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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAAGATGAAGTCAATGTCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTGTTTATGGGACTAAGgtgagtgacaagttaggtcaatatcaaagatggaatgaatattggtatatctgatgcttatgttgaatcacag

Basic information

species Oryza sativa
transcript LOC_Os09g12550.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g12550.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G167886_T01 (Zea mays), 5'ss of exon 12
AGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAAGATGAAGTCAATGTCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTGTTTATGGGACTAAGgtgagtgacaagttagg-tcaatatcaaagatggaatgaatattggtatatctgatgcttatgttgaatcacag
|||||||||||||||||||||| | |||||||  | ||| ||||||||||| |||||||||||||||||||||||  |||||||||||||||||||||||||||||  ||||||| | |||    |||| ||||||| |||||  |     ||||||||| || || |  ||||
AGACATGGAGCTTGTAAGAGTTCTTCCTAGTGTAGGAGAGGAAGTCAATGTTGCATGTTTTCATCCTTCCCCTGGATCAGGTCTTGTTTATGGGACTAAGgtgagtagcaagttaagatcagcgacaaaaatggaataaatatatgctctgctgatgcttctggtgtacaacag

upper sequence: LOC_Os09g12550.1 (Oryza sativa), 5'ss of exon 13
lower sequence: AT5G43930.1 (Arabidopsis thaliana), 5'ss of exon 12
AGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAAGATGAAGTCAATGTCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTGTTTATGGGACTAAGgtgagtgaca---agttaggtcaatatcaaagatggaatgaatattggtatatctgatgcttatgttgaatcacag--------------------
||| ||||||||||| |||||  | || ||| | || |||||||| || || || |||||||||||||| ||||| | |||||||||||||||||| ||||| |   | |   | | || ||| |||| |  |   |       || |   |||||||  |||  | || |||                       
AGATATGGAGCTTGTGAGAGTACTGCCAAGTTCAGAGGATGAAGTGAACGTTGCGTGTTTTCATCCTTCTCCTGGAGGAGGTCTTGTTTATGGGACAAAGgtaaaccatattgaatcagatcattatcgattaacaatgttcggtttgggaatctgatcatta--tcgactcatgactcatgttttttttccgtag

upper sequence: LOC_Os09g12550.1 (Oryza sativa), 5'ss of exon 13
lower sequence: AT1G04140.2 (Arabidopsis thaliana), 5'ss of exon 12
AGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAAGATGAAGTCAATGTCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTGTTTATGGGACTAAGgtgagtgacaagttaggtcaatatcaaagat-----ggaat--gaatattggtatat-ctgatgcttatgt----tgaatcacag
||| ||||| || || |||||  | || ||  | || |||||||| ||||| || || ||||||||||| ||||| | ||||||||| ||||| || ||||| | | |      |    ||| | ||| |      ||      ||| |||   | |  ||||  ||        |  ||| |||
AGATATGGAACTGGTGAGAGTACTTCCAAGCTCAGAGGATGAAGTTAATGTTGCTTGCTTTCATCCTTCTCCTGGGGGAGGTCTTGTCTATGGAACAAAGgtaattaatcctaaatcgtaatgtgaaaaacttctcggcgctaaaatgttgacttgtattgatatttgctcaatatttatctcag

upper sequence: LOC_Os09g12550.1 (Oryza sativa), 5'ss of exon 13
lower sequence: Vv07s0005g04630.t01 (Vitis vinifera), 5'ss of exon 12
AGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAAGATGAAGTCAATGTCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTGTTTATGGGACTAAGgtgagtgacaagttaggtcaatatcaaagatggaatgaatattggtatatctgatgcttatgttgaatcacag--------------------------------------------------------
||| ||||| ||||| |||||  | || |||||||||||||| |||||||| || || ||||||||||  ||||| | ||||||||| ||||| || ||||||     |   |   ||    |   |   |    |  || ||| | | |       | |  | |||| | |                                                         
AGATATGGAACTTGTTAGAGTGCTTCCCAGTGCTGAAGATGAGGTCAATGTAGCTTGCTTTCATCCTTTACCTGGAGGAGGTCTTGTGTATGGAACCAAGgtgtacatctgataccgtttggaaatatttttatttttat-ttgttctcttcttcaataaaatagaataatattaattttttcagcttatatccttacttctgtgtaattcttttgctgaaaattgcag

upper sequence: LOC_Os09g12550.1 (Oryza sativa), 5'ss of exon 13
lower sequence: PP1S58_234V6.1 (Physcomitrella patens), 5'ss of exon 13
AGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAAGATGAAGTCAATGTCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTGTTTATGGGACTAAGgtgagtgacaagttagg--tcaatatcaaagatggaatgaatattggtat-atctgatgct-tatgttgaatcacag-----------------------
||| ||||||||||| |||||  | || |||||||| |||||||| ||||| || |||||||||||      |||||  |||||||| ||||| || |||||||||      |  |   ||   |  |    |   ||  || |  | || |  ||  | | |||  ||  | |                          
AGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAGGATGAAGTGAATGTGGCGTGTTTTCATCCCCAAGTTGGTGGCGGTCTTGTATATGGAACAAAGgtgagttgttcttctgtgttctggactagtatttagatatatgtgtgaatcagttgtagttctatactgtttgaagattcgttatctgagataaagtgtt

upper sequence: LOC_Os09g12550.1 (Oryza sativa), 5'ss of exon 13
lower sequence: EFJ26270 (Selaginella moellendorffii), 5'ss of exon 13
AGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAAGATGAAGTCAATGTCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTGTTTATGGGACTAAGgtgagtgacaagttaggtcaatatcaaaga-tggaatgaatattggtatatctgatgcttatgttgaatcacag
|||  || | || ||  ||||| |||| ||||||||||||||||| ||||| || || |||||||||     ||| | ||| |||||||| || || |||||    | ||| ||   |  | ||  | || | |    |||      ||| | |                    
AGATTTGAAACTAGTGCGAGTTCTCCCAAGTGCTGAAGATGAAGTTAATGTAGCGTGCTTTCATCCTCGAGTTGGCGGAGGGCTTGTTTACGGCACAAAGgt--tcggcaactttccttgagatggatgactcggcctaatgcacaaataacag--------------------

upper sequence: LOC_Os09g12550.1 (Oryza sativa), 5'ss of exon 13
lower sequence: EFJ14567 (Selaginella moellendorffii), 5'ss of exon 12
AGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAAGATGAAGTCAATGTCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTGTTTATGGGACTAAGgtgagtgacaagttaggtcaatatcaaaga-tggaatgaatattggtatatctgatgcttatgttgaatcacag
|||  || | || ||  ||||| |||| ||||||||||||||||| ||||| || || |||||||||     ||| | ||| |||||||| || || |||||   |||||| ||   |  | ||  | || | |    |||      ||| | |                    
AGATTTGAAACTAGTGCGAGTTCTCCCAAGTGCTGAAGATGAAGTTAATGTAGCGTGCTTTCATCCTCGAGTTGGCGGAGGGCTTGTTTACGGCACAAAGgt--ttgacaactttcctttagatggatgactcggcctaatgcacaaataacag--------------------

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|86482193|gb|CI124826.1|CI124826
EST:     TCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTGTTTATGGGACTAAG                         GAAGGAAAGCTCAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAA
genomic: TCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTGTTTATGGGACTAAGgtgagtgaca ... tgaatcacagGAAGGAAAGCTCAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAA
EST: gi|29627251|gb|CB632262.1|CB632262
EST:     TCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTGTTTATGGGACTAAG                         GAAGGAAAGCTCAGGATAATTCAAAACAATGTTGCAGACTACTAGGGGAAA
genomic: TCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTGTTTATGGGACTAAGgtgagtgaca ... tgaatcacagGAAGGAAAGCTCAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAA
EST: gi|87014906|gb|CI271505.1|CI271505
EST:     TCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTGTTTATGGGACTAAG                         GAAGGAAAGCTCAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAA
genomic: TCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTGTTTATGGGACTAAGgtgagtgaca ... tgaatcacagGAAGGAAAGCTCAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAA
EST: gi|66915004|gb|CX101852.1|CX101852
EST:     TCGCATGTTTTCATCCTTCCCCTGGTGCAAGTCTTGTTTATGGGACTAAG                         GAAGGAAAGCTCANGATAATTCAACACAATGTTGCAGACTACTAGGGGAAA
genomic: TCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTGTTTATGGGACTAAGgtgagtgaca ... tgaatcacagGAAGGAAAGCTCAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAA
EST: gi|29673906|gb|CB670181.1|CB670181
EST:     TCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTGTTTATGGGACTAAG                         GAAGGAAAGCTCAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAA
genomic: TCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTGTTTATGGGACTAAGgtgagtgaca ... tgaatcacagGAAGGAAAGCTCAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAA
EST: gi|58653118|gb|CK041798.1|CK041798
EST:     TCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTGTTTATGGGACTAAG                         GAAGGAAAGCTCAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAA
genomic: TCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTGTTTATGGGACTAAGgtgagtgaca ... tgaatcacagGAAGGAAAGCTCAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAA

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: 67 (upstream exon), 58 (downstream exon)
Score: 16

AGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAAGATGAAGTCAATGTCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTGTTTATGGGACTAAGgtgagtgaca ... tgaatcacagGAAGGAAAGCTCAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAATATTCTTGAG




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