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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacactgtgttctgttattggccttccatgactgcaacttatagtattcttttctctcgcttttag

Basic information

species Oryza sativa
transcript LOC_Os04g51610.1
intron # 26
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 26
lower sequence: GRMZM2G391042_T01 (Zea mays), 5'ss of exon 26
GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacactg-----tgttctgttattggccttccatgactgcaacttatagtattcttttctctcgcttttag
|||||||| ||||| || ||||| || ||||||||||||||||| |||||||||||||||||||| |||||||||||||||||||| ||||||||||||||| ||  ||||     | || | || || |||||     |||| |  |||| || ||  ||| |   |  || ||
GCAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGGgtacgttaactgctttatcttttcttgttagccttgtgctactgtagtttatggtgtttgttttt---ggcttcag

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 26
lower sequence: GRMZM2G138195_T01 (Zea mays), 5'ss of exon 2
GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacactg-----tgttctgttattggccttccatgactgcaacttatagtattcttttctctcgcttttag
 ||||||| ||||| || ||||| || ||||||||||||||||| |||||||||||||||||||| |||||||||||||||||||| ||||||||||||||| ||  ||||     | || | || || |||||     |||| |  |||| || ||  ||| |   |  || ||
ACAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGGgtacgttaactgctttatcttttcttgttagccttgtgctactgtagtttatggtgtttgttttt---ggcttcag

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 26
lower sequence: GRMZM2G140328_T03 (Zea mays), 5'ss of exon 26
GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgt---acactgtgttctgttattggccttcc---atgactgcaactt----atagtattcttttctctcgcttttag-----------------------------------------------------------------------------------------------------------------
|||||||| ||||| || |||||||| |||||||||||||||||||||||||||||||||||||| ||||||||||||||||| ||||| |||||||||||| ||     |||   ||  |         ||||   | || |  || ||    |  | | |   |||  |  |  || |                                                                                                                 
GCAGATATTGGTCTATCAATGGGCATTCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTCGCATCAGTCGTGAGGgtacgttaaggactagtttgggaacaccattttcccaaaggattttaattttccaagggaaattagttcattttcccttgggaaaaatagaaatctcttgggaaaattgagttcccaaactagccctaaatgtgtttatatttttttgttagccttctgctactgtagttcatggtgtttgtttctggcttcag

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA13G00420.1 (Glycine max), 5'ss of exon 26
GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacac-tgtgttctgttattggccttccatgactgcaacttatagtattctttt--ctctcgcttttag--------------------------
|| ||||| |||||  | ||||| ||||| || || |||||||| || ||||| |||||||| || || ||||||||||||||||| || || |||| |||  |  | | | | || | | |  |   ||  |    |   |   ||  |   | |||  |     ||||| |                          
GCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAGgttagccctcatttcttatttgagagattttgaactgttcttataaatgatgcacgtttgacatctactttttgaaggttagtactcatttctggcatta

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA17G06520.1 (Glycine max), 5'ss of exon 28
GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacactgtgttctgttattggcctt----ccatgactgcaacttatagtattcttttctctcgcttttag--------------------------
|| ||||| |||||  | ||||| ||||| || || |||||||| || ||||| |||||||| || || ||||||||||||||||| || || |||| |||  || | |  |  |   ||    |  ||    |  |   |  || | || | ||  ||  |     | ||| |                          
GCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAGgttagtcctcatttcttatttggaagattttgaactgttcttataaatgat-gcatgtttaacatctaccttttgaaggactatttctggcattacttgaa

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA07G00630.2 (Glycine max), 5'ss of exon 25
GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacactgtgt--tctgttattggccttc--catgactgcaacttatagtattcttttctctcgcttttag-------------------------
|| ||||| ||||| || ||||||||||| |||||||||||||| || || || || |||||||| ||| | || || || |||||||| || || | |||| ||   || | |  |   || |  | |||    ||||      |||    |     | |||    ||  ||                          
GCTGATATTGGTCTTTCTATGGGCATCCAAGGAACTGAAGTTGCAAAAGAAAGCTCAGATATTATAATCCTAGACGATAACTTTGCATCAGTGGTAAAGgtaggtgttctatttaatacattctcaggcttggatatgatattgtcttccgtttcctgtatcttctcctagtaaattgttgggtaatcaacgctcccac

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA09G06890.1 (Glycine max), 5'ss of exon 25
GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtac-actgtgttctgttattg--------gccttccatgactgcaacttatagtattcttttctctcgcttttag--------------------------------------------------------------------------------------
|| |||||||||||  | ||||| ||||| || || ||||||||||| ||||| |||||||| || || ||||||||||||||||| || || |||| ||| ||||| ||| ||   | || ||         |  ||     | |   | |   | |   |||||    | ||  | |                                                                                      
GCCGATATAGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCCAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAGgtttgtactactttgagatatttttatttgttctgttttttgccattagtagtggaaatgcactttttgaacactgattgtacaatgagaggtttatatagaagtgaggtgcatttaatattgaagcacaactgatgatgacaattgtgtttctccatggttgtag

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA13G44990.1 (Glycine max), 5'ss of exon 27
GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacactgt--gttctgtta--ttggccttccatgactg-caacttatagtattcttttctctcgc--ttttag----------------------
|||||||| ||||| || ||||||||||| ||||| |||||||| || || ||||| |||||||| ||||||||||| || |||||||| || || | |||| |     | |   |||  |||     |  ||  |||  || |   || | || |   |   |    |  ||| |                       
GCAGATATTGGTCTTTCTATGGGCATCCAAGGAACAGAAGTTGCAAAAGAAAGTTCAGATATTATAATCTTGGATGATAACTTTGCATCAGTAGTAAAGgtaagcttgttatttattcacttaagcatgtattatatggttgtctttttttggtgtctgtcattggtacaatttcacatgctcaacttagaagttataa

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA15G00340.1 (Glycine max), 5'ss of exon 27
GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacactgtgttctgttattggccttccatgactgcaacttatagtattcttttctctcgcttttag-----------------------------
|||||||| ||||| || ||||||||||| ||||| |||||||| || || ||||| |||||||| ||||||||||| || |||||||| || || | |||| |     ||| || | ||    | ||  |||   | ||   | |   || ||   ||   |   |||                              
GCAGATATTGGTCTTTCTATGGGCATCCAAGGAACAGAAGTTGCAAAAGAAAGTTCAGATATTATAATCTTGGATGATAACTTTGCATCAGTAGTAAAGgtaagcttgttgtcttttttttggtgtctgtcattggtacatgatttcacatgctcaacttaagaacttatatacatttctttggcaatgatttgcctag

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA08G23760.1 (Glycine max), 5'ss of exon 28
GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacactgtgt--tctgttattggccttc--catgactgcaacttatagtattcttttctctcgcttttag-------------------------
|||||||| ||||| || |||||||||   |||||||||||||| || || || || |||||||| ||| | || ||||| |||||||| || || | |||| ||   || | |  | | || |  |||||    ||||      |||    |     | |||    ||  ||                          
GCAGATATTGGTCTTTCTATGGGCATCTCCGGAACTGAAGTTGCAAAAGAAAGCTCAGATATTATAATCCTAGACGACAACTTTGCATCAGTAGTAAAGgtaggtgttctatttaatatattctcagccttgggtatgatattgtcttccgtttcctgtatcttctcctagtaaaaagttattacttcattttccattg

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA15G18180.1 (Glycine max), 5'ss of exon 25
GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtac-----------actgtgttctgttattggcctt-ccatgactgcaacttatagtattcttttctctcgcttttag---------------------------------------------------------------------------------------
|| |||||||||||  | ||||| ||||| || || ||||||||||| ||||| || ||||| || || ||||||||||||||||| || || |||| |||  ||||           | | |  | |||| |     ||  ||| | |  || |   | |   |||||      ||  | |                                                                                       
GCCGATATAGGTCTAGCAATGGGTATCCAAGGTACAGAAGTTGCCAAAGAGAGCTCCGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAGgttagtactactttgagatattttaatttgttctgttttttgtcattagtagaagtagaaatgcactttttgaatactgattgtacaatgagaggtttatatagaattgaggtgcattgaatatttgaagcacaactgatgatgacaattgtttttctccatggttgtag

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 26
lower sequence: AT5G57110.1 (Arabidopsis thaliana), 5'ss of exon 27
GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtaca------ctgtgttctgttattggccttccatgactgca-----acttatagtattcttttctctcgcttttag----------------------------------------------------------------------------------------------------------------------
|||||||| |||||  | ||||| ||    ||||| ||||| || ||||||||||| || || ||||||||||||||||| ||||| || || || | ||| | | ||      || | ||||  | |     |||  |   || |        |  |  |  | |   || |   || |                                                                                                                       
GCAGATATTGGTCTTGCTATGGGAATAGCAGGAACAGAAGTGGCTAAGGAGAGTTCGGACATCATCATCTTGGATGACAACTTTGCTTCAGTTGTCAAGgtttattcaaattcacttttttctactttatagattcatttgttggataaaggtctgcaagacacataaatccctacttcaatagattttttttgtgaatccatgtatactatgtgtagatccaagaatgcatttttcgtaactgaatttgttgctactaagtattccaaccttaatttgtggtgatatatattatatag

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 26
lower sequence: AT4G29900.1 (Arabidopsis thaliana), 5'ss of exon 27
GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacact--gtgttctgttatt--ggccttccatgactgcaact----tatagtattcttttctctcg-----cttttag-----------------------------------------------------------------------------------------------------------
||||||||||||||| | ||||| ||||| || || |||||||| ||||| |  || || || || |||||||||||||| |||| ||| || |||| ||| ||||  ||  |    |    |||      |   || |  | | ||    | |  || |||| | |  ||     ||||| |                                                                                                           
GCAGATATAGGTCTCGCAATGGGTATCCAAGGCACCGAAGTTGCAAAGGAAAAGTCAGACATCATTATCTTGGATGACAACTTTGAATCCGTTGTGAAGgtttgtatccttagaaaccaaggattcaaatttcttataaaagaagctcctttttgatactcttctgttgcgtgatacttttggaatttcttttcctcgtaaatgtcctcctttgggctttggggctatttgtgatctttttaattatcctgaattagatatccattttaataatcgtctcattcctatag

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 26
lower sequence: AT3G21180.1 (Arabidopsis thaliana), 5'ss of exon 25
GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacactgtgttctgttattggccttccatgactgcaacttatagtattcttttctct-cgcttttag--------------------------
||||||||||||||||| ||||| ||    |||||||||||||| || ||||||||||| || || || ||||||||||||||||| || || || | |||  ||  |||   | |   ||| |           || | || | ||   ||| | | | | |  || ||                           
GCAGATATAGGTCTCTCTATGGGTATATCAGGAACTGAAGTTGCAAAAGAGAGTTCTGACATCATTATTTTGGATGACAATTTTGCTTCAGTAGTAAAGgttagtctactacat-caaatatagaaacatgtgatcttctacat-tatccttcatctttatgcttttctaatcaataaactctgtttactcttccag

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 26
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 5'ss of exon 27
GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacactgtgttctgttattggccttccatgact--gcaacttatagt----attcttttctctcgcttttag-----------------------
||||||||||||||||| |||||||| || |||||||||||||| || || || || || || || ||||||||||| || ||||| || || || | |||  ||  |       |  ||||  |  |    || ||  | || || ||||    |||||    | |    ||||                        
GCAGATATAGGTCTCTCTATGGGCATTCAAGGAACTGAAGTTGCAAAAGAAAGCTCAGACATCATTATCTTGGATGATAACTTTGCCTCAGTTGTAAAGgttagtgtaagcaaaccatttatgtgagtaaattgtcttgggaatttgtagttatgattctaccttgttatatttaaaacaaaaatactgtcaatccttt

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|88351169|gb|CI623391.1|CI623391
EST:     AGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGG                         GTTGTCAGATGGGGTCGCTCGGTTTATGCAAACATTCAGAAATTTATACAG
genomic: AGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacac ... tcgcttttagGTTGTCAGATGGGGTCGCTCGGTTTATGCAAACATTCAGAAATTTATACAG
EST: gi|58594188|gb|CF992496.1|CF992496
EST:     AGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGG                         GTTGTCAGATGGGGTCGCTCAGTTTATGCAAACATTCAGAAATTTATACAG
genomic: AGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacac ... tcgcttttagGTTGTCAGATGGGGTCGCTCGGTTTATGCAAACATTCAGAAATTTATACAG
EST: gi|218500877|gb|FG965670.1|FG965670
EST:     CAATTTTGCATCGGTCGTGAGG                         GTTGTCAGATGGGGTCGCTCGGTTTATGCAAACATTCAGAAATTTATACAG
genomic: CAATTTTGCATCGGTCGTGAGGgtatgtacac ... tcgcttttagGTTGTCAGATGGGGTCGCTCGGTTTATGCAAACATTCAGAAATTTATACAG

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), 74 (downstream exon)
Score: 36

GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacac ... tcgcttttagGTTGTCAGATGGGGTCGCTCGGTTTATGCAAACATTCAGAAATTTATACAGTTTCAGTTAACCGTCAACGTTGCAGCCTTGATTATTAACGTTGTTGCTG




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