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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGTCACTGTTTCTCAACCAATAAATGCTGTTGCGTTTGTGATGGATGGGCTCTACTATGGTGTTTCTGACTTTGCTTTCGTGGCATACTCTACAgttcagatttctattcttatcatgtcccattgtatagtttatcagttatagctgcagcatcctaatcacattagtatttttcttgtttcag

Basic information

species Oryza sativa
transcript LOC_Os12g01580.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01580.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM5G890665_T01 (Zea mays), 5'ss of exon 10
TTTGTCACTGTTTCTCAACCAATAAATGCTGTTGCGTTTGTGATGGATGGGCTCTACTATGGTGTTTCTGACTTTGCTTTCGTGGCATACTCTACAgttcagatttctattcttatcatgtcccattgtatagtt--------tatcagttatagctgcagcatcc-taatcacattagtat--ttttcttgtttcag-------------------------
||||||||  ||||||| ||  | |||||| |||| || |||   |||||||||||||||||||||||||||||||| |  |  ||||| || || |||| ||||  || || ||   |||| |||| |   ||         |||||   ||        ||||  | ||||| | |  |    |||    |   |                          
TTTGTCACCATTTCTCAGCCGGTGAATGCTATTGCATTCGTGGCTGATGGGCTCTACTATGGTGTTTCTGACTTTGCCTATGCTGCATATTCCACGgttctgattcataatcctactctgtcgcattattatgtcaacgatactatcacacattatcatgtcatcaattatcacttcaacacaactttgccatcctaatcgtgtcaaatctttgttgtttcag

upper sequence: LOC_Os12g01580.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G150557_T01 (Zea mays), 5'ss of exon 8
TTTGTCACTGTTTCTCAACCAATAAATGCTGTTGCGTTTGTGATGGATGGGCTCTACTATGGTGTTTCTGACTTTGCTTTCGTGGCATACTCTACAgttcagatttctattcttatcatgtcccattgtatagtttatcagttatagctgcagcatcctaatcacattagtatttttcttgtttcag---------------------------------------
                                             |||||||||||||||||||||||||||||||| |  |  ||||| || || |||| ||||  || |||||   ||||||||| |   || |   |  ||      || |||  | ||   |  |||  |    ||    ||                                        
-------------------------------------------CTGATGGGCTCTACTATGGTGTTTCTGACTTTGCCTATGCTGCATATTCCACGgttctgattcataatcttactctgtcccattattatgtctccaatatactatcaca-cattatcattttagcagttatcactttaacacaactttgtcactaaaataatgttgaatctttgttgtttcag

upper sequence: LOC_Os12g01580.1 (Oryza sativa), 5'ss of exon 10
lower sequence: AT2G38330.1 (Arabidopsis thaliana), 5'ss of exon 11
TTTGTCACTGTTTCTCAACCAATAAATGCTGTTGCGTTTGTGATGGATGGGCTCTACTATGGTGTTTCTGACTTTGCTTTCGTGGCATACTCTACAgttcagatttctattcttatcatgtcccattgtatagtttatcagttatagctgcagcatcctaatcacattagtatttttcttgtttcag
|||||  |||  ||||||||  | |||||| | ||||||||  ||||||||||||| |||||||| |||||||| |  || |  || || ||||  || |   || ||  |      ||    | ||  ||  |   |    |  | ||| |  |   | || |  |      |  | |||   |||
TTTGTGGCTGGATCTCAACCGGTGAATGCTCTAGCGTTTGTTTTGGATGGGCTCTATTATGGTGTCTCTGACTTCGGATTTGCCGCTTATTCTATGgtcccttttccttcttcatcaattggtcgtttgattctcccttttcttcacctggaaaaagttgattatttc-----tcattttggaacag

upper sequence: LOC_Os12g01580.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv08s0058g00510.t01 (Vitis vinifera), 5'ss of exon 11
TTTGTCACTGTTTCTCAACCAATAAATGCTGTTGCGTTTGTGATGGATGGGCTCTACTATGGTGTTTCTGACTTTGCTTTCGTGGCATACTCTACAgttcagatttctattcttatcatgtcccattgtatagtttatcagttatagctgcagcatcctaatcacattagtatttttcttgtttcag
|||||  |||  ||||||||||| |||||| |||| ||||| || ||||| ||||||||||| ||||| |||||||  |  |  || ||||| |  || |    |||| |   ||| ||       | || | ||| ||| |  |  |  || | || |  | |  ||  | ||| |   |   |||
TTTGTTGCTGGATCTCAACCAATGAATGCTATTGCATTTGTTATTGATGGACTCTACTATGGGGTTTCAGACTTTGGATATGCTGCCTACTCCATGgtacca--ttctgtgtatatgat-------tata-aatttttcattctt--ccacatcttctttcttaacttgctgtttgtgacgag-cag

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|29639601|gb|CB644610.1|CB644610
EST:     ATGGGCTCTACTATGGTGTTTCTGACTTTGCTTTCGTGGCATACTCTACA                         TTATTTGCGGGAGCTATCTCATCAGCAGTACTGCTTGTGGCCGCTCCTAAG
genomic: ATGGGCTCTACTATGGTGTTTCTGACTTTGCTTTCGTGGCATACTCTACAgttcagattt ... cttgtttcagTTATTTGCGGGAGCTATCTCATCAGCAGTACTGCTTGTGGCCGCTCCTAAG
EST: gi|25806216|gb|CA762177.1|CA762177
EST:     ATGGGCTCTACTATGGTGTTTCTGACTTCGCTTTCGTGGCATACTCTACA                         TTATTTGCGGGAGCTATCTTATCAGCAGTACTGCTTGTGGCCGCTCCTAAG
genomic: ATGGGCTCTACTATGGTGTTTCTGACTTTGCTTTCGTGGCATACTCTACAgttcagattt ... cttgtttcagTTATTTGCGGGAGCTATCTCATCAGCAGTACTGCTTGTGGCCGCTCCTAAG

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: 45 (upstream exon), 23 (downstream exon)
Score: 3

TTTGTCACTGTTTCTCAACCAATAAATGCTGTTGCGTTTGTGATGGATGGGCTCTACTATGGTGTTTCTGACTTTGCTTTCGTGGCATACTCTACAgttcagattt ... cttgtttcagTTATTTGCGGGAGCTATCTCATCAGCAGTACTGCTTGTGGCCGCTCCTAAGTTTGGTCTTGGTGGCGTCTGGGCTGGCCTTACTCTATTTATGAGTTTGC




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