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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGCTCATGGAACAGCTGTTGGTCTCCCTTCTGATGATGACATGGGTAACAGTGAGGTTGGGCATAACGCACTTGGTGCTGGTCGGATTTTTGCTCAAGGgtacatgtttctcctggttctcttttttattagcacactgtcagttataatctgtggatggccaaaaagtattgcgtttgtttctaaaggtcttattaca...

Basic information

species Oryza sativa
transcript LOC_Os05g40420.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g40420.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA09G40690.1 (Glycine max), 5'ss of exon 2
AGGCTCATGGAACAGCTGTTGGTCTCCCTTCTGATGATGACATGGGTAACAGTGAGGTTGGGCATAACGCACTTGGTGCTGGTCGGATTTTTGCTCAAGGgtacatgtttctcctggttctcttttttattagcacactgtcag--ttataatctgtggatggccaaaaagtattgcgtttgtttctaaaggtcttattaca
 ||||||||| || ||||| || || ||  | || |||||||||||||| ||||| ||||| || || || ||||| |||||||| || |||||||| ||||| |  |    |  |  ||||||||| ||           ||   ||||  |      | ||    ||| | | |      |  ||   | | |    | |
GGGCTCATGGTACCGCTGTAGGCCTTCCAACAGAAGATGACATGGGTAATAGTGAAGTTGGTCACAATGCTCTTGGGGCTGGTCGCATATTTGCTCAGGGgtaaac-taaaactagcctctctttttcatctatttggccccatgcttatgttactaccaaggttttaaattgtggt-cgcatggctgtcgatttagggata

upper sequence: LOC_Os05g40420.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv08s0056g00200.t01 (Vitis vinifera), 5'ss of exon 2
AGGCTCATGGAACAGCTGTTGGTCTCCCTTCTGATGATGACATGGGTAACAGTGAGGTTGGGCATAACGCACTTGGTGCTGGTCGGATTTTTGCTCAAGGgtacatgtttctcctggttctcttttttattagcacactgtca---gttataatctgtggatggccaaaaagtat-tgcgtttgtttctaaaggtcttattaca
|||||||||| |  || || || || ||  |||| ||||||||||| |||||||| ||||| ||||| || ||||||||||| || || | |||||||||||  || | ||| |  | | |  ||| | |||  | | | | |    |||||| || |  |   |||  | ||   | |    ||||    |   ||| ||   
AGGCTCATGGGAGTGCAGTAGGGCTTCCAACTGAGGATGACATGGGCAACAGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATATGCTCAAGGgtgaatttctcttcctgattttatttcttttatgaaatttttacatattataacctttatacacccaggatgtcccttcacaagttt---gattcctttttga-

upper sequence: LOC_Os05g40420.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S145_164V6.2 (Physcomitrella patens), 5'ss of exon 3
AGGCTCATGGAACAGCTGTTGGTCTCCCTTCTGATGATGACATGGGTAACAGTGAGGTTGGGCATAACGCACTTGGTGCTGGTCGGATTTTTGCTCAAGGgta---catgtttctcctggttctcttttttattagcacactgtcagttataatctgtggatggccaaaaagtattgcgtttgtttctaaaggtcttattaca
| || |||||| | || || || || ||| | || || ||||||||||||||||||||||| ||||| ||  | ||||| || || ||||||   ||||||||   |||| |  ||  |    ||   | | ||||    |  |||    |    | | ||  | |||    | | |   | ||| || |  ||    |    
AAGCCCATGGAGCTGCGGTAGGGCTACCTACGGAGGAGGACATGGGTAACAGTGAGGTTGGCCATAATGCTTTGGGTGCAGGCCGCATTTTTAAGCAAGGgtatgtcatgctggtctagtaaatcagatatcttagt-ttccatcatgggtgcgatatcga--gacaatggctttggtaatcgttgctcactgtaggctagtt

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|12622776|gb|AU172989.1|AU172989
EST:     AGTGAGGTTGGGCATAACGCACTTGGTGCTGGTCGGATTTTTGCTCAAGG                         GGCTAAACTTGTGGATACTGCTTTGGCCTCTGGAAAAATTTTTGAAGGAGA
genomic: AGTGAGGTTGGGCATAACGCACTTGGTGCTGGTCGGATTTTTGCTCAAGGgtacatgttt ... tcttttgtagGGCTAAACTTGTGGATACTGCTTTGGCCTCTGGAAAAATTTTTGAAGGAGA
EST: gi|66920720|gb|CX107568.1|CX107568
EST:     AGTGAGGTTGGGCATAACGCACTTGGTGCTGGTCGGATTTTTGCTCAAGG                         GGCTAAACTTGTGGATACTGCTTTGGCCTCTGGA
genomic: AGTGAGGTTGGGCATAACGCACTTGGTGCTGGTCGGATTTTTGCTCAAGGgtacatgttt ... tcttttgtagGGCTAAACTTGTGGATACTGCTTTGGCCTCTGGA

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: 73 (upstream exon), 69 (downstream exon)
Score: 58

AGGCTCATGGAACAGCTGTTGGTCTCCCTTCTGATGATGACATGGGTAACAGTGAGGTTGGGCATAACGCACTTGGTGCTGGTCGGATTTTTGCTCAAGGgtacatgttt ... tcttttgtagGGCTAAACTTGTGGATACTGCTTTGGCCTCTGGAAAAATTTTTGAAGGAGAAGGGTTTAAGTACATTAAGGAGAGTTTTGACCAAGGCACTCTTCATCTT




<











<


<