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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAGgtaagaatttgtttggactttgaaacagtagtttgcagcaaatgcctaatatttatgttggcaacaccag

Basic information

species Oryza sativa
transcript LOC_Os02g58590.1
intron # 16
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|86428491|gb|CI075172.1|CI075172
EST:     ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAG                         GACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
genomic: ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAGgtaagaattt ... gcaacaccagGACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
EST: gi|218480194|gb|FG949561.1|FG949561
EST:     ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAG                         GACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
genomic: ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAGgtaagaattt ... gcaacaccagGACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
EST: gi|88836323|gb|CI078220.1|CI078220
EST:     ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAG                         GACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
genomic: ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAGgtaagaattt ... gcaacaccagGACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
EST: gi|89174306|gb|CI110504.1|CI110504
EST:     ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAG                         GACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
genomic: ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAGgtaagaattt ... gcaacaccagGACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
EST: gi|44665380|gb|CR278814.1|CR278814
EST:     ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAG                         GACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
genomic: ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAGgtaagaattt ... gcaacaccagGACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
EST: gi|88837996|gb|CI371574.1|CI371574
EST:     CTGA-GACCTGAGCTACCTCAAGGAG                         GACAAGTTCCTGATCCAATTTGGG-AAGACGTCGCTAGTGCCACCCCTCTC
genomic: CTGAGGACCTGAGCTACCTCAAGGAGgtaagaattt ... gcaacaccagGACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
EST: gi|29628399|gb|CB633410.1|CB633410
EST:     ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAG                         GACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
genomic: ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAGgtaagaattt ... gcaacaccagGACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
EST: gi|88564789|gb|CI495506.1|CI495506
EST:     TACCTCAAGGAG                         GACAAGTTCCTGATCCAATTTGGGGAAGACGTCGCTAGTGCCACCCCTCTC
genomic: TACCTCAAGGAGgtaagaattt ... gcaacaccagGACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
EST: gi|86433973|gb|CI094316.1|CI094316
EST:     ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAG                         GACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
genomic: ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAGgtaagaattt ... gcaacaccagGACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
EST: gi|86491170|gb|CI133803.1|CI133803
EST:     ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAG                         GACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
genomic: ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAGgtaagaattt ... gcaacaccagGACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
EST: gi|313081063|gb|HO213649.1|HO213649
EST:     ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAG                         GACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
genomic: ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAGgtaagaattt ... gcaacaccagGACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
EST: gi|88222701|gb|CI220842.1|CI220842
EST:     ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAG                         GACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
genomic: ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAGgtaagaattt ... gcaacaccagGACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
EST: gi|29633687|gb|CB638696.1|CB638696
EST:     ATCAAGTGGAATTCTGAGGACTTGAGCTACCTCAAGGAG                         GACAAGTTCTTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
genomic: ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAGgtaagaattt ... gcaacaccagGACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
EST: gi|58688254|gb|CK076941.1|CK076941
EST:     ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAG                         GACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
genomic: ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAGgtaagaattt ... gcaacaccagGACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
EST: gi|88532003|gb|CI461457.1|CI461457
EST:     ATATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAG                         GACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
genomic: ATATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAGgtaagaattt ... gcaacaccagGACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
EST: gi|89176118|gb|CI043139.1|CI043139
EST:     ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAG                         GACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
genomic: ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAGgtaagaattt ... gcaacaccagGACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
EST: gi|88419037|gb|CI508990.1|CI508990
EST:     AGGACCTGAGCTACCTCAAGGAG                         GACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
genomic: AGGACCTGAGCTACCTCAAGGAGgtaagaattt ... gcaacaccagGACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
EST: gi|88840918|gb|CI000880.1|CI000880
EST:     ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAG                         GACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
genomic: ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAGgtaagaattt ... gcaacaccagGACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
EST: gi|88834475|gb|CI077758.1|CI077758
EST:     ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAG                         GACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
genomic: ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAGgtaagaattt ... gcaacaccagGACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
EST: gi|218489065|gb|FG948408.1|FG948408
EST:     ATCAAGTGTAATTCTGAGGACCTGAGCTACCTCAAGGAG                         GACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC
genomic: ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAGgtaagaattt ... gcaacaccagGACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTC

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: 64 (upstream exon), 51 (downstream exon)
Score: 16

ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAGgtaagaattt ... gcaacaccagGACAAGTTCCTGATCCAATTTGGGAAAGACGTCGCTAGTGCCACCCCTCTCCATGGATCTGATGCCGCGTTGAAAGCCCACAATATGGATGCGGATGTAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCAAGTGGAATTCTGAGGACCTGAGCTACCTCAAGGAGgtaagaatttgtttggactttgaaacagtagtttgcagcaaatgcctaatatttatgttggcaacaccag

- - AGTGGA
- - - - - - - - - - - - - - - -  AAGGAG