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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTTTCACTTGGAGGGCAGCGCCGCAAGAGGCGCCAAACAGCTGCAGCAGTTACGCAAGCCCCAGGAGAAAAACGCTACAACCTCAGGCGCACCACAGTgtaagtttctgtatttatcccacgtttaatttctactcaaggttatcatcctttttttaactgacttgtggagtaaattgatttcctttttgctttattttgttggaaag

Basic information

species Oryza sativa
transcript LOC_Os02g48010.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g48010.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G015875_T01 (Zea mays), 5'ss of exon 7
GTGTTTCACTTGGAGGGCAGCGCCGCAAGAGGCGCCAAACAGCTGCAGCAGTTACGCAAGCCCCAGGAGAAAAACGCTACAACCTCAGGCGCACCACAGTgtaagtttctgtatttatcccacgtttaatttctactcaaggtta--tcatcctttttttaactgacttgtggagtaaattgatttcctttttgctttattttgttggaaag
||||||||||||||||||||||||| |||||||| ||||| ||||  ||||| ||  | ||||||||||||| ||| |||||  | || | ||  | || |||||| ||| ||||  ||||    || || ||||||    |||   |   | | | |||        ||   |  ||| | || |  |||||  ||    |||||  ||||
GTGTTTCACTTGGAGGGCAGCGCCGTAAGAGGCGGCAAACTGCTGGGGCAGTGACAGATGCCCCAGGAGAAAGACGTTACAATTTGAGACACAGTAGAGCgtaagtatctttattggtccc-taattcatatctacttggcgttgggttgacttatgtttcctaattctgcttatcaaactaatatttttttt--ttggcattgttccaaag
















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|29644320|gb|CB649327.1|CB649327
EST:     GTTACGCAAGCCCCAGGAGAAAAACGCTACAACCTCAGGCGCACCACAGT                         TGCAAATGCGGCAACTGCAGCCCAAACCAACAAAAAGAAAGCTGCGAAAAA
genomic: GTTACGCAAGCCCCAGGAGAAAAACGCTACAACCTCAGGCGCACCACAGTgtaagtttct ... tgttggaaagTGCAAATGCGGCAACTGCAGCCCAAACCAACAAAAAGAAAGCTGCGAAAAA
EST: gi|29672013|gb|CB668288.1|CB668288
EST:     GTTACGCAAGCCCCAGGAGAAAAACGCTACAACCTCAGGCGCACCACAGT                         TGCAAATGCGGCAACTGCAGCCCAAACCAACAAAAAGAAAGCTGCGAAAAA
genomic: GTTACGCAAGCCCCAGGAGAAAAACGCTACAACCTCAGGCGCACCACAGTgtaagtttct ... tgttggaaagTGCAAATGCGGCAACTGCAGCCCAAACCAACAAAAAGAAAGCTGCGAAAAA
EST: gi|29658107|gb|CB654382.1|CB654382
EST:     GTTACGCAAGCCCCAGGAGAAAAACGCTACAACCTCAGGCGCACCACAGT                         TGCAAATGCGGCAACTGCAGCCCAAACCAACAAAAAGAAAGCTGCGAAAAA
genomic: GTTACGCAAGCCCCAGGAGAAAAACGCTACAACCTCAGGCGCACCACAGTgtaagtttct ... tgttggaaagTGCAAATGCGGCAACTGCAGCCCAAACCAACAAAAAGAAAGCTGCGAAAAA
EST: gi|29658106|gb|CB654381.1|CB654381
EST:     GTTACGCAAGCCCCAGGAGAAAAACGCTACAACCTCAGGCGCACCACAGT                         TGCAAATGCGGCAACTGCAGCCCAAACCAACAAAAAGAAAGCTGCGAAAAA
genomic: GTTACGCAAGCCCCAGGAGAAAAACGCTACAACCTCAGGCGCACCACAGTgtaagtttct ... tgttggaaagTGCAAATGCGGCAACTGCAGCCCAAACCAACAAAAAGAAAGCTGCGAAAAA
EST: gi|88588258|gb|CI706064.1|CI706064
EST:     GTTACGCAAGCCCCAGGAGAAAAACGCTACAACCTCAGGCGCACCACAGT                         TGCAAATGCGGCAACTGCAGCCCAAACCAACAAAAAGAAAGCTGCGAAAAA
genomic: GTTACGCAAGCCCCAGGAGAAAAACGCTACAACCTCAGGCGCACCACAGTgtaagtttct ... tgttggaaagTGCAAATGCGGCAACTGCAGCCCAAACCAACAAAAAGAAAGCTGCGAAAAA
EST: gi|29638045|gb|CB643054.1|CB643054
EST:     GTTACGCAAGCCCCAGGAGAAAAACGCTACAACCTCAGGCGCACCACAGT                         TGCAAATGCGGCAACTGCAGCCCAAACCAACAAAAAGAAAGCTGCGAAAAA
genomic: GTTACGCAAGCCCCAGGAGAAAAACGCTACAACCTCAGGCGCACCACAGTgtaagtttct ... tgttggaaagTGCAAATGCGGCAACTGCAGCCCAAACCAACAAAAAGAAAGCTGCGAAAAA
EST: gi|87015180|gb|CI273578.1|CI273578
EST:     GTTACGCAAGCCCCAGGAGAAAAACGCTACAACCTCAGGCGCACCACAGT                         TGCAAATGCGGCAACTGCAGCCCAAACCAACAAAAAGAAAGCTGCGAAAAA
genomic: GTTACGCAAGCCCCAGGAGAAAAACGCTACAACCTCAGGCGCACCACAGTgtaagtttct ... tgttggaaagTGCAAATGCGGCAACTGCAGCCCAAACCAACAAAAAGAAAGCTGCGAAAAA
EST: gi|9886237|gb|AU102130.1|AU102130
EST:     GTTACGCAAGCCCCAGGAGAAAAACGCTACAACCTCAGGCGCACCACAGT                         TGCAAATGCGGCAACTGCAGCCCAAACCAAC
genomic: GTTACGCAAGCCCCAGGAGAAAAACGCTACAACCTCAGGCGCACCACAGTgtaagtttct ... tgttggaaagTGCAAATGCGGCAACTGCAGCCCAAACCAAC
EST: gi|29623423|gb|CB628434.1|CB628434
EST:     GTTACGCAAGCCCCAGGAGAAAAACGCTACAACCTCAGGCGCACCACAGT                         TGCAAATGCGGCAACTGCAGCCCAAACCAACAAAAGGAAAGCTGCGAAAAA
genomic: GTTACGCAAGCCCCAGGAGAAAAACGCTACAACCTCAGGCGCACCACAGTgtaagtttct ... tgttggaaagTGCAAATGCGGCAACTGCAGCCCAAACCAACAAAAAGAAAGCTGCGAAAAA
EST: gi|87015133|gb|CI273531.1|CI273531
EST:     GGAGAAAAACGCTACAACCTCAGGCGCACCACAGT                         TGCAAATGCGGCAACTGCAGCCCAAACCTACAAAAAGAAAGCTGCGAAAAA
genomic: GGAGAAAAACGCTACAACCTCAGGCGCACCACAGTgtaagtttct ... tgttggaaagTGCAAATGCGGCAACTGCAGCCCAAACCAACAAAAAGAAAGCTGCGAAAAA
EST: gi|3766585|gb|AU030695.1|AU030695
EST:     GAAAAACGCTACACCCTCA-GCGCACCACAGT                         TGCAAATNCGGCAACTGCAGCCCAANCCAACAAAAAGAAAGCTGCGAAAAA
genomic: GAAAAACGCTACAACCTCAGGCGCACCACAGTgtaagtttct ... tgttggaaagTGCAAATGCGGCAACTGCAGCCCAAACCAACAAAAAGAAAGCTGCGAAAAA
EST: gi|9864891|gb|AU100641.1|AU100641
EST:     GTTACGCAAGCCCCAGGAGAAAAACGCTACAACCTCAGGCGCACCACAGT                         TGCAAATGCGGCAACTGCAGCCCAAACCAAC
genomic: GTTACGCAAGCCCCAGGAGAAAAACGCTACAACCTCAGGCGCACCACAGTgtaagtttct ... tgttggaaagTGCAAATGCGGCAACTGCAGCCCAAACCAAC
EST: gi|29661394|gb|CB657669.1|CB657669
EST:     GTTACGCAAGCCCCAGGAGAAAAACGCTACAACCTCAGGCGCACCACAGT                         TGCAAATGCGGCAACTGCAGCCCAAACCAACAAAAAGAAAGCTGCGAAAAA
genomic: GTTACGCAAGCCCCAGGAGAAAAACGCTACAACCTCAGGCGCACCACAGTgtaagtttct ... tgttggaaagTGCAAATGCGGCAACTGCAGCCCAAACCAACAAAAAGAAAGCTGCGAAAAA

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: 59 (upstream exon), 62 (downstream exon)
Score: 19

GTGTTTCACTTGGAGGGCAGCGCCGCAAGAGGCGCCAAACAGCTGCAGCAGTTACGCAAGCCCCAGGAGAAAAACGCTACAACCTCAGGCGCACCACAGTgtaagtttct ... tgttggaaagTGCAAATGCGGCAACTGCAGCCCAAACCAACAAAAAGAAAGCTGCGAAAAAGGGAAGTAAACAGACAGTAGAGGCTACCGCAGATGACACAGAAGGAACC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTTTCACTTGGAGGGCAGCGCCGCAAGAGGCGCCAAACAGCTGCAGCAGTTACGCAAGCCCCAGGAGAAAAACGCTACAACCTCAGGCGCACCACAGTgtaagtttctgtatttatcccacgtttaatttctactcaaggttatcatcctttttttaactgacttgtggagtaaattgatttcctttttgctttattttgttggaaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA