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'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGGAGGTATTCAGCTTTTATCCAGAGAACCGCCCATGCAACGGATTTGAAGAGGCATTAGAAAGATACAGAGAAATTGTTCCGACTCTTCGATTAGCTGgttcgtttcagtaatttcacaatttagatgtttattcttcctttatttttttaaagaaggatcttgaatttagctggttatatataagattgcagtagtaactacagatcttcagaaaaataatgtatgcaaaaattgcaacag

Basic information

species Oryza sativa
transcript LOC_Os06g40650.4
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g40650.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G071659_T01 (Zea mays), 5'ss of exon 5
CAGGAGGTATTCAGCTTTTATCCAGAGAACCGCCCATGCAACGGATTTGAAGAGGCATTAGAAAGATACAGAGAAATTGTTCCGACTCTTCGATTAGCTGgttcgtttcagtaatttcacaatttagatgtttattcttcctttattt--ttttaaagaaggatcttgaatttagctggttatatataagattgcagtagtaactacagatcttcagaaaaataatgtatgcaaaaattgcaacag
|||||||||||||||||||| |||||||||||||||||||| ||||||||||||||  |||| |||||||||||||| ||||| |||||||||||||| |||| |||| ||| |      ||| || ||| || ||  ||  |  |||  ||||    |  ||  |  |||||      | ||| |  |||    || ||                                              
CAGGAGGTATTCAGCTTTTACCCAGAGAACCGCCCATGCAATGGATTTGAAGAGGCGCTAGACAGATACAGAGAAATCGTTCCAACTCTTCGATTAGCAGgtttgttt-agtgaagatttaatataaatgcttttttctctctcttttgtttttctgaatcgaaataaaatttgttctttcataaaagagagaaaaggagc---------------------------------------------

upper sequence: LOC_Os06g40650.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G345544_T02 (Zea mays), 5'ss of exon 5
CAGGAGGTATTCAGCTTTTATCCAGAGAACCGCCCATGCAACGGATTTGAAGAGGCATTAGAAAGATACAGAGAAATTGTTCCGACTCTTCGATTAGCTGgttcgtttcagtaatttcacaatttagatgtttattct-tcctttatttttttaaagaaggatcttgaatttagctggttatatataagattgcagtagtaactacagatcttcagaaaaataatgtatgcaaaaattgcaacag
|||||||||||||||||||| |||||||||||||||||||||||||||||||||||| |||| |||||||||||||| ||||| |||||||||||||| |||| |||| ||| |      ||| |||||  || |||| || ||| ||||| | ||  |  | |   |  ||      |  || |   ||    || || |                                            
CAGGAGGTATTCAGCTTTTACCCAGAGAACCGCCCATGCAACGGATTTGAAGAGGCACTAGACAGATACAGAGAAATCGTTCCAACTCTTCGATTAGCAGgtttgttt-agtgaagatttaatatagattatttttctctcttttgtttttctgaaccaaaacc--aagcttgctctttcgtaaaagggagaaaaggagcaga------------------------------------------
















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|116875559|gb|EC366067.1|EC366067
EST:     AGAGGCATTAGAAAGATACAGAGAAATTGTTCCGACTCTTCAATTAGCTG                         GACCAACATCTTTTGCCCCGATGATTGAAACAGCAATTGGTATTGTAGACA
genomic: AGAGGCATTAGAAAGATACAGAGAAATTGTTCCGACTCTTCGATTAGCTGgttcgtttca ... attgcaacagGACCAACATCTTTTGCCCCGATGATTGAAACAGCAATTGGTATTGTAGACA
EST: gi|58692386|gb|CK081073.1|CK081073
EST:     AGAGGCATTAGAAAGATACAGAGAAATTGTTCCGACTCTTCGATTAGCTG                         GAGCAACATCTTTTGCCCCGATGATTGAAACAGCAATTGGTATTGTAGACA
genomic: AGAGGCATTAGAAAGATACAGAGAAATTGTTCCGACTCTTCGATTAGCTGgttcgtttca ... attgcaacagGACCAACATCTTTTGCCCCGATGATTGAAACAGCAATTGGTATTGTAGACA
EST: gi|66928286|gb|CX115134.1|CX115134
EST:     AGAGGCATTAGAAAGATACAGAGAAATTGTTCCGACTCTTCGATTAGCTG                         GACCAACATCTTTTGCCCCGATGATTGAAACAGCAATTGGTATTGTAGACA
genomic: AGAGGCATTAGAAAGATACAGAGAAATTGTTCCGACTCTTCGATTAGCTGgttcgtttca ... attgcaacagGACCAACATCTTTTGCCCCGATGATTGAAACAGCAATTGGTATTGTAGACA
EST: gi|29632713|gb|CB637722.1|CB637722
EST:     AGAGGCATTAGAAAGATACAGAGAAATTGTTCCGACTCTTCGATTAGCTG                         GACCAACATCTTTTGCCCCGATGATTGAAACAGCAATTGGTATTGTAGACA
genomic: AGAGGCATTAGAAAGATACAGAGAAATTGTTCCGACTCTTCGATTAGCTGgttcgtttca ... attgcaacagGACCAACATCTTTTGCCCCGATGATTGAAACAGCAATTGGTATTGTAGACA
EST: gi|300216150|gb|HO087935.1|HO087935
EST:     AGAGGCATTAGAAAGATACAGAGAAATTGTTCCGACTCTTCGATTAGCTG                         GACCAACATCTTTTGCCCCGATGATTGAAACAGCAATTGGTATTGTAGACA
genomic: AGAGGCATTAGAAAGATACAGAGAAATTGTTCCGACTCTTCGATTAGCTGgttcgtttca ... attgcaacagGACCAACATCTTTTGCCCCGATGATTGAAACAGCAATTGGTATTGTAGACA
EST: gi|58695004|gb|CK083691.1|CK083691
EST:     AGAGGCATTAGAAAGATACAGAGAAATTGTTCCGACTCTTCGATTAGCTG                         GACCAACATCTTTTGCCCCGATGATTGAAACAGCAATTGGTATTGTAGACA
genomic: AGAGGCATTAGAAAGATACAGAGAAATTGTTCCGACTCTTCGATTAGCTGgttcgtttca ... attgcaacagGACCAACATCTTTTGCCCCGATGATTGAAACAGCAATTGGTATTGTAGACA
EST: gi|33677349|gb|CF305588.1|CF305588
EST:     AGAGGCATTAGAAAGATACAGAGAAATTGTTCCGACTCTTCGATTAGCTG                         GACCAACATCTTTTGCCCCGATGATTGAAACAGCAATTGGTATT
genomic: AGAGGCATTAGAAAGATACAGAGAAATTGTTCCGACTCTTCGATTAGCTGgttcgtttca ... attgcaacagGACCAACATCTTTTGCCCCGATGATTGAAACAGCAATTGGTATT
EST: gi|116875525|gb|EC366033.1|EC366033
EST:     AGAGGCATTAGAAAGATACAGAGAAATTGTTCCGACTCTTCGATTAGCTG                         GACCAACATCTTTTGCCCCGATGATTGAAACAGCAATTGGTATTGTAGACA
genomic: AGAGGCATTAGAAAGATACAGAGAAATTGTTCCGACTCTTCGATTAGCTGgttcgtttca ... attgcaacagGACCAACATCTTTTGCCCCGATGATTGAAACAGCAATTGGTATTGTAGACA
EST: gi|58678137|gb|CK066824.1|CK066824
EST:     AGAGGCATTAGAAAGATACAGAGAAATTGTTCCGACTCTTCGATTAGCTG                         GACCAACATCTTTTGCCCCGATGATTGAAACAGCAATTGGTATTGTAGACA
genomic: AGAGGCATTAGAAAGATACAGAGAAATTGTTCCGACTCTTCGATTAGCTGgttcgtttca ... attgcaacagGACCAACATCTTTTGCCCCGATGATTGAAACAGCAATTGGTATTGTAGACA

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), 75 (downstream exon)
Score: 17

CAGGAGGTATTCAGCTTTTATCCAGAGAACCGCCCATGCAACGGATTTGAAGAGGCATTAGAAAGATACAGAGAAATTGTTCCGACTCTTCGATTAGCTGgttcgtttca ... attgcaacagGACCAACATCTTTTGCCCCGATGATTGAAACAGCAATTGGTATTGTAGACAGCACTGGTGGTCAGTATCATGTTCTTCTGATAATAGCCGATGGACAG




<











<


<