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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAAATGGAACACTGGTGAAAAAATTGGTGAAAGGgtcagaactgatctctctctctctctctctctctctcgtgtaaattctgtggattatgtcctaacatatcatgtcaacatttttgcag

Basic information

species Oryza sativa
transcript LOC_Os01g67220.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g67220.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G044092_T01 (Zea mays), 5'ss of exon 10
AAAAATGGAACACTGGTGAAAAAATTGGTGAAAGGgtcagaactgatctctctctctctctctctctctctcgtgtaaattctgtggattatgtcctaacatatcatgtcaacatttttgcag
|||||||||| | |||||||||||||||||||||||||||||     | ||     ||| ||||  |     ||||||||| | ||| || | ||||||||||   | |||| |||| |||||
AAAAATGGAATAGTGGTGAAAAAATTGGTGAAAGGgtcagaatgctgcactgaacttctttctccgt-----gtgtaaattatctgg-ttctctcctaacatactgtctcaa-atttgtgcag
















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|25806962|gb|CA762923.1|CA762923
EST:     AAAAATGGAACACCGGGTGAAAAAATTGGTGAAAGG                         GCCGCATTTGAGTGGCTTTTCATAGTTCCTTGGGGCCTCCGGAAATTACTT
genomic: AAAAATGGAACA-CTGGTGAAAAAATTGGTGAAAGGgtcagaactg ... atttttgcagGCCGCATCTGAGTGGCTTTTCATAGTTCCTTGGGGCCTCCGGAAATTACTT
EST: gi|88591557|gb|CI709596.1|CI709596
EST:     AAAAATGGAACACTGGTGAAAAAATTGGTGAAAGG                         GCCGCATCTGAGTGGCTTTTCATAGTTCCTTGGGGCCTCCGGAAATTACTT
genomic: AAAAATGGAACACTGGTGAAAAAATTGGTGAAAGGgtcagaactg ... atttttgcagGCCGCATCTGAGTGGCTTTTCATAGTTCCTTGGGGCCTCCGGAAATTACTT
EST: gi|396941166|gb|HO188375.1|HO188375
EST:     AAAAATGGAACACCGGTGAAAAAATTGGTGAAAGG                         GCCGCATCTGAGTGGCTTTTCATAGTTCCTTGGGGCCTCCGGAAATTACTT
genomic: AAAAATGGAACACTGGTGAAAAAATTGGTGAAAGGgtcagaactg ... atttttgcagGCCGCATCTGAGTGGCTTTTCATAGTTCCTTGGGGCCTCCGGAAATTACTT

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: 35 (upstream exon), 75 (downstream exon)
Score: 33

AAAAATGGAACACTGGTGAAAAAATTGGTGAAAGGgtcagaactg ... atttttgcagGCCGCATCTGAGTGGCTTTTCATAGTTCCTTGGGGCCTCCGGAAATTACTTAATTATGCAGCAAAGAGATATGGAAATCCTGTGATATATGTAACTGAGA




<











<


<