Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAGTTCAAGATGGTCCGCGATATGCAGTCCAACATCAAGCGCATCGTCAACCTCGAGACGCTCGCCGCCGGGACCAACAAGCGGCGCATCATCCAGCAGgtgagcccccctgcccccttcgcatcggtgtaatttgcgggtaatttgcagcatcttgttgactgatggtttgatggttag

Basic information

species Oryza sativa
transcript LOC_Os01g56600.1
intron # 1
splice site 5'
intron type U2

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|218491046|gb|FG951983.1|FG951983
EST:     ACCTCGAGACGCTCGCCGCCGGGACCAACAAGCGGCGCATCATCCAGCAG                         GCCGTCTTCACGGAGCTCTGCAACATGTTGGATCCCGGGAAGCCTTCCTTC
genomic: ACCTCGAGACGCTCGCCGCCGGGACCAACAAGCGGCGCATCATCCAGCAGgtgagccccc ... tgatggttagGCCGTCTTCACGGAGCTCTGCAACATGTTGGATCCCGGGAAGCCTTCCTTC
EST: gi|88422690|gb|CI573852.1|CI573852
EST:     ACCTCGAGACGCTCGCCGCCGGGACCAACAAGCGGGGCATCATCCAGCAG                         GCCGTCTTCACGGAGCTCTGCAAGATGTTGGATCCCGGGAAGCCTTCCTTC
genomic: ACCTCGAGACGCTCGCCGCCGGGACCAACAAGCGGCGCATCATCCAGCAGgtgagccccc ... tgatggttagGCCGTCTTCACGGAGCTCTGCAACATGTTGGATCCCGGGAAGCCTTCCTTC
EST: gi|86891894|gb|CI310072.1|CI310072
EST:     ACCTCGAGACGCTCGCCGCCGGGACCAACAAGCGGCGCATCATCCAGCAG                         GCCGTCTTCACGGAGCTCTGCAACATGTTGGATCCCGGGAAGCCTTCCTTC
genomic: ACCTCGAGACGCTCGCCGCCGGGACCAACAAGCGGCGCATCATCCAGCAGgtgagccccc ... tgatggttagGCCGTCTTCACGGAGCTCTGCAACATGTTGGATCCCGGGAAGCCTTCCTTC
EST: gi|88420692|gb|CI564528.1|CI564528
EST:     ACCTCGAGACGCTCGCCGCCGGGACCAACAAGCGGCGCATCATCCAGCAG                         GCCGTCTTCACGGAGCTCTGCAACATGTTGGATCCCGGGAAGCCTTCCTTC
genomic: ACCTCGAGACGCTCGCCGCCGGGACCAACAAGCGGCGCATCATCCAGCAGgtgagccccc ... tgatggttagGCCGTCTTCACGGAGCTCTGCAACATGTTGGATCCCGGGAAGCCTTCCTTC
EST: gi|88392343|gb|CI612817.1|CI612817
EST:     ACCTCGAGACGCTCGCCGCCGGGACCAACAAGCGGCGCATCATCCAGCAG                         GCCGTCTTCACGGAGCTCTGCAACATGTTGGATCCCGGGAAGCCTTCCTTC
genomic: ACCTCGAGACGCTCGCCGCCGGGACCAACAAGCGGCGCATCATCCAGCAGgtgagccccc ... tgatggttagGCCGTCTTCACGGAGCTCTGCAACATGTTGGATCCCGGGAAGCCTTCCTTC
EST: gi|88359738|gb|CI622428.1|CI622428
EST:     ACCTCGAGACGCTCGCCGCCGGGACCAAAAAGCGGGGCATCATCCAGCAG                         GCCGTCTTCACGGAGCTCTGCAACATGTTGGATCCCGGGAAGCCTTCCTTC
genomic: ACCTCGAGACGCTCGCCGCCGGGACCAACAAGCGGCGCATCATCCAGCAGgtgagccccc ... tgatggttagGCCGTCTTCACGGAGCTCTGCAACATGTTGGATCCCGGGAAGCCTTCCTTC

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: 56 (upstream exon), 74 (downstream exon)
Score: 16

CCAGTTCAAGATGGTCCGCGATATGCAGTCCAACATCAAGCGCATCGTCAACCTCGAGACGCTCGCCGCCGGGACCAACAAGCGGCGCATCATCCAGCAGgtgagccccc ... tgatggttagGCCGTCTTCACGGAGCTCTGCAACATGTTGGATCCCGGGAAGCCTTCCTTCACTCCCAAGAAGGGGAAACCTTGCGTGGTCATGTTCGTTGGTTTGCAAG




<











<


<