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'   		29  
 5'  3'   		30  
 5'  3'   		31  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCCAAGAAAGGGATGCTTTTTATTGACTTCCCTCCAGTCCTGCAAGTTCAATTAAAGCGGTTTGAATATGATTTTGTGCGGGATACCATGGTTAAGgtctgaaattcactctatattttctctggcttgtttctagatttcatctatgatttatccttttcattgtggcgcttgctaatatttaacataggctaca...

Basic information

species Oryza sativa
transcript LOC_Os01g56490.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56490.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA20G11330.1 (Glycine max), 5'ss of exon 1
-GATGCCAAGAAAGGGATGCTTTTTATTGACTTCCCTCCAGTCCTGCAAGTTCAATTAAAGCGGTTTGAATATGATTTTGTGCGGGATACCATGGTTAAGgtctgaaattcactctata---ttttctctggcttgtttctagatttcatctatgatttatccttttcattgtggcgcttgctaatatttaacataggctaca
 ||||| ||||||||  | || |||||||| || ||||| ||||| ||| | ||  ||||  | ||||||||||| ||| |||||||||| |||||||||||  |   | || |  |||   || | | || ||| | |  | ||||  |  |   ||  | | | ||  | | |    |   ||| |||| ||   | |   
GGATGCTAAGAAAGGTGTCCTATTTATTGATTTTCCTCCTGTCCTTCAACTCCAGCTAAAAAGATTTGAATATGACTTTATGCGGGATACTATGGTTAAGgttggctgtccaatggataaatttctttatgccttatcttgatatttgtttgacagttagtacctatctatttaggttgtagaaat-tttaccacttgatg--

upper sequence: LOC_Os01g56490.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 5'ss of exon 9
GATGCCAAGAAAGGGATGCTTTTTATTGACTTCCCTCCAGTCCTGCAAGTTCAATTAAAGCGGTTTGAATATGATTTTGTGCGGGATACCATGGTTAAGgtctgaaattcactctatattttctctggcttgtttctagatttcatctatgatttatccttttcattg--tggcg-cttgctaatatttaacataggctaca-
||||| | ||| ||  |  | || |||||||||||||| ||||| ||| ||||  | ||||| ||||||||||||||| ||||||| || ||||| |||||| | | |  | |    |   |  |||   | || | |  | || | ||| |||  | | |  |||    ||||  ||| || || ||| | | | | |  | 
GATGCTAGGAAGGGTGTCTTATTCATTGACTTCCCTCCTGTCCTTCAACTTCAGCTGAAGCGATTTGAATATGATTTTATGCGGGACACTATGGTAAAGgtcagcagtctaata---accgttcctgctctattacaaagtgtcctatatcattggtgcatcgcatgaattggcttctttcttat-tttcatacaaggtgtaa

upper sequence: LOC_Os01g56490.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 5'ss of exon 9
GATGCCAAGAAAGGGATGCTTTTTATTGACTTCCCTCCAGTCCTGCAAGTTCAATTAAAGCGGTTTGAATATGATTTTGTGCGGGATACCATGGTTAAGgtctgaaattc-actctatattttctctggcttgtttctagatttcatctatgatttatccttttcattgtggcgcttgctaatatttaacataggctaca
||||| ||||| ||  |  | |||||||||||||| ||||| || ||| ||||  ||||||||||||| ||||| ||  ||||||| || ||||| |||||| | | |   |   | | ||| ||    | || ||   | |      | || || |   ||||  ||||  | ||||    |  |||  || |  |   
GATGCTAAGAAGGGTGTCTTATTTATTGACTTCCCACCAGTTCTTCAACTTCAGCTAAAGCGGTTTGAGTATGACTTCATGCGGGACACTATGGTGAAGgtcagtactaggaaattctctttgcttcatcatgattagtgttacatggtttggttgaatgttttgcttgtctc-cttgtatttcattagtattgattgtg

upper sequence: LOC_Os01g56490.1 (Oryza sativa), 5'ss of exon 9
lower sequence: PP1S104_2V6.1 (Physcomitrella patens), 5'ss of exon 8
-GATGCCAAGAAAGGGATGCTTTTTATTGACTTCCCTCCAGTCCTGCAAGTTCAATTAAAGCGGTTTGAATATGATTTTGTGCGGGATACCATGGTTAAGgtctga--aattcactctatattttctctggcttgtttctagatttcatctatgatttatccttttcattgtggcg--cttgctaatatttaacataggctaca--
 ||||||||||||||| | ||||| ||||| |||||||||||||| ||  | || || || || ||||| || || |   |||| || |  ||||| |||||  |     || |  ||    | | || ||| || ||  |     || ||||   |||     |  |      |   ||| | |||  ||  ||       ||  
GGATGCCAAGAAAGGGGTTCTTTTCATTGATTTCCCTCCAGTCCTTCAGTTGCAGTTGAAACGTTTTGAGTACGACTACATGCGAGACAGTATGGTCAAGgtaggcctggtttatactgcgctgtatc-ggcatgcttgaa-----cagctatacgttaagaagtcaaaaactaccttctttcaaatgattgccacctatagcact

upper sequence: LOC_Os01g56490.1 (Oryza sativa), 5'ss of exon 9
lower sequence: EFJ18164 (Selaginella moellendorffii), 5'ss of exon 7
GATGCCAAGAAAGGGATGCTTTTTATTGACTTCCCTCCAGTCCTGCAAGTTCAATTAAAGCGGTTTGAATATGATTTTGTGCGGGATACCATGGTTAAGgtctgaaattca-ctctatattttctctggcttgtttctagatttcatctat--gatttatccttttcattgtggcgcttgctaatatttaacataggctaca
|||||    || ||  |||| ||| | || || || || || || ||  ||||| | |||||||||||||||||||||||||| || || |||||||||||   |  || | ||   |  | |   ||| | ||| |||| || |||  |    ||||   || || ||||   |  |  |||||  |      ||      
GATGCACGCAAGGGCGTGCTCTTTGTGGATTTTCCCCCTGTTCTCCAGCTTCAACTCAAGCGGTTTGAATATGATTTTGTGCGAGACACAATGGTTAAGgtaatagcttgaactacgttgtgttggtggatggttcctag-ttccattcactgaatttgggctgtttattg-aacagtgcctaattatgctggcag------

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|89163644|gb|CI100534.1|CI100534
EST:     GGTTTGAATATGATTTTGTGCGGGATACCATGGTTAAG                         ATAAATGACCGCTATGAGTTCCCATTACAATTAGATCTTGACAAGGATGAT
genomic: GGTTTGAATATGATTTTGTGCGGGATACCATGGTTAAGgtctgaaatt ... gacaatgtagATAAATGACCGCTATGAGTTCCCATTACAATTAGATCTTGACAAGGATGAT
EST: gi|88223226|gb|CI223075.1|CI223075
EST:     TTCAATTAAAGCGGTTTGAATATGATTTTGTGCGGGATACCATGGTTAAG                         ATAAATGACCGCTATGAGTTCCCATTACAATTAGATCTTGACAAGGATGAT
genomic: TTCAATTAAAGCGGTTTGAATATGATTTTGTGCGGGATACCATGGTTAAGgtctgaaatt ... gacaatgtagATAAATGACCGCTATGAGTTCCCATTACAATTAGATCTTGACAAGGATGAT
EST: gi|29639377|gb|CB644386.1|CB644386
EST:     TTCAATTAAAGCGGTTTGAATATGATTTTGTGCGGGATACCATGGTTAAG                         ATAAATGACCGCTATGAGTTCCCATTACAATTAGATCTTGACAAGGATGAT
genomic: TTCAATTAAAGCGGTTTGAATATGATTTTGTGCGGGATACCATGGTTAAGgtctgaaatt ... gacaatgtagATAAATGACCGCTATGAGTTCCCATTACAATTAGATCTTGACAAGGATGAT
EST: gi|8955595|gb|BE229401.1|BE229401
EST:     -TCAATTAAAGCGGTTTGAATATGATTTTGTGCCGGRDAMCATGGTTAAG                         ATAAATGACCSCTATGAGTTCCCATTACAATTAGATCTTGACAAGGATGAT
genomic: TTCAATTAAAGCGGTTTGAATATGATTTTGTGCGGGATACCATGGTTAAGgtctgaaatt ... gacaatgtagATAAATGACCGCTATGAGTTCCCATTACAATTAGATCTTGACAAGGATGAT
EST: gi|86260523|gb|CI066396.1|CI066396
EST:     TTCAATTAAAGCGGTTTGAATATGATTTTGTGCGGGATACCATGGTTAAG                         ATAAATGACCGCTATGAGTTCCCATTACAATTAGATCTTGACAAGGATGAT
genomic: TTCAATTAAAGCGGTTTGAATATGATTTTGTGCGGGATACCATGGTTAAGgtctgaaatt ... gacaatgtagATAAATGACCGCTATGAGTTCCCATTACAATTAGATCTTGACAAGGATGAT
EST: gi|86504086|gb|CI146719.1|CI146719
EST:     TTCAATTAAAGCGGTTTGAATATGATTTTGTGCGGGATACCATGGTTAAG                         ATAAATGACCGCTATGAGTTCCCATTACAATTAGATCTTGACAAGGATGAT
genomic: TTCAATTAAAGCGGTTTGAATATGATTTTGTGCGGGATACCATGGTTAAGgtctgaaatt ... gacaatgtagATAAATGACCGCTATGAGTTCCCATTACAATTAGATCTTGACAAGGATGAT

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: 67 (upstream exon), 74 (downstream exon)
Score: 7

GATGCCAAGAAAGGGATGCTTTTTATTGACTTCCCTCCAGTCCTGCAAGTTCAATTAAAGCGGTTTGAATATGATTTTGTGCGGGATACCATGGTTAAGgtctgaaatt ... gacaatgtagATAAATGACCGCTATGAGTTCCCATTACAATTAGATCTTGACAAGGATGATGGAAAATACCTCTCTCCAGAAGCTGACAGGAGGGTGCGTAACCTCTATA




<











<


<