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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTCAATGCTCTGGGCAGAAGGGAGGAGTGAATGGATGCCATTGTCGTCGATTCCTGACCTACTTGCGGTGGTCACAAAAAAGGATCAACCTGATGAAGgttactgatttctaccttctgttttaaggaaataatacagaatacacttcacgtgatctcctgacattttctttaatctttctgatgccccag

Basic information

species Oryza sativa
transcript LOC_Os04g41910.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g41910.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G171660_T03 (Zea mays), 5'ss of exon 2
AGCTCAATGCTCTGGGCAGAAGGGAGGAGTGAATGGATGCCATTGTCGTCGATTCCTGACCTACTTGCGGTGGTCACAAAAAAGGATCAACCTGATGAAGgttactgatttctaccttctgttttaaggaaataatacagaatacacttcacgtgatctcctgacattttctttaatctttctgatgccccag
||| ||||||||||||||||||||||||  |||||||||||| | ||||| ||  |||| ||||   | |  ||| ||   ||||||||| ||||  |||||||    || || |||  |||  |  |    ||||  | |      |      | | | ||     ||   | ||  | | ||  |      
AGCACAATGCTCTGGGCAGAAGGGAGGAAGGAATGGATGCCACTCTCGTCCATCTCTGAGCTACACTCCGCAGTCGCAGCGAAGGATCAATCTGAACAAGgttaaatgttgctgcct--tgtactgtgcctgtaatggaaa-----ttctgtaaggttttcttctcattcactgaacttctgtgcag------
















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|88393636|gb|CI619928.1|CI619928
EST:     GATTCCTGACCTACTTGCGGTGGTCACAAAAAAGGATCAACCTGATGAAG                         GAATTGAAGATGATTTCG
genomic: GATTCCTGACCTACTTGCGGTGGTCACAAAAAAGGATCAACCTGATGAAGgttactgatt ... gatgccccagGAATTGAAGATGATTTCG
EST: gi|29636733|gb|CB641742.1|CB641742
EST:     GATTCCTGACCTACTTGCGGTGGTCACAAAAAAGGATCAACCTGATGAAG                         GAATTGAAGATGATTTCGATAAATTTCAAAAGGAGGTTATAGAAGCTGAGG
genomic: GATTCCTGACCTACTTGCGGTGGTCACAAAAAAGGATCAACCTGATGAAGgttactgatt ... gatgccccagGAATTGAAGATGATTTCGATAAATTTCAAAAGGAGGTTATAGAAGCTGAGG
EST: gi|88347690|gb|CI655043.1|CI655043
EST:     ATCCCTGACCTACCTGCGGTGGTCACAAAAAAGGATCAACCCTGATGAAG                         GAATTGAAGATGATTTCGATAAATTTCAAAAGGAGGTTATAGAAGCT
genomic: ATTCCTGACCTACTTGCGGTGGTCACAAAAAAGGATCAACC-TGATGAAGgttactgatt ... gatgccccagGAATTGAAGATGATTTCGATAAATTTCAAAAGGAGGTTATAGAAGCT
EST: gi|86903824|gb|CI302470.1|CI302470
EST:     GATTCCTGACCTACTTGCGGTGGTCACAAAAAAGGATCAACCTGATGAAG                         GAATTGAAGATGATTTCGATCAATTTCACAAGGAGGTTATAGAAGCTGAGG
genomic: GATTCCTGACCTACTTGCGGTGGTCACAAAAAAGGATCAACCTGATGAAGgttactgatt ... gatgccccagGAATTGAAGATGATTTCGATAAATTTCAAAAGGAGGTTATAGAAGCTGAGG
EST: gi|29676260|gb|CB672535.1|CB672535
EST:     GATTCCTGACCTACTTGCGGTGGTCACAAAAAAGGATCAACCTGATGAAG                         GAATTGAAGATGATTTCGATAAATTTCAAAAGGAGGTTATAGAAGCTGAGG
genomic: GATTCCTGACCTACTTGCGGTGGTCACAAAAAAGGATCAACCTGATGAAGgttactgatt ... gatgccccagGAATTGAAGATGATTTCGATAAATTTCAAAAGGAGGTTATAGAAGCTGAGG

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: 56 (upstream exon), 68 (downstream exon)
Score: 13

AGCTCAATGCTCTGGGCAGAAGGGAGGAGTGAATGGATGCCATTGTCGTCGATTCCTGACCTACTTGCGGTGGTCACAAAAAAGGATCAACCTGATGAAGgttactgatt ... gatgccccagGAATTGAAGATGATTTCGATAAATTTCAAAAGGAGGTTATAGAAGCTGAGGCAGAGGTGGAAGCCTCGACAGACAAGGCTGCAGATAACGACATAAACCA




<











<


<