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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGGTAGAGgtgggctgcgcttcgttcaacatcgcacgtgcaatctttgacacacctgaataattccctgttatttcatatcccag

Basic information

species Oryza sativa
transcript LOC_Os12g40830.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g40830.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G069758_T02 (Zea mays), 5'ss of exon 4
GGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGGTAGAGgtgggctgcgcttcgttcaacatcgcacgtgcaatctttgacacacctgaataattccctgttatttcatatcccag
|| || |||||||||||||| || |||||||||||||| ||||| ||||||||||||||||| |||||||| ||||||||||||||||||||||||| | ||     | |  | || ||  ||| |           |||  |||| | || ||||||  ||| | |  |||| |||
GGGTATGTTGGCAACAAATCGGCCGTCTTTCCCCTGCAGCTCCTTGGCTTTGATGTGGATCCAATAAACTCTGTACAGTTTTCTAATCATACAGgtaaatgtatatcgtggat-gtacacaatctcgtacaattcacttgggacacataaacaattcca-gttgtgtgttatctcag

upper sequence: LOC_Os12g40830.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA18G04360.1 (Glycine max), 5'ss of exon 3
GGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGGTAGAGgtgggctgcg---cttcgttcaacatcgcacgtgcaatctttgacacacctgaataattccctgttatttcatatcccag---------------------------------------------------------------------------------
 | || ||||| || ||||| || ||||| || |||||||| ||||| | |||||| ||||| || || || || |||||||| ||||||||||| |      | ||       ||| |||| | || || |   | ||| || |     | | |  |     | | | |   | |                                                                                     
-GGTATGTTGGTAATAAATCCGCTGTCTTCCCTCTGCAACTACTGGGATATGATGTCGATCCAATTAATTCCGTGCAGTTTTCGAATCATACAGGcaagctgagtctttaatttttcattcagcttctcagg---actctgtggcttgattta-tggtgtgacgctgtctgtcaacgtgaataagttttggtgtggtatggtgtgcttgattaagtaattctgcagttgtggtttgataaatttgatggctataatgcagg

upper sequence: LOC_Os12g40830.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA11G33970.1 (Glycine max), 5'ss of exon 3
GGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGGTAGAGgtgggctgcg---cttcgttcaacatcgcacg--tgcaatctttgacacacc-tgaataattccctgttatttcatat---cccag----------------------------------------------------------------------
|| || ||||| || ||||| || ||||| || |||||| | ||||| | |||||||||||| || || || || |||||||| ||||||||||| |      | ||       ||| |||| | || || |  |       |||| | ||  ||      |  |||| | |    ||      ||                                                                      
GGGTATGTTGGTAATAAATCCGCTGTCTTCCCTCTGCAATTACTGGGATATGATGTGGATCCAATTAATTCTGTGCAGTTTTCGAATCATACAGgcaagctgagtctttaatttttcattcagcttctcaggattctgtggcttgatatacggtgtgacgctgtctgtcaatgtgaataagtttaggtgtggtatggtatgcttgattaagtaattctgcagttgtggtttgataaatttgatggttataatgcag

upper sequence: LOC_Os12g40830.3 (Oryza sativa), 5'ss of exon 3
lower sequence: AT5G37850.3 (Arabidopsis thaliana), 5'ss of exon 3
GGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGGTAGAGgtgggctgcgcttc------gttcaacatcgcacgtgcaatctttgacacacctgaataattccctgttatttcatatcccag---------------------------
||||| ||||| ||||||||||| |||||||| || ||| |  |||| | |||||||||||| || ||||| ||||| || || |||||||||||||    | ||   |  |        |   ||  |  |       |   ||| |  | ||   | |||   |||   |  || | |                              
GGATATGTTGGTAACAAATCAGCTGTCTTTCCTCTTCAATTGTTGGGGTATGATGTGGATCCAATCAACTCTGTACAATTCTCGAATCATACAGgtaatatttggtcacagtaatgtagagcctaatgttcctgaaattactgttgtcgtatcttcgttattgg-tgtatctgaatctactgatttggcattactaaaacttttttccag

upper sequence: LOC_Os12g40830.3 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv14s0006g01660.t01 (Vitis vinifera), 5'ss of exon 3
GGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGGTAGAGgtgggctgcgcttcgttcaa----catcgcacgtgcaatctttgacacacc-tgaataattccctgttatttcatat---cccag-------------------------------------------------------------
||||| |||||||| ||||| || ||||||||||| || || ||||||| |||||| ||||| || || || |||||||| || ||||| ||||| |   |  |  |   ||||  ||||      ||  |  |   |    ||| | |   ||     |   |||  | |  ||||     |||                                                             
GGATATGTTGGCAATAAATCGGCTGTCTTTCCCCTCCAGCTACTGGGCTATGATGTCGATCCAATCAATTCAGTACAGTTCTCAAATCACACAGgca--agctgcttatacttcactcaaacagtctcagaactctgaagcctgaaatatggtgcgaggtcaactgccaatctatatgagttcaggcatgagatcctagtagcaattgaggttaaattatggttagtcaacttgaatatcttgcag

upper sequence: LOC_Os12g40830.3 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ27991 (Selaginella moellendorffii), 5'ss of exon 2
GGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGGTAGAGgtgggctgcgcttcgttcaacatcgcacgtgcaatctttgacacacctgaataattccctgttatttcatatcccag
||||||||||| || ||||| || ||||||||| |||| |||||||| || ||||| |||||||| ||||| |||||||| || ||||| || || |   |      || | ||| |     |  | |||    |||||  |     ||  ||                        
GGATACGTTGGAAATAAATCGGCGGTCTTTCCCTTGCAGCTCCTGGGATTCGATGTTGATCCGATCAACTCCgtacagttctccaatcacacgggcaagagcaatgcgctcctcgct-----tttctcgttt--tcttttcccagtttgtttag-----------------------

upper sequence: LOC_Os12g40830.3 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ29421 (Selaginella moellendorffii), 5'ss of exon 2
GGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGGTAGAGgtgggctgcgcttcgttcaacatcgcacgtgcaatctttgacacacctgaataattccctgttatttcatatcccag
||||||||||| || ||||| || ||||||||| |||| |||||||| || ||||| |||||||| ||||| |||||||| || ||||| ||||| |          || | ||| |     || |   | |  |        |   |                             
GGATACGTTGGAAATAAATCGGCGGTCTTTCCCTTGCAGCTCCTGGGATTCGATGTTGATCCGATCAACTCCgtacagttctccaatcacacaggcaagaccaatgcgctcctcgctt---ttctctttttcttttcccagtgcgtttag---------------------------

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|58661072|gb|CK049752.1|CK049752
EST:     TGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATAC------AG                         GGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: TGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGGTAGAGgtgggctgcg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
EST: gi|88448481|gb|CI693864.1|CI693864
EST:     TGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGG--G--                         --TACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: TGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGGTAGAGgtgggctgcg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
EST: gi|88301040|gb|CI592220.1|CI592220
EST:     TGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGG--G--                         --TACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: TGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGGTAGAGgtgggctgcg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
EST: gi|88443713|gb|CI591938.1|CI591938
EST:     TGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGG--G--                         --TACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: TGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGGTAGAGgtgggctgcg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
EST: gi|88580749|gb|CI697698.1|CI697698
EST:     TGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGG--G--                         --TACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: TGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGGTAGAGgtgggctgcg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
EST: gi|88424098|gb|CI689800.1|CI689800
EST:     TGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGG--G--                         --TACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: TGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGGTAGAGgtgggctgcg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
EST: gi|88335844|gb|CI645445.1|CI645445
EST:     TGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGG--G--                         --TACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: TGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGGTAGAGgtgggctgcg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
EST: gi|66924011|gb|CX110859.1|CX110859
EST:     TGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATAC------AG                         GGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: TGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGGTAGAGgtgggctgcg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC

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: 19 (upstream exon), 75 (downstream exon)
Score: 2

GGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGGTAGAGgtgggctgcg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATCTTATTGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATT




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