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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGATgtaagtatcatgatactgcttcagtgtaatgtatcaagcatctgcagatatgggcatgcttcagcattttctaacattaaacgtttgaatatcatggcag

Basic information

species Oryza sativa
transcript LOC_Os08g29370.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g29370.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G015967_T01 (Zea mays), 5'ss of exon 6
GAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGATgtaagtatcatgatactgcttcagtgtaatgtatcaagcatctgcagat-atgggcatgct--tcagcattttctaacattaaacgtttgaatatcatggcag
|||||||| |||||||||||||||||||| || ||||| || || |||||||||||||| ||||| ||||| |||||    |      |||   | || |   ||||| |||| ||||||  ||  ||||  |    |   | ||||||| | | |    |  |   |||| |||
GAACTTGGTCGCTACAAGGCTCAAACAAAACTCCCTTTCAACGCTTTTGGAACAATGGCTATGGCAAGAGAAgtaagagagaca----tgcaagattgca-catatca-gcatatgcagacgatctgcatcgtatctaatgtattctaacctgagataacttcactgcatgacag

upper sequence: LOC_Os08g29370.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA19G01260.1 (Glycine max), 5'ss of exon 6
GAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGATgtaagtatcatgatactgcttcagtgtaatgtatcaagcatctgcagatatgggcatgctt--cagcattttctaacattaaac-gtttgaatatcatggcag
|| ||||| |  ||||||||||||||||||||||| |||||||| || || |||||||||||||| |||||||| || |  ||        | || ||   |   | ||||||    |  | |     | |||      |||| ||    |||    |||||||||         
GAGCTTGGTCTATACAAGGCTCAAACAAAGCTTCCGTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGATgtgaggagaatctattctttgcattgctgttctttaagcatgataatcttttttttttcttgcttttatttactccttttatgttgtttgaatag--------

upper sequence: LOC_Os08g29370.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA13G23850.1 (Glycine max), 5'ss of exon 6
GAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGATgtaagtatcatg-atactgcttcagtgtaatgtatcaagcatctgcagatatgggcatgcttcagcattttctaacattaaac-gtttgaatatcatggcag
|| ||||| |  ||||||||||||||||||||||| |||||||| || || |||||||||||||| |||||||| || |  ||  || ||    || ||   |   | ||||||    |  | |              |||| ||    |||    |||||||||         
GAGCTTGGTCTATACAAGGCTCAAACAAAGCTTCCCTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGATgtgaggagaatctattctttgacattgctgttctttaagcatgctaatcttttttttcttgcttctatttactccttttatgttgtttgaatag--------

upper sequence: LOC_Os08g29370.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv14s0066g01410.t01 (Vitis vinifera), 5'ss of exon 6
GAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGATgtaagtatcatgatactgcttcagtgtaatgtatcaagcatctgcagatatgggcatgcttcagcattttctaacattaaacgtttgaatatcatg--gcag
|| ||||| |  ||||||||||||||||||||||| ||||||||||||||||||||||| ||||| ||||||||||| |   | || |       |  || |    ||    | |   ||  ||             ||||  |    ||     |||  || | |    ||||
GAGCTTGGTCTGTACAAGGCTCAAACAAAGCTTCCATTTAATGCATTTGGAACAATGGCCATGGCAAGAGATgtaagaactctaattcataccatggctatttctacatatgtgtatggacttgatggctaaatgatatttgttctttttttgttttttcattttactctgcag

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|86848897|gb|CI295714.1|CI295714
EST:     AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGAT                         GAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
genomic: AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGATgtaagtatca ... atcatggcagGAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
EST: gi|88221803|gb|CI221759.1|CI221759
EST:     AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGAT                         GAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
genomic: AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGATgtaagtatca ... atcatggcagGAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
EST: gi|313084044|gb|HO213827.1|HO213827
EST:     AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGAT                         GAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
genomic: AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGATgtaagtatca ... atcatggcagGAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
EST: gi|25804245|gb|CA760206.1|CA760206
EST:     AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGAT                         GAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
genomic: AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGATgtaagtatca ... atcatggcagGAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
EST: gi|86500872|gb|CI143505.1|CI143505
EST:     AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGAT                         GAATTTGATGACAATTCTGCTTCTAGCCAATTCTTTTGGTTGTTAAAAGAG
genomic: AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGATgtaagtatca ... atcatggcagGAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
EST: gi|29658080|gb|CB654355.1|CB654355
EST:     AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGAT                         GAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
genomic: AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGATgtaagtatca ... atcatggcagGAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
EST: gi|29613721|gb|CB618734.1|CB618734
EST:     AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGAT                         GAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
genomic: AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGATgtaagtatca ... atcatggcagGAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
EST: gi|29657974|gb|CB654249.1|CB654249
EST:     AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGAT                         GAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
genomic: AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGATgtaagtatca ... atcatggcagGAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
EST: gi|86831350|gb|CI297619.1|CI297619
EST:     AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGAT                         GAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
genomic: AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGATgtaagtatca ... atcatggcagGAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
EST: gi|86257246|gb|CI004064.1|CI004064
EST:     AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGAT                         GAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
genomic: AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGATgtaagtatca ... atcatggcagGAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
EST: gi|29622079|gb|CB627090.1|CB627090
EST:     AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGAT                         GAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
genomic: AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGATgtaagtatca ... atcatggcagGAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG

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), 73 (downstream exon)
Score: 9

GAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGATgtaagtatca ... atcatggcagGAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAGAGTGAGCTAACACCAAGCAATGCCAATATACTGGATGGGCGGTATGCCG




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