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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTCCCTATCAGTGCTAGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggcttcttctcatgccttcctaatcttgcattaagtttcttttagatgatagacaacttatgtttttcaacatgggaaggaactagactgggag...

Basic information

species Oryza sativa
transcript LOC_Os01g07950.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g07950.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AC208327.4_FGT002 (Zea mays), 5'ss of exon 6
ATGTCCCTATCAGTGCTAGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggcttcttctcatgccttcctaatcttgcattaagtttcttttagatgatagacaacttatgtttttcaacatgggaaggaactagactgggag
  ||||||| | ||| |||||| ||| | || || ||||||||||||||| |||| ||||||||||||||||||||||  |   |  ||| |   ||  || |||   |   ||||||                                                 
GCGTCCCTACCTGTGGTAGAGACATTCTTGGGGATCTCAAGCTCAAAGAGAGTGTTAAAGCCCACACgtaagtggctttgt---agacctcctggatgatgtatttt-taatttttag-------------------------------------------------

upper sequence: LOC_Os01g07950.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G880300_T02 (Zea mays), 5'ss of exon 5
ATGTCCCTATCAGTGCTAGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggcttcttctcatgccttcctaatcttgcattaagtttcttttagatgatagacaacttatgtttttcaacatgggaaggaactagactgggag-----
  |||||| || ||| |||||| ||| | || || || ||||||||||||||||| ||||||||||||||||||   ||||   || ||| |   ||  || |||   |      ||  ||  |    |||| ||| |   ||  ||  || |  | |   |  |       
GCGTCCCTGTCTGTGGTAGAGACATTCTTGGGGATCTTAAGCTCAAAGAGTGTGTTAAAGCCCACACgtaagtg---tctttgtatacctcctggatgatgtatttt-taaacagtaagtggcaacacacttgtgtctcagaat-tgaaaatggtccatggtaaggtagatt
















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|88528217|gb|CI454441.1|CI454441
EST:     AAGCTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|33687689|gb|CF315928.1|CF315928
EST:     AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTC
genomic: AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTC
EST: gi|86869918|gb|CI316646.1|CI316646
EST:     AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|86595567|gb|CI264664.1|CI264664
EST:     AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|88538548|gb|CI467587.1|CI467587
EST:     GAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: GAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|88552434|gb|CI482440.1|CI482440
EST:     TGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: TGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|88955766|gb|CI092055.1|CI092055
EST:     AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCNTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|88542355|gb|CI471679.1|CI471679
EST:     AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|88541651|gb|CI470933.1|CI470933
EST:     AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|88532187|gb|CI461652.1|CI461652
EST:     CTCAAGCTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCAACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: CTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|88476854|gb|CI414125.1|CI414125
EST:     AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|88491403|gb|CI428675.1|CI428675
EST:     AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|88523023|gb|CI450822.1|CI450822
EST:     GAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: GAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|88199623|gb|CI199473.1|CI199473
EST:     AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|88836536|gb|CI010792.1|CI010792
EST:     AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|88239324|gb|CI240486.1|CI240486
EST:     AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|33685064|gb|CF313303.1|CF313303
EST:     AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|87013732|gb|CI269231.1|CI269231
EST:     AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|88278368|gb|CI399368.1|CI399368
EST:     CTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: CTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|86545203|gb|CI185409.1|CI185409
EST:     AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|88531278|gb|CI459743.1|CI459743
EST:     AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACNTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|86539017|gb|CI179223.1|CI179223
EST:     AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|88542312|gb|CI471634.1|CI471634
EST:     AGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|87031444|gb|CI261818.1|CI261818
EST:     AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|55441732|gb|CV734193.1|CV734193
EST:     AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|88504962|gb|CI432468.1|CI432468
EST:     AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|88530878|gb|CI459305.1|CI459305
EST:     CCTCAAGCTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: CCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|86602178|gb|CI260648.1|CI260648
EST:     AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|87033132|gb|CI187756.1|CI187756
EST:     AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|88277353|gb|CI398155.1|CI398155
EST:     AGAGATATTTT-GGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCCACCAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|88842800|gb|CI371700.1|CI371700
EST:     AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|88532069|gb|CI461527.1|CI461527
EST:     GCTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCAACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: GCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|88241295|gb|CI241144.1|CI241144
EST:     AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTTTTGGGGG
genomic: AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|88902750|gb|CI088288.1|CI088288
EST:     AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|33660934|gb|CF291901.1|CF291901
EST:     AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: AGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
EST: gi|88546330|gb|CI475956.1|CI475956
EST:     CAAAGAGTGTGTCAAAGCCCACAC                         CAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG
genomic: CAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGG

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: 67 (upstream exon), 75 (downstream exon)
Score: 64

ATGTCCCTATCAGTGCTAGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggct ... gcttgtgcagCAACTGGCCTACGTTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGGGTCTGATATCATATTAGATATGCATCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTCCCTATCAGTGCTAGAGATATTTTGGGAGACCTCAAGCTCAAAGAGTGTGTCAAAGCCCACACgtaagtggcttcttctcatgccttcctaatcttgcattaagtttcttttagatgatagacaacttatgtttttcaacatgggaaggaactagactgggag

- - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggaagg