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'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttttttttcatttacatatttgatttcttcttaagttgcatgttgacactaacatgggatgttactgccacagGCACTGCAGAGATTTTTTGCTTCACTGGTCCAGTCTGCAAATACAAGCTTTGACACTTTGTTGGATTCTCTTATTTCTACTGCTAAACCATCGCAGTCAG

Basic information

species Oryza sativa
transcript LOC_Os02g07120.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G168629_T01 (Zea mays), 3'ss of exon 20
gtattttttttttcatttacatatttgatttctt-----cttaagttgcatgttgacactaacatgggatgtta---ctgccacagGCACTGCAGAGATTTTTTGCTTCACTGGTCCAGTCTGCAAATACAAGCTTTGACACTTTGTTGGATTCTCTTATTTCTACTGCTAAACCATCGCAGTCAG
|||          |    | | |   ||     |     ||| | ||  | ||    ||||||||  |||||||    ||  |||||| || ||||| |||||||| ||||| || || ||||||||||| ||||||||  |||||||||| || ||||||||| ||||||| ||||| || ||||
gtacccccacccacccacaaaaaagagaggatctgagcactttatttttaggtgactactaacatatgatgttaatattgttacagGCTCTTCAGAGGTTTTTTGCATCACTTGTTCAATCTGCAAATACTAGCTTTGATGCTTTGTTGGAGTCCCTTATTTCTGCTGCTAAGCCATCACATTCAG
















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|88730915|gb|CI754528.1|CI754528
EST:     AGGCCCTTATTTTGATCAGGAGTGCTCTCTTGCAAGGGCAGGCACTACAG                         GCACTGCAGAGATTTTT
genomic: AGGCCCTTATTTTGATCAGGAGTGCTCTCTTGCAAGGGCAGGCACTACAGgtattttttt ... actgccacagGCACTGCAGAGATTTTT
EST: gi|163929098|gb|EG712647.1|EG712647
EST:     GCTCTCTTGCAAGGGCAGGCACTACAG                         GCACTGCAGAGATTTTTTGCTTCACTGGTCCAGTCTGCAAATACAAGCTTT
genomic: GCTCTCTTGCAAGGGCAGGCACTACAGgtattttttt ... actgccacagGCACTGCAGAGATTTTTTGCTTCACTGGTCCAGTCTGCAAATACAAGCTTT
EST: gi|29634555|gb|CB639564.1|CB639564
EST:     AGGCCCTTATTTTGATCAGGAGTGCTCTCTTGCAAGGGCAGGCACTACAG                         GCACTGCAGAGATTTTTTGCTTCACTGGTCCAGTCTGCAAATACAAGCTTT
genomic: AGGCCCTTATTTTGATCAGGAGTGCTCTCTTGCAAGGGCAGGCACTACAGgtattttttt ... actgccacagGCACTGCAGAGATTTTTTGCTTCACTGGTCCAGTCTGCAAATACAAGCTTT
EST: gi|88730224|gb|CI753839.1|CI753839
EST:     AGGCCCTTATTTTGATCAGGAGTGCTCTCTTGCAAGGGCAGGCACTACAG                         GCACTGCAGAGATTTTTTGCTTCACTGGTC
genomic: AGGCCCTTATTTTGATCAGGAGTGCTCTCTTGCAAGGGCAGGCACTACAGgtattttttt ... actgccacagGCACTGCAGAGATTTTTTGCTTCACTGGTC

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: 51 (upstream exon), 75 (downstream exon)
Score: 33

AAAATCCATCCAAAATGTTGGTCTTGCAGTGAGGTACAAGGTTTTGCCCCAGGCCCTTATTTTGATCAGGAGTGCTCTCTTGCAAGGGCAGGCACTACAGgtattttttt ... actgccacagGCACTGCAGAGATTTTTTGCTTCACTGGTCCAGTCTGCAAATACAAGCTTTGACACTTTGTTGGATTCTCTTATTTCTACTGCTAAACCATCGCAGTCAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgatttcttcttaagttgcatgttgacactaacatgggatgttactgccacagGCACTGCAGAGATTTTTTGCTTCACTGGTCCAGTCTGCAAATACAAGCTTTGACACTTTGTTGGATTCTCTTATTTCTACTGCTAAACCATCGCAGTCAG
                            cactaac  putative branch site (score: 33)
         ttcttaa  TA-rich tract