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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTAAGCAGTTGGCTGAAAAGGCACGTGCTGGGAAGCTTGCTCCTAATGAATTTCAGGGAGGGACTTTCAGgcatgtgatattttacccttttgtcattgcttttgggaaatcctgtactgctgttgatatttgaatgttttgacattgcttctgcag

Basic information

species Oryza sativa
transcript LOC_Os06g30460.4
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g30460.4 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G082664_T01 (Zea mays), 5'ss of exon 16
GTTAAGCAGTTGGCTGAAAAGGCACGTGCTGGGAAGCTTGCTCCTAATGAATTTCAGGGAGGGACTTTCAGgcatgtgatattttacccttttgtcattgcttttgggaaatcctgtactgctgttga-------tatttgaatgttttgaca--ttg--cttctgcag
||||||||| |||||||||||||| | |||||||||||||| ||||| |||||||| || || ||||||||||| |  |  || | ||  |||  ||||| | ||  |  |     | ||    ||||       ||||| ||  |||| |    |||  ||| |||||
GTTAAGCAGCTGGCTGAAAAGGCAAGAGCTGGGAAGCTTGCACCTAACGAATTTCAAGGGGGAACTTTCAGgcaagcaac-ttgtgcctgtttaccattgttcttcagggagttctttctatcattgaaattctatattttaacattttaatgatttgttcttatgcag

upper sequence: LOC_Os06g30460.4 (Oryza sativa), 5'ss of exon 14
lower sequence: Vv13s0074g00150.t01 (Vitis vinifera), 5'ss of exon 19
GTTAAGCAGTTGGCTGAAAAGGCACGTGCTGGGAAGCTTGCTCCTAATGAATTTCAGGGAGGGACTTTCAGgca----tgtgatattttacccttttgtcattgcttttgggaaatcctgt-----actgctgttgatatttgaatgttttgacattgcttctgcag
|| ||  | || |||||||||||||| || |||||||||   || ||||||||||| ||||| |||||||||      |||  |||  | ||  | ||  | |  |  | |    |  |||      | ||  |    ||||   | ||||   ||  ||| | |||
GTCAAAGAATTAGCTGAAAAGGCACGAGCAGGGAAGCTTAAGCCCAATGAATTTCAAGGAGGAACTTTCAGgtgaatgtgtcttataattccagtatgatactattacttgtgtcttttgttaaaagcagccatcataattttttttttttttaat--cttatacag
















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|58692196|gb|CK080883.1|CK080883
EST:     GCACGTGCTGGGAAGCTTGCTCCTAATGAATTTCAGGGAGGGACTTTCAG                         CATCTCAAATTTGGGAATGTACCCAGTCGACCACTTCTGTGCAATCATCAA
genomic: GCACGTGCTGGGAAGCTTGCTCCTAATGAATTTCAGGGAGGGACTTTCAGgcatgtgata ... gcttctgcagCATCTCAAATTTGGGAATGTACCCAGTCGACCACTTCTGTGCAATCATCAA
EST: gi|88849307|gb|CI087829.1|CI087829
EST:     GCACGTGCTGGGAAGCTTGCTCCTAATGAATTTCAGGGAGGGACTTTCAG                         CATCTCAAATTTGGGAATGTACCCAGTCGACCACTTCTGTGCAATCATCAA
genomic: GCACGTGCTGGGAAGCTTGCTCCTAATGAATTTCAGGGAGGGACTTTCAGgcatgtgata ... gcttctgcagCATCTCAAATTTGGGAATGTACCCAGTCGACCACTTCTGTGCAATCATCAA
EST: gi|218482631|gb|FG947596.1|FG947596
EST:     GCACGTGCTGGGAAGCTTGCTCCTAATGAATTTCAGGGAGGGACTTTCAG                         CATCTCAAATTTGGGAATGTACCCAGTCGACCACTTCTGTGCAATCATCAA
genomic: GCACGTGCTGGGAAGCTTGCTCCTAATGAATTTCAGGGAGGGACTTTCAGgcatgtgata ... gcttctgcagCATCTCAAATTTGGGAATGTACCCAGTCGACCACTTCTGTGCAATCATCAA

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: 45 (upstream exon), 50 (downstream exon)
Score: 35

GTTAAGCAGTTGGCTGAAAAGGCACGTGCTGGGAAGCTTGCTCCTAATGAATTTCAGGGAGGGACTTTCAGgcatgtgata ... gcttctgcagCATCTCAAATTTGGGAATGTACCCAGTCGACCACTTCTGTGCAATCATCAATCCTCCTCAG




<











<


<