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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcctaagcttgatttagattttttactacaattggttacatgtagcttgatgctaacggtgagctgcatgaattactttagGTGGATTCATCTGTTGGAGGGAAGACCGGCATTAACCATCCATTGGGGAAGAACTTAATTGGGGCGTTCTACCAGCCACAGTGTGTACTGATAGACACCG

Basic information

species Oryza sativa
transcript LOC_Os09g36800.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g36800.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G573867_T01 (Zea mays), 3'ss of exon 3
gtcctaagcttgatttagattttttactacaattgg-ttacatgtagcttgatgctaacggtga-gctgcatgaat---tactttagGTGGATTCATCTGTTGGAGGGAAGACCGGCATTAACCATCCATTGGGGAAGAACTTAATTGGGGCGTTCTACCAGCCACAGTGTGTACTGATAGACACCG
||| || |||||||||   |  || |||| | |||| |||||| ||  | | | ||     ||| | |||  | ||   | ||||||||||||||||||||||| ||||| || || |||||||| ||| | ||||||||||| ||||| || |||||||||||||| ||||| || || ||||| |
gtcatatgcttgatttg--tggttcactaaagttgggttacatatatataggt-ctggttctgatgttgctcggatgactgctttagGTGGATTCATCTGTTGGCGGGAAAACTGGGATTAACCACCCACTAGGGAAGAACTTGATTGGAGCATTCTACCAGCCACAATGTGTTCTAATTGACACAG

upper sequence: LOC_Os09g36800.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G051129_T01 (Zea mays), 3'ss of exon 2
gtcctaagcttgatttagattttttactacaattggtt-acatgtag-cttgatgctaacggtgagctgcatgaattactttagGTGGATTCATCTGTTGGAGGGAAGACCGGCATTAACCATCCATTGGGGAAGAACTTAATTGGGGCGTTCTACCAGCCACAGTGTGTACTGATAGACACCG
||| |||||||||||||   |  |  ||| | |||||| |||| |||  ||| | || | | ||  | | ||||  | ||||||||||||||||||||||| ||||| ||||| |||||||| ||| | || |||||||| |||||||| || ||||||||||| ||||| || || |||||  
gtcataagcttgattta---tggtccctaaagttggtttacatataggtttggttctgatgttgctc-ggatga-ctgctttagGTGGATTCATCTGTTGGTGGGAAAACCGGGATTAACCACCCACTAGGAAAGAACTTGATTGGGGCATTTTACCAGCCACAATGTGTTCTAATTGACACAA

upper sequence: LOC_Os09g36800.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv04s0023g03820.t01 (Vitis vinifera), 3'ss of exon 3
--------gtcctaagcttgatttag-attttttactacaattgg---ttacatgtagcttgat---gctaacggtgagctgcatgaattacttt---agGTGGATTCATCTGTTGGAGGGAAGACCGGCATTAACCATCCATTGGGGAAGAACTTAATTGGGGCGTTCTACCAGCCACAGTGTGTACTGATAGACACCG
          |  || ||   ||||  ||| |||  || | ||||   |||  |  |  || |    |||   |   |  |   |   ||  |||   |||||||||| || |||||||| || || ||||| ||||||||  | || || || || ||||| || |||||||| || ||||||||||| |||||||| |
aaaaaaaaaccaaaaactaactttaatattcttttttaaacttggcacttatgttgaatttcagctggcttctgaaaaaataactattttttttttctagGTGGATTCTTCAGTTGGAGGCAAAACTGGCATAAACCATCCTCTAGGAAAAAATTTGATTGGTGCTTTCTACCAACCTCAGTGTGTACTTATAGACACTG

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|11026098|gb|AU162699.1|AU162699
EST:     TCCTGCGTGGTGTCAATTTCATACAGATTCCTACTACTCTGATGGCCCAG                         GTGGATTCATCTGTTGGAGGGAAGACCGGCATTAACCATCCATTGGGGAAG
genomic: TCCTGCGTGGTGTCAATTTCATACAGATTCCTACTACTCTGATGGCCCAGgtcctaagct ... attactttagGTGGATTCATCTGTTGGAGGGAAGACCGGCATTAACCATCCATTGGGGAAG
EST: gi|58613221|gb|CK040933.1|CK040933
EST:     TCCTGCGTGGTGTCAATTTCATACAGATTCCTACTACTCTGATGGCCCAG                         GTGGATTCATCTGTTGGAGGGAAGACCGGCATTAACCATCCATTGGGGAAG
genomic: TCCTGCGTGGTGTCAATTTCATACAGATTCCTACTACTCTGATGGCCCAGgtcctaagct ... attactttagGTGGATTCATCTGTTGGAGGGAAGACCGGCATTAACCATCCATTGGGGAAG
EST: gi|25798307|gb|CA754268.1|CA754268
EST:     TCCTGCGTGGTGTCAATTTCATACAGATTCCTACTACTCTGATGGCCCAG                         GTGGATTCATCTGTTGGAGGGAAGACCGGCATTAACCATCCATTGGGGAAG
genomic: TCCTGCGTGGTGTCAATTTCATACAGATTCCTACTACTCTGATGGCCCAGgtcctaagct ... attactttagGTGGATTCATCTGTTGGAGGGAAGACCGGCATTAACCATCCATTGGGGAAG
EST: gi|58602132|gb|CK012660.1|CK012660
EST:     TCCTGCGTGGTGTCAATTTCATACAGATTCCTACTACTCTGATGGCCCAG                         GTGGATTCATCTGTTGGAGGGAAGACCGGCATTAACCATCCATTGGGGAAG
genomic: TCCTGCGTGGTGTCAATTTCATACAGATTCCTACTACTCTGATGGCCCAGgtcctaagct ... attactttagGTGGATTCATCTGTTGGAGGGAAGACCGGCATTAACCATCCATTGGGGAAG
EST: gi|218479549|gb|FG949471.1|FG949471
EST:     TCCTGCGTGGTGTCAATTTCATACAGATTCCTACTACTCTGATGGCCCAG                         GTGGATTCATCTGTTGGAGGGAAGACCGGCATTAACCATCCATTGGGGAAG
genomic: TCCTGCGTGGTGTCAATTTCATACAGATTCCTACTACTCTGATGGCCCAGgtcctaagct ... attactttagGTGGATTCATCTGTTGGAGGGAAGACCGGCATTAACCATCCATTGGGGAAG
EST: gi|218496360|gb|FG958514.1|FG958514
EST:     TCCTGCGTGGTGTCAATTTCATACAGATTCCTACTACTCTGATGGCCCAG                         GTGGATTCATCTGTTGGAGGGAAGACCGGCATTAACCATCCATTGGGGAAG
genomic: TCCTGCGTGGTGTCAATTTCATACAGATTCCTACTACTCTGATGGCCCAGgtcctaagct ... attactttagGTGGATTCATCTGTTGGAGGGAAGACCGGCATTAACCATCCATTGGGGAAG

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: 60 (upstream exon), 75 (downstream exon)
Score: 45

GTTGGGAGGTGGCGTTATTGGGGACATGTGCGGTTTTGCAGCTGCTGCGTTCCTGCGTGGTGTCAATTTCATACAGATTCCTACTACTCTGATGGCCCAGgtcctaagct ... attactttagGTGGATTCATCTGTTGGAGGGAAGACCGGCATTAACCATCCATTGGGGAAGAACTTAATTGGGGCGTTCTACCAGCCACAGTGTGTACTGATAGACACCG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacaattggttacatgtagcttgatgctaacggtgagctgcatgaattactttagGTGGATTCATCTGTTGGAGGGAAGACCGGCATTAACCATCCATTGGGGAAGAACTTAATTGGGGCGTTCTACCAGCCACAGTGTGTACTGATAGACACCG
                        tgctaac  putative branch site (score: 45)
                                              ttacttt  putative PPT
                                            aattacttta  TA-rich tract