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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACTTCGCCGCCCACGCCGCCGGCGGCGAGGACGACGGCGGCCTCTTCGGCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGACgtgagtgccctagctttgtcgatttcgatccccttttgccgcgatctgattctcttaagtttctaaaccctcgattgatctctggtggtgtgtgtgggtgggggatgcgggcag

Basic information

species Oryza sativa
transcript LOC_Os06g06030.1
intron # 1
splice site 5'
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|163927773|gb|EG710541.1|EG710541
EST:     CCCACCTGCCCCGCCGAC                         TTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
genomic: CCCACCTGCCCCGCCGACgtgagtgccc ... atgcgggcagTTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
EST: gi|2428687|gb|C73150.1|C73150
EST:     GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGAC                         TTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
genomic: GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGACgtgagtgccc ... atgcgggcagTTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
EST: gi|58597702|gb|CK008230.1|CK008230
EST:     GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGAC                         TTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
genomic: GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGACgtgagtgccc ... atgcgggcagTTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
EST: gi|88301098|gb|CI594624.1|CI594624
EST:     GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGAC                         TTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGGAGGGA
genomic: GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGACgtgagtgccc ... atgcgggcagTTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
EST: gi|58600214|gb|CK010742.1|CK010742
EST:     GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGAC                         TTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
genomic: GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGACgtgagtgccc ... atgcgggcagTTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
EST: gi|58595565|gb|CK006093.1|CK006093
EST:     GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGAC                         TTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAGGGACAAGAAGGGA
genomic: GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGACgtgagtgccc ... atgcgggcagTTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
EST: gi|86830088|gb|CI290291.1|CI290291
EST:     GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGAC                         TTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
genomic: GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGACgtgagtgccc ... atgcgggcagTTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
EST: gi|568280|gb|D39117.1|D39117
EST:     GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGAC                         TTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
genomic: GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGACgtgagtgccc ... atgcgggcagTTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
EST: gi|29669742|gb|CB666017.1|CB666017
EST:     GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGAC                         TTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
genomic: GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGACgtgagtgccc ... atgcgggcagTTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
EST: gi|87023733|gb|CI286484.1|CI286484
EST:     GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGAC                         TTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
genomic: GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGACgtgagtgccc ... atgcgggcagTTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
EST: gi|218491233|gb|FG953090.1|FG953090
EST:     GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGAC                         TTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
genomic: GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGACgtgagtgccc ... atgcgggcagTTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
EST: gi|58604003|gb|CK014531.1|CK014531
EST:     AGCTCCCCACCTGCCCCGCCGAGCG                         TTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGG
genomic: AGCTCCCCACCTGCCCCGCCGA-C-gtgagtgccc ... atgcgggcagTTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGG
EST: gi|58604003|gb|CK014531.1|CK014531
EST:     AGCTCCCCACCTGCCCCGCCGAGCG                         TTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGG
genomic: AGCTCCCCACCTGCCCCGCCGA-C-gtgagtgccc ... atgcgggcagTTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGG
EST: gi|88377147|gb|CI597931.1|CI597931
EST:     GCGCCGGCGCCGACCTG-CCGCCATGGAGCTCCCCACCTGCCCCGCCGAC                         TTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
genomic: GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGACgtgagtgccc ... atgcgggcagTTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
EST: gi|58600793|gb|CK011321.1|CK011321
EST:     GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGAC                         TTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
genomic: GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGACgtgagtgccc ... atgcgggcagTTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
EST: gi|2443151|gb|C74922.1|C74922
EST:     GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGAC                         TTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
genomic: GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGACgtgagtgccc ... atgcgggcagTTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
EST: gi|88402829|gb|CI613277.1|CI613277
EST:     GCGCCGGCGCCGACCTGCCCGACATGGAGCTCCCCACCTGCCCCGCCGAC                         TTCGACCGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCAAAAGAAGGG
genomic: GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGACgtgagtgccc ... atgcgggcagTTCGAC-GGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGG
EST: gi|8858756|gb|AU096074.1|AU096074
EST:     GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGAC                         TTCGACGGGTTCCAGAAGGAGACCAAGGAGATNCTGAAGCACAAGAAGGGA
genomic: GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGACgtgagtgccc ... atgcgggcagTTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
EST: gi|58604785|gb|CK015313.1|CK015313
EST:     CGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCCACCTGCCCCGGCGAC                         TTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
genomic: CGCCGGCGCCGACCTGCCCGCCATGGAGCT-CCCCACCTGCCCCGCCGACgtgagtgccc ... atgcgggcagTTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
EST: gi|88744778|gb|CI768138.1|CI768138
EST:     GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGAC                         TTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
genomic: GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGACgtgagtgccc ... atgcgggcagTTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
EST: gi|8858107|gb|AU095425.1|AU095425
EST:     GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGAC                         TTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
genomic: GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGACgtgagtgccc ... atgcgggcagTTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
EST: gi|88400394|gb|CI593469.1|CI593469
EST:     GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGAC                         TTCGA-GGGTTCCAGAAGGAGACCAA-GAGATGCTGAAGCACAAGAATGGA
genomic: GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGACgtgagtgccc ... atgcgggcagTTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
EST: gi|218499941|gb|FG967251.1|FG967251
EST:     GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGAC                         TTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
genomic: GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGACgtgagtgccc ... atgcgggcagTTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
EST: gi|58595613|gb|CK006141.1|CK006141
EST:     GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGAC                         TTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
genomic: GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGACgtgagtgccc ... atgcgggcagTTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
EST: gi|88745098|gb|CI768458.1|CI768458
EST:     GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGAC                         TTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
genomic: GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGACgtgagtgccc ... atgcgggcagTTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
EST: gi|55411406|gb|CV723782.1|CV723782
EST:     GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGAC                         TTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
genomic: GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGACgtgagtgccc ... atgcgggcagTTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
EST: gi|86887603|gb|CI294237.1|CI294237
EST:     GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGAC                         TTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
genomic: GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGACgtgagtgccc ... atgcgggcagTTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
EST: gi|42592131|gb|CK738617.1|CK738617
EST:     GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGAC                         TTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
genomic: GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGACgtgagtgccc ... atgcgggcagTTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
EST: gi|10931155|gb|AU161429.1|AU161429
EST:     GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGAC                         TTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
genomic: GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGACgtgagtgccc ... atgcgggcagTTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
EST: gi|33801628|gb|CF326686.1|CF326686
EST:     GCGCCGGCGCCGACCTGCCCGCCATGTAGCTCCCCACCTGCCCCGCCGAC                         TTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA
genomic: GCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGACgtgagtgccc ... atgcgggcagTTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGA

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: 75 (upstream exon), 74 (downstream exon)
Score: 83

CAACTTCGCCGCCCACGCCGCCGGCGGCGAGGACGACGGCGGCCTCTTCGGCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGACgtgagtgccc ... atgcgggcagTTCGACGGGTTCCAGAAGGAGACCAAGGAGATGCTGAAGCACAAGAAGGGAACGACCACGCTCGCGTTCATCTTCGACAAGGGCGTCATCGTCGCCGCCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAACTTCGCCGCCCACGCCGCCGGCGGCGAGGACGACGGCGGCCTCTTCGGCGCCGGCGCCGACCTGCCCGCCATGGAGCTCCCCACCTGCCCCGCCGACgtgagtgccctagctttgtcgatttcgatccccttttgccgcgatctgattctcttaagtttctaaaccctcgattgatctctggtggtgtgtgtgggtgggggatgcgggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT