Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAATGCGACTGTTTGTTGGCGATCCTGTTTGGACACCCTACAACCGTCCCCATGACCATCTTCCTGCAAGgtaagcccaggatttcgacgtcattctcattgctgcctaccatcaatttttgtttccctccttttcttgttcctctacggagccttgctgtattctttcag

Basic information

species Oryza sativa
transcript LOC_Os10g28350.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g28350.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv05s0020g04080.t01 (Vitis vinifera), 5'ss of exon 6
GCAATGCGACTGTTTGTTGGCGATCCTGTTTGGACACCCTACAACCGTCCCCATGACCATCTTCCTGCAAGgtaagcccag----gatttcgacgtcattctcat----tgctgcctaccatcaatttttgtttccctccttttcttgttcctctacggagccttgctg-tattctttcag------
|||||| | ||||||||||| |||||||||||||| ||||  || ||||| |||||  |||| ||||||||||| | |       | | || |  |  ||   ||    |  |  | ||| | |    | ||  ||       ||||  |  |||   ||  ||  | | |   |||| |       
GCAATGAGGCTGTTTGTTGGTGATCCTGTTTGGACTCCCTTTAATCGTCCTCATGATAATCTACCTGCAAGgtatggctttttctgttctccatcttgtttatatcttttaatctccaccttaatacctggtggccaattaagtcttcgtattctt--gaatctcacagatggccttttatttgcag
















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|88270931|gb|CI380231.1|CI380231
EST:     GATCCTGTTTGGACACCCTACAACCGTCCCCATGACCATCTTCCTGCAAG                         AAAGGAGTTTTTGGCTAAACTTCTCAAGTCAGAAGGTGAAAATCAAGCAAG
genomic: GATCCTGTTTGGACACCCTACAACCGTCCCCATGACCATCTTCCTGCAAGgtaagcccag ... attctttcagAAAGGAGTTTTTGGCTAAACTTCTCAAGTCAGAAGGTGAAAATCAAGCA-G
EST: gi|87036234|gb|CI190856.1|CI190856
EST:     GATCCTGTTTGGACACCCTACAACCGTCCCCATGACCATCTTCCTGCAAG                         AAAGGAGTTTTTGGCTAAACTTCTCAAGTCAGAAGGTGAAAATCAAGCAGT
genomic: GATCCTGTTTGGACACCCTACAACCGTCCCCATGACCATCTTCCTGCAAGgtaagcccag ... attctttcagAAAGGAGTTTTTGGCTAAACTTCTCAAGTCAGAAGGTGAAAATCAAGCAGT
EST: gi|88509164|gb|CI436670.1|CI436670
EST:     GATCCTGTTTGGACACCCTACAACCGTCCCCATGACCATCTTCCTGCAAG                         AAAGGAGTTTTTGGCTAAACTTCTCAAGTCAGAAGGTGAAAATCAAGCAGT
genomic: GATCCTGTTTGGACACCCTACAACCGTCCCCATGACCATCTTCCTGCAAGgtaagcccag ... attctttcagAAAGGAGTTTTTGGCTAAACTTCTCAAGTCAGAAGGTGAAAATCAAGCAGT
EST: gi|33693837|gb|CF322076.1|CF322076
EST:     GATCCTGTTTGGACACCCTACAACCGTCCCCATGACCATCTTCCTGCAAG                         AAAGGAGTTTTTGGCTAAACTTCTCAAGTCAGAAGGTGAAAATCAAGCAGT
genomic: GATCCTGTTTGGACACCCTACAACCGTCCCCATGACCATCTTCCTGCAAGgtaagcccag ... attctttcagAAAGGAGTTTTTGGCTAAACTTCTCAAGTCAGAAGGTGAAAATCAAGCAGT
EST: gi|88489103|gb|CI426375.1|CI426375
EST:     GATCCTGTTTGGACACCCTACAACCGTCCCCATGACCATCTTCCTGCAAG                         AAAGGAGTTTTTGGCTAAACTTCTCAAGTCAGAAGGTGAAAATCAAGCAGT
genomic: GATCCTGTTTGGACACCCTACAACCGTCCCCATGACCATCTTCCTGCAAGgtaagcccag ... attctttcagAAAGGAGTTTTTGGCTAAACTTCTCAAGTCAGAAGGTGAAAATCAAGCAGT
EST: gi|9865230|gb|AU100980.1|AU100980
EST:     GATCCTGTTTGGACACCCTACAACCGTCCCCATGACCATCTTCCTGCAAG                         AAAGGAGTTTTTGGCTAAACTTCTCAAGTCAGAAGGTGAAAATCAAGCAGT
genomic: GATCCTGTTTGGACACCCTACAACCGTCCCCATGACCATCTTCCTGCAAGgtaagcccag ... attctttcagAAAGGAGTTTTTGGCTAAACTTCTCAAGTCAGAAGGTGAAAATCAAGCAGT
EST: gi|33682516|gb|CF310755.1|CF310755
EST:     GATCCTGTTTGGACACCCTACAACCGTCCCCATGACCATCTTCCTGCAAG                         AAAGGAGTTTTTGGCTAAACTTCTCAAGTCAGAAGGTGAAAATCAAGCAGT
genomic: GATCCTGTTTGGACACCCTACAACCGTCCCCATGACCATCTTCCTGCAAGgtaagcccag ... attctttcagAAAGGAGTTTTTGGCTAAACTTCTCAAGTCAGAAGGTGAAAATCAAGCAGT
EST: gi|88275016|gb|CI395620.1|CI395620
EST:     GATCCTGTTTGGACACCCTACAACCGTCCCCATGACCATCTTCCTGCAAG                         AAAGGAGTTTTTGGCTAAACTTCTCAAGTCAGAAGGTGAAAATCAAGCAGT
genomic: GATCCTGTTTGGACACCCTACAACCGTCCCCATGACCATCTTCCTGCAAGgtaagcccag ... attctttcagAAAGGAGTTTTTGGCTAAACTTCTCAAGTCAGAAGGTGAAAATCAAGCAGT
EST: gi|10931130|gb|AU161404.1|AU161404
EST:     CCCATGACCATCTTCCTGCAAG                         AAAGGAGTTTTTGGCTAAACTTCTCAAGTCAGAAGGTGAAAATCAAGCAGT
genomic: CCCATGACCATCTTCCTGCAAGgtaagcccag ... attctttcagAAAGGAGTTTTTGGCTAAACTTCTCAAGTCAGAAGGTGAAAATCAAGCAGT
EST: gi|88271996|gb|CI388049.1|CI388049
EST:     GATCCTGTTTGGACACCCTACAACCGTCCCCATGACCATCTTCCTGCAAG                         AAAGGAGTTTTTGGCTAAACTTCTCAAGTCAGAAGGTGAAAATCAAGCAGT
genomic: GATCCTGTTTGGACACCCTACAACCGTCCCCATGACCATCTTCCTGCAAGgtaagcccag ... attctttcagAAAGGAGTTTTTGGCTAAACTTCTCAAGTCAGAAGGTGAAAATCAAGCAGT
EST: gi|10930577|gb|AU160851.1|AU160851
EST:     CCATCTTCCTGCAAG                         AAAGGAGTTTTTGGCTAAACTTCTCAAGTCAGAAGGTGAAAATCAAGCAGT
genomic: CCATCTTCCTGCAAGgtaagcccag ... attctttcagAAAGGAGTTTTTGGCTAAACTTCTCAAGTCAGAAGGTGAAAATCAAGCAGT
EST: gi|88992645|gb|CI035679.1|CI035679
EST:     GATCCTGTTTGGACACCCTACAACCGTCCCCATGACCATCTTCCTGCAAG                         AAAGGAGTTTTTGGCTAAACTTCTCAAGTCAGAAGGTGAAAATCAAGCAGT
genomic: GATCCTGTTTGGACACCCTACAACCGTCCCCATGACCATCTTCCTGCAAGgtaagcccag ... attctttcagAAAGGAGTTTTTGGCTAAACTTCTCAAGTCAGAAGGTGAAAATCAAGCAGT

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: 75 (upstream exon), 43 (downstream exon)
Score: 16

GCAATGCGACTGTTTGTTGGCGATCCTGTTTGGACACCCTACAACCGTCCCCATGACCATCTTCCTGCAAGgtaagcccag ... attctttcagAAAGGAGTTTTTGGCTAAACTTCTCAAGTCAGAAGGTGAAAATCAAGCAGTTGAAGGCTTCTGAGGGTTTTGTTGGGCTCCTGCACTGCGGTTCTATATT




<











<


<