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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACTTCTATCTGCAAGAGCATCCTGATCTCATCAATGACCTTCTCAATGTACTTGCGCTTCGTTTGGATCATACAAGAGTCGTGGACATAATGCGCAAGgtttgtttcttatggcagggccttctattggtctatcagttttgctctgtttcaaaattttgaactgtttaattattatttgtacag

Basic information

species Oryza sativa
transcript LOC_Os11g01380.1
intron # 25
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 25
lower sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 10
GCACTTCTATCTGCAAGAGCATCCTGATCTCATCAATGACCTTCTCAATGTACTTGCGCTTCGTTTGGATCATACAAGAGTCGTGGACATAATGCGCAAGgtttgtttcttatggcagggccttctat----tggtctatcagtttt-gctctgtttcaaaatttt-----gaactg--tttaattattatttgtacag---------------------------------------------------------------------------------------------------
 || || ||| ||||||||||||||||||||||||||||  | || || || ||||| |||||||| ||||| || ||||| || |||||||||||||||||  |  ||| || | |   |  | | |    ||  || | | |    || |||||||||    |       | |||  | |  ||  | |||| ||||                                                                                                   
TCAGTTTTATTTGCAAGAGCATCCTGATCTCATCAATGATATGCTAAACGTGCTTGCACTTCGTTTAGATCACACCAGAGTTGTAGACATAATGCGCAAGgtaagcatctgattgaaaatctatttctgcagtgcactttgaatagaagccctgtttcaattcctcccaaaaatctgattcttgttgctctttggacaggctggtcagttgcatcttgtgaaaccatatatggttgcaattcagagtaacaatgtctctgccatgaatggagccttgaatgagctttatgtctgagag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 25
lower sequence: GRMZM5G822591_T01 (Zea mays), 5'ss of exon 2
GCACTTCTATCTGCAAGAGCATCCTGATCTCATCAATGACCTTCTCAATGTACTTGCGCTTCGTTTGGATCATACAAGAGTCGTGGACATAATGCGCAAGgtttgtttctta-tggcagggccttctattggtctatc---------agttttgct---------ctgtttcaaaattttgaactgtttaattattatttgtacag
 ||||||||| |||| |||||||||||||||||||||||  | || ||||| ||||| |||||||| |||||||| ||||| || |||||||||||||||||| |  ||| | ||  |     ||   || |   |           ||   || |         ||    | ||| | |||  ||| |  ||  | |||| ||||
TCACTTCTATTTGCAGGAGCATCCTGATCTCATCAATGATATGCTGAATGTGCTTGCACTTCGTTTAGATCATACCAGAGTTGTAGACATAATGCGCAAGgttagcatctgaatgaaaatttatttccttagcgcactttggatagaagccctgttttcaaattccttcccccaaaatctgacttgtcttgttgctctttggacag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 25
lower sequence: GRMZM2G057576_T01 (Zea mays), 5'ss of exon 24
GCACTTCTATCTGCAAGAGCATCCTGATCTCATCAATGACCTTCTCAATGTACTTGCGCTTCGTTTGGATCATACAAGAGTCGTGGACATAATGCGCAAGgtttgtttcttatggcagggc----cttctattggtctatcagtttt-gctctgtttcaaa---attttgaa---ctg--tttaattattatttgtacag
 ||||| ||||||||||||||||||||||||||||||||  | || || || ||||| |||||||| ||||| || | ||| || |||||||||||||||||| |  ||| || | |   |    | |  | ||  || | | |    || |||||||||     |    ||   |||  | |  ||  | |||| ||||
TCACTTTTATCTGCAAGAGCATCCTGATCTCATCAATGATATGCTAAACGTGCTTGCACTTCGTTTAGATCACACCATAGTTGTAGACATAATGCGCAAGgttagcatctgattgaaaatctattcctgcagtgcactttgaatagaagccctgtttcaattccgtcccaaaaatctgattcttgttgctctttggacag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 25
lower sequence: GRMZM5G804382_T01 (Zea mays), 5'ss of exon 2
GCACTTCTATCTGCAAGAGCATCCTGATCTCATCAATGACCTTCTCAATGTACTTGCGCTTCGTTTGGATCATACAAGAGTCGTGGACATAATGCGCAAGgtttgtttctta-tggcagggccttctattggt---ctatcagtttt-gctctgtttcaaaattttga---------actgtttaattattatttgtacag
 ||||||||| ||||||||||||||||||||||||||||  | || ||||| ||||| |||||||| |||||||| ||||| || |||||||||||||||||| |  ||| | ||| |     ||   || |    || | | |    || |||||||||| |  |           ||||| |  ||  | |||| ||||
TCACTTCTATTTGCAAGAGCATCCTGATCTCATCAATGATATGCTGAATGTGCTTGCACTTCGTTTAGATCATACCAGAGTTGTAGACATAATGCGCAAGgttagcatctgaatggaaatttatttccttagcgcactttgaatagaagccctgtttcaaattccttccaaaatcttactgtcttgttgctctttggacag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 25
lower sequence: GLYMA14G37510.1 (Glycine max), 5'ss of exon 23
GCACTTCTATCTGCAAGAGCATCCTGATCTCATCAATGACCTTCTCAATGTACTTGCGCTTCGTTTGGATCATACAAGAGTCGTGGACATAATGCGCAAGgtttgtt--tcttatggcagggccttctattggtctatcagttttgctctgtttc----aaaattttgaactgtttaattattatttgtacag-------------------------------------
 ||||||||  ||||||| ||||||||| | || ||||| ||||| ||||||||||| |||||| |||| || ||  | || ||||| |||||||| ||||| |||   ||| ||   |     ||||| ||   ||  ||||||  |||  ||      || ||   |||||||| |  ||  ||| | ||                                      
TCACTTCTACTTGCAAGAACATCCTGATATTATAAATGATCTTCTTAATGTACTTGCCCTTCGTGTGGACCACACCCGTGTTGTGGATATAATGCGGAAGgtctgtaggtctcattcta---ttttctaatgtgtta--agttttaatcttcttttggtgaagttaataactgtttgaaaatattttatgcaatattcttatttgttgcttgattttttctggtttttag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 25
lower sequence: GLYMA11G35460.1 (Glycine max), 5'ss of exon 24
GCACTTCTATCTGCAAGAGCATCCTGATCTCATCAATGACCTTCTCAATGTACTTGCGCTTCGTTTGGATCATACAAGAGTCGTGGACATAATGCGCAAGgtttgtttctta-tggcagggccttc-tattggtctatcagttttgctctgtttcaaaattt-----tgaactgtttaattattatttgt-acag
 ||||||||| | ||||||||||| ||||| ||||||||  || | ||||| ||||| |||||| | |||||| || | || || ||||| ||||| |||||    ||  || || ||     ||| | || || | |   || |   ||||||   | ||      ||||   |||   | | || | | | ||
TCACTTCTATTTACAAGAGCATCCAGATCTTATCAATGATGTTTTGAATGTCCTTGCACTTCGTGTTGATCATGCACGTGTTGTTGACATCATGCGAAAGgtagcattaatactgtcaacaatttcattttagtttttactttataacctgttttccatttcactgatgaatattttccctgtgatgtattatag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 25
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 25
GCACTTCTATCTGCAAGAGCATCCTGATCTCATCAATGACCTTCTCAATGTACTTGCGCTTCGTTTGGATCATACAAGAGTCGTGGACATAATGCGCAAGgtttgtttcttatggcagggcc--ttctattggtctatcagttttgctctgt--ttcaaaattttgaactgtttaattattatttgtacag--------
 ||||||||  |||||||||| |||||| | ||||| || ||||||||||| ||||| || || || ||||| ||  | ||||| || || |||||||||||| |   || |     |      |  | |  ||  |  | || |   | ||   | || | | |  |     | ||||||  ||||            
TCACTTCTACTTGCAAGAGCACCCTGATATAATCAACGATCTTCTCAATGTGCTTGCTCTGCGGTTAGATCACACGCGTGTCGTTGATATTATGCGCAAGgttagaggctgaccattgatttaatattttctgttaaaaacttatcaccagtggcttaacaatctatatctgatgattatttcttgtttctgatctcag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 25
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 25
GCACTTCTATCTGCAAGAGCATCCTGATCTCATCAATGACCTTCTCAATGTACTTGCGCTTCGTTTGGATCATACAAGAGTCGTGGACATAATGCGCAAGgtttgtttcttatggcagggccttctattggtctatcagttttgctctgtttcaaaattttgaactgtttaattattatttgtacag
|||||||||  ||||||||||||| ||| | ||||| || |||||||| ||||||||| | || || || |||||  | || || || |||||||| |||||| |   || |  | | | | || | ||  ||||| |      ||  | | ||  | ||  |||  ||   || || |     |||
GCACTTCTACTTGCAAGAGCATCCGGATATAATCAACGATCTTCTCAACGTACTTGCGTTGCGGTTAGACCATACTCGTGTTGTTGATATAATGCGGAAGgttagaagctgactg-atgactttgtttttttctataaaaacaactgagctacattactt--aacaattggtttcttctgatctcag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 25
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 25
GCACTTCTATCTGCAAGAGCATCCTGATCTCATCAATGACCTTCTCAATGTACTTGCGCTTCGTTTGGATCATACAAGAGTCGTGGACATAATGCGCAAGgtttgtttcttatggcagggccttctattg-gtctatcagttt-tgctctgtttca-------aaattttgaactgtttaattattatttgtacag-----------------------------------
||||||||| ||||| || ||||||||||| || ||||| || || ||||| ||||| |||||| |||| || ||  | || || ||||||||||| ||||| ||  | || ||      | || | |   |  |||   | | ||||   |||         ||||  | ||  ||||||  ||  |||   ||                                    
GCACTTCTACCTGCAGGAACATCCTGATCTTATTAATGATCTCCTTAATGTGCTTGCTCTTCGTGTGGACCACACTCGGGTTGTTGACATAATGCGAAAGgtctgcatgtt-tgcttactctttatgtgatggatattgctgtgtgcttcttttagtgggaacaaatgattaaaagtttaaaaatggttttgtcaatggtatcttatgcttatgatctctttgggtttcag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 25
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 25
GCACTTCTATCTGCAAGAGCATCCTGATCTCATCAATGACCTTCTCAATGTACTTGCGCTTCGTTTGGATCATACAAGAGTCGTGGACATAATGCGCAAGgtttgtttcttatggcagggccttctattggtctatcagttttgctctgtttcaaaattttgaactgtttaattatt------atttgtacag---------------------------------
|||||| ||  |||||||||||||||||||||| ||||| ||||| ||||| ||||| |||||  | || |||||  | || || ||||||||||| ||||||| ||  || || | ||   || | ||  ||  |   | ||  ||||    |   |  |    |  || | | ||       ||| |  |                                  
GCACTTTTACTTGCAAGAGCATCCTGATCTCATTAATGATCTTCTAAATGTGCTTGCACTTCGAGTAGACCATACTCGTGTGGTTGACATAATGCGGAAGgttt-ttgtttgtg-ctggcttttttgtt--tcctttcttcttcttctgaagtatgttacttgtttccttgactcttctagacgtttatgtactcttttggttatgcgttttttgttggattccag

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|29624172|gb|CB629183.1|CB629183
EST:     TACTTGCGCTTCGTTTGGATCATACAAGAGTCGTGGACATAATGCGCAAG                         GCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAAC
genomic: TACTTGCGCTTCGTTTGGATCATACAAGAGTCGTGGACATAATGCGCAAGgtttgtttct ... atttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAAC
EST: gi|12622957|gb|AU173170.1|AU173170
EST:     GGATCATACAAGAGTCGTGGACATAATGCGCAAG                         GCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAAC
genomic: GGATCATACAAGAGTCGTGGACATAATGCGCAAGgtttgtttct ... atttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAAC
EST: gi|5005228|gb|AU070390.1|AU070390
EST:     CAAGAGTCGTGGACATAATGCGCAAG                         GCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAAC
genomic: CAAGAGTCGTGGACATAATGCGCAAGgtttgtttct ... atttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAAC
EST: gi|29685119|gb|CB681394.1|CB681394
EST:     GGATCATACAAGAGCCCTGGACATAATGCGCAAG                         GCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAAC
genomic: GGATCATACAAGAGTCGTGGACATAATGCGCAAGgtttgtttct ... atttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAAC
EST: gi|29664581|gb|CB660856.1|CB660856
EST:     TACTTGCGCTTCGTTTGGATCATACAAGAGTCGTGGACATAATGCGCAAG                         GCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAAC
genomic: TACTTGCGCTTCGTTTGGATCATACAAGAGTCGTGGACATAATGCGCAAGgtttgtttct ... atttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAAC
EST: gi|87017011|gb|CI286147.1|CI286147
EST:     TACTTGCGCTTCGTTTGGATCATACAAGAGTCGTGGACATAATGCGCAAG                         GCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAAC
genomic: TACTTGCGCTTCGTTTGGATCATACAAGAGTCGTGGACATAATGCGCAAGgtttgtttct ... atttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAAC

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), 75 (downstream exon)
Score: 84

GCACTTCTATCTGCAAGAGCATCCTGATCTCATCAATGACCTTCTCAATGTACTTGCGCTTCGTTTGGATCATACAAGAGTCGTGGACATAATGCGCAAGgtttgtttct ... atttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG




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