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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGAACGCATCTTTCCTGCCTTTCCTCCTCCCAAAGCTCCAAATCGCGCCCCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATGgtaaagatcccgcattcagcctcttctgttccccccctctccgcgatctgaaaccgtacctgttcttcccggaatgggctgcag

Basic information

species Oryza sativa
transcript LOC_Os12g10560.1
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|33669786|gb|CF298025.1|CF298025
EST:     CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATG                         ATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
genomic: CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATGgtaaagatcc ... tgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
EST: gi|428995|gb|D25151.1|D25151
EST:     CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATG                         ATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
genomic: CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATGgtaaagatcc ... tgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
EST: gi|86899168|gb|CI298074.1|CI298074
EST:     CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATG                         ATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
genomic: CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATGgtaaagatcc ... tgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
EST: gi|88414379|gb|CI691539.1|CI691539
EST:     CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATG                         ATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
genomic: CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATGgtaaagatcc ... tgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
EST: gi|33693746|gb|CF321985.1|CF321985
EST:     CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATG                         ATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
genomic: CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATGgtaaagatcc ... tgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
EST: gi|33659105|gb|CF281718.1|CF281718
EST:     CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATG                         ATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
genomic: CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATGgtaaagatcc ... tgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
EST: gi|33689089|gb|CF317328.1|CF317328
EST:     CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATG                         ATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
genomic: CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATGgtaaagatcc ... tgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
EST: gi|66923463|gb|CX110311.1|CX110311
EST:     CCGTCATCCTCCGCCATG                         ATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
genomic: CCGTCATCCTCCGCCATGgtaaagatcc ... tgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
EST: gi|88310668|gb|CI672531.1|CI672531
EST:     CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATG                         ATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
genomic: CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATGgtaaagatcc ... tgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
EST: gi|88352823|gb|CI678848.1|CI678848
EST:     CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATG                         ATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
genomic: CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATGgtaaagatcc ... tgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
EST: gi|4881090|gb|AU065389.1|AU065389
EST:     CGCCCCCCAAATCCACGAGCACCAGCGAGTCGCCGTCATCCTCCGCCATG                         ATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
genomic: CGCCCCCCAAATCCACGAGCACCAGCGA-TCGCCGTCATCCTCCGCCATGgtaaagatcc ... tgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
EST: gi|88353193|gb|CI654459.1|CI654459
EST:     CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATG                         ATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
genomic: CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATGgtaaagatcc ... tgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
EST: gi|33663155|gb|CF294122.1|CF294122
EST:     CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATG                         ATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
genomic: CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATGgtaaagatcc ... tgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
EST: gi|88307351|gb|CI641991.1|CI641991
EST:     CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATG                         ATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
genomic: CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATGgtaaagatcc ... tgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG

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: 71 (upstream exon), 47 (downstream exon)
Score: 9

AAGAACGCATCTTTCCTGCCTTTCCTCCTCCCAAAGCTCCAAATCGCGCCCCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATGgtaaagatcc ... tgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAGTACTACGTCCCGCTCGAGGACTCGGAGAAGCACAAGGTCGAGTACGAG




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