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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAGgtaaacacatcctatcctccatggatgaccatttctgatcaagctgctacttaactgtatgcatctgacgatgaactgattactgaatcgatatgatccaaaattaatgaaaaaaaaag

Basic information

species Oryza sativa
transcript LOC_Os02g02560.1
intron # 2
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|88370657|gb|CI590235.1|CI590235
EST:     TGACAACGAGAAGT-CGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG                         TGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
genomic: TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAGgtaaacacat ... aaaaaaaaagTGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
EST: gi|88401596|gb|CI588537.1|CI588537
EST:     TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG                         TGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
genomic: TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAGgtaaacacat ... aaaaaaaaagTGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
EST: gi|88417942|gb|CI596619.1|CI596619
EST:     TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG                         TGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
genomic: TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAGgtaaacacat ... aaaaaaaaagTGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
EST: gi|88371009|gb|CI595121.1|CI595121
EST:     TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG                         TGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
genomic: TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAGgtaaacacat ... aaaaaaaaagTGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
EST: gi|88294742|gb|CI604614.1|CI604614
EST:     TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG                         TGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
genomic: TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAGgtaaacacat ... aaaaaaaaagTGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
EST: gi|88377046|gb|CI597830.1|CI597830
EST:     TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG                         TGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
genomic: TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAGgtaaacacat ... aaaaaaaaagTGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
EST: gi|88426949|gb|CI601910.1|CI601910
EST:     TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG                         TGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
genomic: TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAGgtaaacacat ... aaaaaaaaagTGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
EST: gi|88433235|gb|CI591675.1|CI591675
EST:     TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCTGCTACCTCAG                         TGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
genomic: TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAGgtaaacacat ... aaaaaaaaagTGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
EST: gi|88415469|gb|CI589061.1|CI589061
EST:     TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG                         TGGGGAGGAGGAGCATGTGGAATGGGCAAAGAT-CACACGCCGACGGACGA
genomic: TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAGgtaaacacat ... aaaaaaaaagTGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
EST: gi|3090613|gb|C93600.1|C93600
EST:     TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG                         TGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
genomic: TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAGgtaaacacat ... aaaaaaaaagTGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
EST: gi|88391611|gb|CI600800.1|CI600800
EST:     TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG                         TGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
genomic: TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAGgtaaacacat ... aaaaaaaaagTGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
EST: gi|88433205|gb|CI591645.1|CI591645
EST:     TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCTGCTACCTCAG                         T
genomic: TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAGgtaaacacat ... aaaaaaaaag-
EST: gi|88433205|gb|CI591645.1|CI591645
EST:     TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCTGCTACCTCAG                         T
genomic: TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAGgtaaacacat ... aaaaaaaaag-
EST: gi|88389523|gb|CI600692.1|CI600692
EST:     TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG                         TGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
genomic: TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAGgtaaacacat ... aaaaaaaaagTGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
EST: gi|88387609|gb|CI585312.1|CI585312
EST:     TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG                         TGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
genomic: TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAGgtaaacacat ... aaaaaaaaagTGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
EST: gi|88314463|gb|CI604947.1|CI604947
EST:     TGACAACGAGAAGTCCGGGTTCATCAGCCTCGCTCGCCCGCTACCTCAG                         TGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
genomic: TGACAACGAGAAGTCCGGGTTCATCAGCCTCG-TCGCCCGCTACCTCAGgtaaacacat ... aaaaaaaaagTGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
EST: gi|88314385|gb|CI604869.1|CI604869
EST:     TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG                         TGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
genomic: TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAGgtaaacacat ... aaaaaaaaagTGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
EST: gi|88300805|gb|CI589797.1|CI589797
EST:     TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG                         TGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
genomic: TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAGgtaaacacat ... aaaaaaaaagTGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
EST: gi|66922584|gb|CX109432.1|CX109432
EST:     TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG                         TGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
genomic: TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAGgtaaacacat ... aaaaaaaaagTGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
EST: gi|88434257|gb|CI589322.1|CI589322
EST:     TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG                         TGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
genomic: TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAGgtaaacacat ... aaaaaaaaagTGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
EST: gi|88433214|gb|CI591654.1|CI591654
EST:     TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG                         TGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
genomic: TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAGgtaaacacat ... aaaaaaaaagTGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
EST: gi|88389649|gb|CI603148.1|CI603148
EST:     TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG                         TGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
genomic: TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAGgtaaacacat ... aaaaaaaaagTGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
EST: gi|88370364|gb|CI587754.1|CI587754
EST:     TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG                         TGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
genomic: TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAGgtaaacacat ... aaaaaaaaagTGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
EST: gi|88405310|gb|CI586131.1|CI586131
EST:     TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG                         TGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA
genomic: TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAGgtaaacacat ... aaaaaaaaagTGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGA

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: 72 (upstream exon), 36 (downstream exon)
Score: 22

TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAGgtaaacacat ... aaaaaaaaagTGGCGAGGAGGAGCATGTGGAATGGGCAAAGATCCACACGCCGACGGACGAGGTGGTGGTGCCGTACGACACCCTGGCGGCGCCGCCGGAGGACTTGGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAGgtaaacacatcctatcctccatggatgaccatttctgatcaagctgctacttaactgtatgcatctgacgatgaactgattactgaatcgatatgatccaaaattaatgaaaaaaaaag

- - - - AGAAGT