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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtctgctttccaatggtttaatctaccattcatttttggcaatcacaccccatttgtatacgaaatttatcattgaatgaaagatgcagctaggtttgaaatattttttcagGCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGATTGCTGTGCAGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAG

Basic information

species Oryza sativa
transcript LOC_Os12g13590.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g13590.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM5G823484_T01 (Zea mays), 3'ss of exon 2
gtatgtctgctttccaatggtttaatctaccattcatttttggcaatcacaccccatttgtatacgaaatttatcattgaatgaaagatgcagctaggtttgaaatattttttcagGCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGATTGCTGTGCAGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAG
            |  ||  |    | | ||  | || ||| |        |   ||| | |||| | | || ||||||  |||  | ||  |  |   ||| ||||||||   |||  ||||| ||||||| | || |||||||| |||||||||||||| ||||||||||||||||||||| | || || || |||||||||||||||
------------tagaaaagcaagaacgact-tacaatttagatggaaggagtacatctatataaggagtt-atcattttatgtgaaatttatttgaatttcaaatatttg--cagCAAGAGGTGGCAGCTTCAGCTGGTGAGAGCAGCTTTAGATCCTTTATGATTGCTGTGCAGCGTTGTACCAGTAGCGTAGCTATTCTTCAGCAG

upper sequence: LOC_Os12g13590.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA16G01660.1 (Glycine max), 3'ss of exon 16
gtatgtctgctttccaatggtttaatctaccattcatttttggcaatcacaccccatttgtatacgaaatttatcattga-atgaaagatgcagctaggtttgaaatattttttcagGCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGATTGCTGTGCAGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAG
        |   |   ||| |||  | |  ||| |  || |   ||  | |    |  | |   |  | || | |||  | ||  |||||  |  |    |||| ||       |||||||||||||| || ||||| ||||| ||||| || ||||| ||||||||||||||||| |||| ||  |||||||| |||||| |||| || 
--------gtaattacatgattt--ttttgcatgctcttgtta-aagtatatagtacatatgagcacatttcaccatacatattcaagatttatttg---ttgatatg------cagGCAGAGGCGGCGGCAGCTGCTGGTGAAAGTAGTTTCAGATCTTTCATGATTGCTGTGCAACGTTCTGGAAGCAGTGTAGCTATTATTCAACAA

upper sequence: LOC_Os12g13590.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA07G05160.1 (Glycine max), 3'ss of exon 16
gtatgtctgctttccaatggtttaatctaccattcatttttggcaatcacaccccatttgtatacgaaatttatcattga-atgaaagatgcagctaggtttgaaatattttttcagGCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGATTGCTGTGCAGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAG
        |   |   ||  |||  | |  ||| |  || |   ||  | |    || | |   |  | || | ||   | ||  |||||  |  |    |||| ||       ||||||||||||||||| ||||| ||||| ||||| || ||||| || ||||||||||| || |||| ||  |||||||| |||||| |||| || 
--------gtaattacataattt--ttttgcatactcttgtta-aagtatatagtatatatgagcacatttcaccagacatattcaagatttatttg---ttgatatg------cagGCAGAGGCGGCAGCAGCTGCTGGTGAAAGTAGTTTCAGATCTTTTATGATTGCTGTACAACGTTCTGGAAGCAGTGTAGCTATTATTCAACAA

upper sequence: LOC_Os12g13590.1 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv15s0046g02200.t01 (Vitis vinifera), 3'ss of exon 16
---------------------gtatgtctgctttccaatggtttaatctaccattcatttttgg-caat-cacaccccattt-----gtatacga-aatttatcattgaatgaa-agatgcagctaggtttgaaatattttttcagGCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGATTGCTGTGCAGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAG
                        | ||||| ||  ||   |||| ||||| |   |  |     ||||  | |  |   ||     ||||   | ||||||||    ||| |   |    |      ||||  |    | |  ||||||| || || |||||||| ||||| || || || ||||| |||||| | ||||| ||||||||||||||||||||||||||| ||||||| 
gtaattacttgatcacatggccattttctgcattttaa-aatttactctactacatacctcaattcaatgtatatgcttcttagaaagtattgaataatttatctagaaattatcgggcataagagaatttgttactgatgtgtagGCAGAAGCTGCTGCTGCTGCTGGTGAAAGCAGTTTCAGATCTTTCATGGTGGCTGTACAGCGTTGTGCTAGCAGTGTGGCTATTGTTCAGCAA

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|33822211|gb|CF336920.1|CF336920
EST:     TCATTGGAACAAGTG-TAGTAGAAGGGTTGCTACTGCTGCTGCTAATGCT                         GCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGANT
genomic: TCATTGGAACAAGTGTTAGTAGAAGGGTTGCTACTGCTGCTGCTAATGCTgtatgtctgc ... attttttcagGCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGA-T
EST: gi|29669745|gb|CB666020.1|CB666020
EST:     TCATTGGAACAAGTGTTAGTAGAAGGGTTGCTACTGCTGCTGCTAATGCT                         GCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGATT
genomic: TCATTGGAACAAGTGTTAGTAGAAGGGTTGCTACTGCTGCTGCTAATGCTgtatgtctgc ... attttttcagGCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGATT
EST: gi|33822202|gb|CF336916.1|CF336916
EST:     TCATTGGAACAAGTGTTAGTAGAAGGGTTGCTACTGCTGCTGCTAATGCT                         GCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGATT
genomic: TCATTGGAACAAGTGTTAGTAGAAGGGTTGCTACTGCTGCTGCTAATGCTgtatgtctgc ... attttttcagGCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacgaaatttatcattgaatgaaagatgcagctaggtttgaaatattttttcagGCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGATTGCTGTGCAGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAG
                                            tattttttc  CT-rich tract
                                     tttgaaatattttttc  TA-rich tract