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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGATCGAGGCATGGAAGGAGATCCCGGATGTTGAAGAGGACGAATGCTCCTCCGGTGCGCCACCGGCATCGCACTCTCAACGACGATCTTCTCTTGCAGgttatttactattttggagctgtgttgttattctgtagttctaattgctgcttttgttgctacttttgttactcagatctggtaatttagcttggactct...

Basic information

species Oryza sativa
transcript LOC_Os02g50640.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g50640.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G398809_T02 (Zea mays), 5'ss of exon 6
-ATGATCGAGGCATGGAAGGAGATCCCGGATGTTGAAGAGGACGAATGCTCCTCCGGTGCGCCACCGGCATCGCACTCTCAACGACGATCTTCTCTTGCAGgttatttactattttggagctgtgttgttattctgtagttctaattg-ctgcttttgttgctacttttgt-tactcagatctggtaat--ttagcttggactct--------
 ||||| |||||  ||||||||||||| | || |||||||||||| |||||||| | |  |||||| || || || || |||||| ||||||||||| ||||| |           | | |    | ||  ||||  |  | || ||| || ||||   | ||||||  |  |   |||||||| ||||  ||  | |  ||  |        
GATGATTGAGGCGGGGAAGGAGATCCCAGGTGCTGAAGAGGACGAGTGCTCCTC-GCTCTGCCACCAGCGTCCCAGTCACAACGAAGATCTTCTCTTACAGgtga--------ggggtatccccttcgtagttct--aactgtacttggctacttt--ctactacttccgcatgtacagatctgctaatctttttcctataccttgcaagagg

upper sequence: LOC_Os02g50640.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G078725_T01 (Zea mays), 5'ss of exon 2
ATGATCGAGGCATGGAAGGAGATCCCGGATGTTGAAGAGGACGAATGCTCCTCCGGTGCGCCACCGGCATCGCACTCTCAACGACGATCTTCTCTTGCAGgttatttac--tattttggagctgtgttgttattctg-tagttctaattgctgcttttgttgctacttttgtta-ctcagatctggtaattta--gctt--ggactct---------------------------------------------------------------------
||||| ||||| |||||||||||||||| || |||||||||||| |||||||||| | ||||| | || || || || |||||| ||| ||||||| ||||| |   ||  |  |||| || | |     || |  | || ||   | |  | | |    | |   | | || |  | |  ||| ||  ||||   |||  | | |||                                                                     
ATGATTGAGGCGTGGAAGGAGATCCCGGGTGCTGAAGAGGACGAGTGCTCCTCCGCTCCGCCATCAGCGTCCCAGTCACAACGAAGATATTCTCTTACAGgtgaggaacattcctttgtagtttttgctctacttggctacttgctactagttcatcatgtacagatctggtaaatttatctcttgttctttactacttatgaagtcttgatgaatagttgggtaaatgctacacctatttctttttttatatacaaattatcttgtaactaatcag

upper sequence: LOC_Os02g50640.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G328831_T01 (Zea mays), 5'ss of exon 3
ATGATCGAGGCATGGAAGGAGATCCCGGATGTTGAAGAGGACGAATGCTCCTCCGGTGCGCCACCGGCATCGCACTCTCAACGACGATCTTCTCTTGCAGgttatttactattttggagctgtgttgttattctgtagttctaattg-ctgcttttgttgctacttttgt-tactcagatctggtaat--ttagcttggactct--------
||||| ||||  |||||||||||| ||| || |||||||||||| |||||||||| |  |||||| || || || || |||||| || |||||||| ||||| |           | | |    | ||  ||||  |  | || ||| || ||||   | ||||||     |   |||||||| ||||  ||  | |  ||  |        
ATGATTGAGGTGTGGAAGGAGATCTCGGGTGCTGAAGAGGACGAGTGCTCCTCCGCTCTGCCACCAGCGTCCCAGTCACAACGAAGACCTTCTCTTACAGgtga--------ggggtatccccttcgtagttct--aactgtacttggctacttt--ctactacttccacatgtacagatctgctaatctttttcctataccttgcaagagg

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|58597010|gb|CK007538.1|CK007538
EST:     CTCCGGTGCGCCACCGGCATCGCACTCTCAACGACGATCTTCTCTTGCAG                         GGAGTGCAAGTGATGGGCGATATCCGGTTGCATCGTCGACCAGGAGGAATA
genomic: CTCCGGTGCGCCACCGGCATCGCACTCTCAACGACGATCTTCTCTTGCAGgttatttact ... gattctatagGGAGTGCAAGTGATGGGCGATATCCGGTTGCATCGTCGACCAGGAGGAATA
EST: gi|58670019|gb|CK058705.1|CK058705
EST:     CTCCGGTGCGCCACCGGCATCGCACTCTCAACGACGATCTTCTCTTGCAG                         GGAGTGCAAGTGATGGGCGATATCCGGTTGCATCGTCGACCAGGAGGAATA
genomic: CTCCGGTGCGCCACCGGCATCGCACTCTCAACGACGATCTTCTCTTGCAGgttatttact ... gattctatagGGAGTGCAAGTGATGGGCGATATCCGGTTGCATCGTCGACCAGGAGGAATA
EST: gi|23380890|gb|BU667335.1|BU667335
EST:     CTCCGGTGCGCCACCGGCATCGCACTCTCAACGACGATCTTCTCTTGCAG                         GGAGTGCAAGTGATGGGCGATATCCGGTTGCATCGTCGAC-AGGAGGAATA
genomic: CTCCGGTGCGCCACCGGCATCGCACTCTCAACGACGATCTTCTCTTGCAGgttatttact ... gattctatagGGAGTGCAAGTGATGGGCGATATCCGGTTGCATCGTCGACCAGGAGGAATA

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: 61 (upstream exon), 73 (downstream exon)
Score: 21

ATGATCGAGGCATGGAAGGAGATCCCGGATGTTGAAGAGGACGAATGCTCCTCCGGTGCGCCACCGGCATCGCACTCTCAACGACGATCTTCTCTTGCAGgttatttact ... gattctatagGGAGTGCAAGTGATGGGCGATATCCGGTTGCATCGTCGACCAGGAGGAATAGTCTACCTGCAAGCAGGTCGCCTCCTCCTGATGCCTCACCCAGTGTCAA




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