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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGGAAACTATTGGTCCCTGGGAACAGAGACCTGGGCACTTTGGAGATGTTTGGAATTATTGGACCGATGATGGCCTAGGATATTACGAGTTTCTCCAGgtgtatgttagttaatgccatctgagtgtttttttttcatctcttctgctatcaacatatctaacgaaatatttctaccgaaattttcatggaaag

Basic information

species Oryza sativa
transcript LOC_Os11g03780.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g03780.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA19G30470.1 (Glycine max), 5'ss of exon 7
GAGGGAAACTATTGGTCCCTGGGAACAGAGACCTGGGCACTTTGGAGATGTTTGGAATTATTGGACCGATGATGGCCTAGGATATTACGAGTTTCTCCAGgtgtatgttagttaatgccatctgagtgtttttttttcatctcttctgctatcaacatatctaacgaaatatttctaccgaaattttcatggaaag
||  || |   |||| ||||||||||||||||||||||||||||| ||||||||||  |||||||| ||||| ||  | || ||||  |||  ||| || ||   |   | ||| |   ||   | |    |||| |  | | || ||  ||  |   ||   || |   |||| |       |||   ||   ||
GAAAGATAGAGTTGGACCCTGGGAACAGAGACCTGGGCACTTTGGTGATGTTTGGAGCTATTGGACAGATGAAGGATTTGGTTATTTTGAGGGTCTTCAAgtaagtac-atttattatgataacaatcacattttgttgt-tattgtgaaattcaatcat--gacaagccattttttt-----tttgtgtgtgtag

upper sequence: LOC_Os11g03780.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA19G30150.1 (Glycine max), 5'ss of exon 8
GAGGGAAACTATTGGTCCCTGGGAACAGAGACCTGGGCACTTTGGAGATGTTTGGAATTATTGGACCGATGATGGCCTAGGATATTACGAGTTTCTCCAGgtgtatgttagtta-atgccatctgagtgtttttttttcatctcttctgctatcaacatatctaacgaaatatttctaccgaaattttcatggaaag
||  || ||  |||| ||||||||| ||||||| |||||||||   ||||| |||||||||||||| || |||||  | || | ||  |||   ||||| ||   | ||  ||  ||  ||    |     |  |    || |  | |  |  | |   |  | |  || |  |||| | |   || || || |   
GAAAGACACGGTTGGACCCTGGGAAGAGAGACCAGGGCACTTTAATGATGTATGGAATTATTGGACTGACGATGGATTTGGTTTTTTTGAGGGCCTCCAAgtaggttttcctttcatatcagtaaataaactcatgggtatttaattt--ttcctattgaattgaaaaacttattcttctgt--ttctcgtgcag--

upper sequence: LOC_Os11g03780.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA19G30450.1 (Glycine max), 5'ss of exon 8
GAGGGAAACTATTGGTCCCTGGGAACAGAGACCTGGGCACTTTGGAGATGTTTGGAATTATTGGACCGATGATGGCCTAGGATATTACGAGTTTCTCCAGgtgtatgttagttaatgc-catctgagtgtttttttttcatctcttctgcta-tcaacata-tctaacgaaatatttctaccgaaattttcatggaaag-----------------------
||    | | ||||| || |||||  ||||||||||||||||||| ||||||||||  || ||||| |||||||| || || ||||| ||||||||||| ||   ||    || |     ||   ||  |    || | || |      ||| || |  || ||||         | |||  |||||  | ||  | |                        
GAAAACATCCATTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTGGATGTACTGGACTGATGATGGACTTGGTTATTATGAGTTTCTCCAAgtaagtgcctctttacatatattgtagcttaggattatgatgttcgtatctagtcgaattactctagttgtgctatgctagtgaaatgat-atatataattattattataatttttgagcag

upper sequence: LOC_Os11g03780.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA03G00630.1 (Glycine max), 5'ss of exon 7
GAGGGAAACTATTGGTCCCTGGGAACAGAGACCTGGGCACTTTGGAGATGTTTGGAATTATTGGACCGATGATGGCCTAGGATATTACGAGTTTCTCCAGgtgtatgttagtt----aatgccatctgagtgtttttttttcatctcttctgct--atcaacatatctaacgaaatatttctaccgaaattttcatggaaag
||  || ||  |||| || |||||| ||||||| || |||| ||||||||| |||||||||||||  ||||| ||  | || |  |  |||   || || ||     ||  ||    ||   |||     | |   | ||| || | |  |  |  ||  | | ||| | | |  | |||||   | |              
GAAAGACACAGTTGGACCATGGGAAGAGAGACCAGGACACTATGGAGATGTATGGAATTATTGGAGTGATGACGGATTTGGTTTCTTTGAGGGCCTTCAAgtagggtttccttttataaactcatgcatatatggatatttaatttttcttattgaattgagaaatcgatctatttgtttctcgagcag-------------

upper sequence: LOC_Os11g03780.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA03G27460.3 (Glycine max), 5'ss of exon 8
GAGGGAAACTATTGGTCCCTGGGAACAGAGACCTGGGCACTTTGGAGATGTTTGGAATTATTGGACCGATGATGGCCTAGGATATTACGAGTTTCTCCAGgtgtatg-------ttagttaatgccatctgagtgtttttttttcatctcttctgctatcaa-catatctaacgaaatatttctaccgaaattttcatggaaag-------------------
||  | | || |||| || |||||  ||||||||||||||||||| ||||||||||  || ||||| |||||||| || || ||||| ||||||||||| ||   ||       | |  || ||        |  | |  | ||||| |||  |   || |  | | | |   |  ||  |  |      || |  ||    |                    
GAAAGCATCTGTTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTGGATGTACTGGACTGATGATGGACTTGGCTATTATGAGTTTCTCCAAgtaagtgcctcttttcatatattgtagctgaggaatatgatgttcatatctagttgaattactcttgttttgtgctatgctagtgaaatgatatatattattattattattatttttgagcag

upper sequence: LOC_Os11g03780.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA19G30460.1 (Glycine max), 5'ss of exon 7
GAGGGAAACTATTGGTCCCTGGGAACAGAGACCTGGGCACTTTGGAGATGTTTGGAATTATTGGACCGATGATGGCCTAGGATATTACGAGTTTCTCCAGgtgtatgttagttaatgccatctgagtgtttttttttcatctcttctgctatcaacata-tctaacgaaatatttctaccgaaattttcatggaaag
||  || |||||||| || |||||  |||||||||||||| |||| ||||||||||| |||||||  ||||||||  | || | ||  |||| ||||| ||||  | ||  || |   | | | | |   ||| |       || |||  || || ||| | | |   |||||||||   | |              
GAAAGATACTATTGGACCATGGGAGGAGAGACCTGGGCACCTTGGTGATGTTTGGAACTATTGGAGTGATGATGGAATTGGTTTTTTTGAGTATCTCCTGgtgagtattcttttacaac-tataattaaatttgtc------ctgctga-ataaatataatatgatttaatatttcttgagcag-------------

upper sequence: LOC_Os11g03780.2 (Oryza sativa), 5'ss of exon 8
lower sequence: AT5G26120.1 (Arabidopsis thaliana), 5'ss of exon 8
GAGGGAAACTATTGGTCCCTGGGAACAGAGACCTGGGCACTTTGGAGATGTTTGGAATTATTGGACCGATGATGGCCTAGGATATTACGAGTTTCTCCAGgtgtatgttagttaatgccatctgagtgtttttttttcatctcttctgctatcaacatatctaacgaaatatttctaccgaaattttcatggaaag
||  |||||  |  |  | |||||| |||||||||| || | ||| ||||||||||| || ||||| ||||||||||| ||  | |  || ||  | || ||  | |  | ||  | |  |  |   ||| | | | ||| |    || |   |  ||  ||||        |   | | ||  |||| || |   
GAAAGAAACCGTGAGAGCTTGGGAAGAGAGACCTGGCCATTATGGTGATGTTTGGAAGTACTGGACTGATGATGGCCTTGGCCACTTTGAATTCTTTCAAgt--aagggatttttttcttttcg---gttctatatccatttaaagtgtttcaataattactaa------gctcgaaacaaatatttcttgtag--

upper sequence: LOC_Os11g03780.2 (Oryza sativa), 5'ss of exon 8
lower sequence: AT3G10740.1 (Arabidopsis thaliana), 5'ss of exon 8
GAGGGAAACTATTGGTCCCTGGGAACAGAGACCTGGGCACTTTGGAGATGTTTGGAATTATTGGACCGATGATGGCCTAGGATATTACGAGTTTCTCCAGgtgtatgttagttaatgccatctgagtgtttttttttcatctcttct-gctatcaacatatctaacgaaatatttctaccgaaattttcatggaaag
||  |||||  | || || |||||| ||||||| || || ||||| ||||||||||| |||||||||||||||||||| ||  | |  |||||  | || |||    ||  |   | | || |||||   |  |  ||  |    || | |||  | ||||  || |||  |||  | | |                
GAAAGAAACCGTAGGACCTTGGGAAGAGAGACCGGGCCATTTTGGTGATGTTTGGAAGTATTGGACCGATGATGGCCTTGGCCACTTTGAGTTCTTTCAAgtgagacttcttcttttctat-tgagtacataatgatccccgaagctcgttattga-atattaaatgaa-cattcttgcag----------------

upper sequence: LOC_Os11g03780.2 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv08s0040g00320.t01 (Vitis vinifera), 5'ss of exon 9
GAGGGAAACTATTGGTCCCTGGGAACAGAGACCTGGGCACTTTGGAGATGTTTGGAATTATTGGACCGATGATGGCCTAGGATATTACGAGTTTCTCCAGgtgtatgttagttaa-tgccatctg---agtgtttttttttcatctcttctgctatcaacatatctaacgaaatatttctaccgaaattttcatggaaag-----------
||   | || ||||| ||||||||  |||||||||| |||||||| ||||||||||| || ||||| |||||||| || || ||||  ||||| || || || | | |     |  || ||  ||   |   |||| |||  ||||       | |  |||  |   | || ||  | ||   | ||||| ||                  
GAAACAGACAATTGGGCCCTGGGAGGAGAGACCTGGACACTTTGGTGATGTTTGGAAGTACTGGACTGATGATGGACTTGGTTATTTTGAGTTCCTTCAAgtatgtatcttccacctgtcaattgtgaaagattttatttatatcttagtgattgt--acaatttccatgagatgctgcttaggtaatttacaaatgttttgtttctgtag

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|33796127|gb|CF323929.1|CF323929
EST:     TTTGGAATTATTGGACCGATGATGGCCTAGGATATTACGAGTTTCTCCAG                         CTTTCTGAAGACCTGGGTGCTGCCCCTATTTGGGTGTTCAATGGTTG
genomic: TTTGGAATTATTGGACCGATGATGGCCTAGGATATTACGAGTTTCTCCAGgtgtatgtta ... tcatggaaagCTTTCTGAAGACCTGGGTGCTGCCCCTATTTGGGTGTTCAATG-TTG
EST: gi|33796277|gb|CF324005.1|CF324005
EST:     TTTGGAATTATTGGACCGATGATGGCCTAGGATATTACGAGTTTCTCCAG                         CTTTCTGAAGACCTGGGTGCTGCCC-TATTTTGGGGTGTTCAATGGCTG
genomic: TTTGGAATTATTGGACCGATGATGGCCTAGGATATTACGAGTTTCTCCAGgtgtatgtta ... tcatggaaagCTTTCTGAAGACCTGGGTGCTGCCCCTATTT-GGG-TGTTCAATGT-TG
EST: gi|27548162|gb|CA766165.2|CA766165
EST:     GAGTTTCTCCAG                         CTTTCTGAAGACCTGGGTGCTGCCCCTATTTGGGTGTTCAATGTTG
genomic: GAGTTTCTCCAGgtgtatgtta ... tcatggaaagCTTTCTGAAGACCTGGGTGCTGCCCCTATTTGGGTGTTCAATGTTG
EST: gi|88722894|gb|CI746404.1|CI746404
EST:     TTTGGAATTATTGGACCGATGATGGCCTAGGATATTACGAGTTTCTCCAG                         CTTTCTGAAGACCTGGGTGCTGCCCCTATTTGGGTGTTCAATGTTG
genomic: TTTGGAATTATTGGACCGATGATGGCCTAGGATATTACGAGTTTCTCCAGgtgtatgtta ... tcatggaaagCTTTCTGAAGACCTGGGTGCTGCCCCTATTTGGGTGTTCAATGTTG

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), 46 (downstream exon)
Score: 36

GAGGGAAACTATTGGTCCCTGGGAACAGAGACCTGGGCACTTTGGAGATGTTTGGAATTATTGGACCGATGATGGCCTAGGATATTACGAGTTTCTCCAGgtgtatgtta ... tcatggaaagCTTTCTGAAGACCTGGGTGCTGCCCCTATTTGGGTGTTCAATGTTG




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