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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_Os12g40830.3
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|88580749|gb|CI697698.1|CI697698
EST:     GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAG                         GGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGgtagaggtgg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
EST: gi|88443713|gb|CI591938.1|CI591938
EST:     GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAG                         GGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGgtagaggtgg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
EST: gi|88339276|gb|CI633847.1|CI633847
EST:     GGGCTTTGATGTGGATCCGATAAANTCGGTACAGTTTTCTAATCATACAG                         GGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGgtagaggtgg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
EST: gi|88448481|gb|CI693864.1|CI693864
EST:     GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAG                         GGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGgtagaggtgg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
EST: gi|88355870|gb|CI625499.1|CI625499
EST:     GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAG                         GGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGgtagaggtgg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
EST: gi|88341926|gb|CI644263.1|CI644263
EST:     GGGCTTTGATGTGGATCCGATAAACTCGGTANAGTTTTCTAATCATACAG                         GGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGgtagaggtgg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
EST: gi|88301040|gb|CI592220.1|CI592220
EST:     GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAG                         GGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGgtagaggtgg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
EST: gi|88337186|gb|CI628272.1|CI628272
EST:     GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAG                         GGTACCCAAAATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGgtagaggtgg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
EST: gi|58661072|gb|CK049752.1|CK049752
EST:     GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAG                         GGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGgtagaggtgg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
EST: gi|88335844|gb|CI645445.1|CI645445
EST:     GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAG                         GGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGgtagaggtgg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
EST: gi|88385774|gb|CI566636.1|CI566636
EST:     GGCTTTGATGTGGATCCGATAAACCTCGGTACAGTTTTCTAATCATACAG                         GGTACCCAACATTTACAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: GGCTTTGATGTGGATCCGATAAAC-TCGGTACAGTTTTCTAATCATACAGgtagaggtgg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
EST: gi|88424098|gb|CI689800.1|CI689800
EST:     GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAG                         GGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGgtagaggtgg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
EST: gi|66924011|gb|CX110859.1|CX110859
EST:     GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAG                         GGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGgtagaggtgg ... 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: 74 (upstream exon), 75 (downstream exon)
Score: 19

GGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGgtagaggtgg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATCTTATTGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATT




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