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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaacttcaagtgatcttatttgttcacatggaaaatgcagaaatgtagtgctcgttacacccgggcatcccatttttttcctgattatccaagagctgttcttactgcattctcatactaagcatcagttccaacttaacgtgaaatcttcccttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCGAGGCTGCTATCATCAACCAACCAGCCAAGCTTCCTAAGCCAGAAGGACA

Basic information

species Oryza sativa
transcript LOC_Os05g44922.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g44922.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G004932_T01 (Zea mays), 3'ss of exon 13
gtgagtaacttcaagtgatcttatttgttcacatggaaaatgcagaaatgtagtgctcgttacacccgggcatcccatttttttcctgattatccaagagctgttcttactgcattctcatactaagcatcagttccaacttaacgtgaaatcttcccttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCGAGGCTGCTATCATCAACCAACCAGCCAAGCTTCCTAAGCCAGAAGGACA
                                                             |   |  |  |    | |   |   | |   |  || |  ||   |||||| ||   || ||| |  || ||  ||||          | ||||    |||||||||||||||||||||||| |||||||||| ||  ||||||| ||||||||||| ||||| || || || |||||||||||||| ||||| || |||||||| |
--------------------------------------------------------gaaccatgtcacgaaacataactagatcaattaaattaaaaaaagtgca-ttactg-atctgcacactgatgatgagcaccaa----------attcttgttctgatggcagAGGGTGACATCCACAAGGAACAAGGTTAAAGTCACTGACAGGATGTGGGCAAGGCTTCTGTCGTCCACCAACCAGCCAAGTTTCCTGAGTCAGAAGGATA

upper sequence: LOC_Os05g44922.2 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 12
gtgagtaacttcaagtgatcttatttgttcacatggaaaatgcagaaatgtagtgctcgttacacccgggcatcccatttttttcctgattatccaagagctgttcttactgcattctcatactaagcatcagttccaacttaacgtgaaatcttcccttgatg-gcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCGAGGCTGCTATCATCAACCAACCAGCCAAGCTTCCTAAGCCAGAAGGACA
                                                                       |   |||  | | |    ||     |  | | ||  |  |   || | | ||  | ||   |     ||  ||| |    | ||    ||||| |||| |  | |     |  |||||||||||   ||| || || ||||||||||| ||||| || || ||||| ||||||||||||||||  | ||  || ||  
--------------------------------------------------------------------aagaattcatggtgtcctctcttgaatgaatgattttgctcttaggttttgacacagaacagttgaggttacaaaacttttg-tatttgactgatgtgcagCGCATCAATGAGAGTCGGAACAAGGTTGTGATAACCGACAGGATGTGGGCAAGGCTCCTTTCGTCAACAAACCAGCCAAGCTTCCAGAACCCCAAAGATG
















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|33678216|gb|CF306455.1|CF306455
EST:     GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
genomic: GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|88249313|gb|CI249162.1|CI249162
EST:     GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
genomic: GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|88263040|gb|CI366814.1|CI366814
EST:     ATGCCTACATACCTTTCTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
genomic: ATGCCTACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|7645974|gb|AU090538.1|AU090538
EST:     AACGGCAGACATGCCTACATNCCTTTCTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATNTGGGCG
genomic: AACGGCAGACATGCCTACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|58603975|gb|CK014503.1|CK014503
EST:     GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
genomic: GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|8527571|gb|AU092386.1|AU092386
EST:     GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
genomic: GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|86866480|gb|CI343433.1|CI343433
EST:     ACATGCCTACATACCTTTCTAT                         AGGGTGACATCCACAC-GAACAAGGTCAAGATCACTGATAGGATGTGGGCG
genomic: ACATGCCTACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|89180637|gb|CI044916.1|CI044916
EST:     GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
genomic: GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|88839064|gb|CI377988.1|CI377988
EST:     GTTGGAAATGTCAACGCCAGACATGCCTACATACCTTTCTAT                         A-GGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTTGGCG
genomic: GTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|86528719|gb|CI168925.1|CI168925
EST:     TGTCAACGGCAGACATGCGTACATACCTTTCTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
genomic: TGTCAACGGCAGACATGCCTACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|88252866|gb|CI350291.1|CI350291
EST:     TACATACCTTTCTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
genomic: TACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|88990194|gb|CI107620.1|CI107620
EST:     GGAAATGTCAACGGCAGACATGCCTACATACCTTTCTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
genomic: GGAAATGTCAACGGCAGACATGCCTACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|89180079|gb|CI044358.1|CI044358
EST:     GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGACG
genomic: GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|88243154|gb|CI244276.1|CI244276
EST:     GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
genomic: GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|88248407|gb|CI248256.1|CI248256
EST:     CACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
genomic: CACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|88838253|gb|CI373613.1|CI373613
EST:     GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
genomic: GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|88249459|gb|CI249308.1|CI249308
EST:     GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
genomic: GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|88214751|gb|CI214600.1|CI214600
EST:     GCCTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
genomic: GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|10611679|gb|AU108415.1|AU108415
EST:     CTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCCTTTCTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGC
genomic: CTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATA-CCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGC
EST: gi|89186474|gb|CI048146.1|CI048146
EST:     GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
genomic: GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|88245544|gb|CI245393.1|CI245393
EST:     GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
genomic: GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|88214204|gb|CI214053.1|CI214053
EST:     GTCAACGGCAGACATGCCTACATACCTTTCTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
genomic: GTCAACGGCAGACATGCCTACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|89182329|gb|CI113698.1|CI113698
EST:     GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
genomic: GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|86255849|gb|CI068298.1|CI068298
EST:     GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCGTTCTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
genomic: GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|88838254|gb|CI373614.1|CI373614
EST:     CTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTACTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGC
genomic: CTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTT-CTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGC
EST: gi|88250125|gb|CI249974.1|CI249974
EST:     GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
genomic: GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|89177325|gb|CI250774.1|CI250774
EST:     GCTTCACTGTTGGAAATGTCAACGTCAGACATGCCTACATACCTTTCTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
genomic: GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|88244619|gb|CI243741.1|CI243741
EST:     GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
genomic: GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|88248233|gb|CI248082.1|CI248082
EST:     GCTTCACTGTTGGGAATGTCAACGGCAGACATGCCTACATACCTTTCTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
genomic: GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|89164298|gb|CI101386.1|CI101386
EST:     GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
genomic: GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|86260211|gb|CI066084.1|CI066084
EST:     CTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
genomic: CTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|86492894|gb|CI135527.1|CI135527
EST:     GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
genomic: GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|89173815|gb|CI041708.1|CI041708
EST:     GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
genomic: GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|86487041|gb|CI129674.1|CI129674
EST:     GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
genomic: GCTTCACTGTTGGAAATGTCAACGGCAGACATGCCTACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|89188382|gb|CI115631.1|CI115631
EST:     GCAGACATGCCTACATACCTTTCTAT                         AGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
genomic: GCAGACATGCCTACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCG
EST: gi|86845059|gb|CI341017.1|CI341017
EST:     TACATACCTTTCTAT                         AGGGTGACATCCACACGCGAAGCAAGGTCAAGATCACTGATAGGATGTGGG
genomic: TACATACCTTTCTATgtgagtaact ... ttgatggcagAGGGTGACATCCACACG-GAA-CAAGGTCAAGATCACTGATAGGATGTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctcatactaagcatcagttccaacttaacgtgaaatcttcccttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCGAGGCTGCTATCATCAACCAACCAGCCAAGCTTCCTAAGCCAGAAGGACA
                                      tcttccctt  CT-rich tract
      atactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtaacttcaagtgatcttatttgttcacatggaaaatgcagaaatgtagtgctcgttacacccgggcatcccatttttttcctgattatccaagagctgttcttactgcattctcatactaagcatcagttccaacttaacgtgaaatcttcccttgatggcagAGGGTGACATCCACACGGAACAAGGTCAAGATCACTGATAGGATGTGGGCGAGGCTGCTATCATCAACCAACCAGCCAAGCTTCCTAAGCCAGAAGGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT