGAGCCTCTGCTATCAACTACCTGCTGTACTTCATGATG
   tgcttac  putative branch site (score: 2)
                                               ccttcc  putative PPT
          agtttctttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtactgttgagcctagccctagatgtacataccacaacttgctatactgcttacagtttctttattttgcatccttttaagcatattgcaaccttccagATAATCAATGCCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCTGGTGGAGGGAAGAGCCTCTGCTATCAACTACCTGCTGTACTTCATGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - ctgttga
- - - - - - - - - - - gatgtac
- - - - - - - - - - - - - - - -accacaa
- - - - - - - - - - - - - - - - - - - cttgcta
- - - - - - - - - - - - - - - - - - - - - - - -ctgctta