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

CTGCAACTATGATTGGCACAGAAGATCGGATTTTGAATAGATGGGCACAGTTTGCCAAAAATTGGGGTTTCCTCCCTCTTGTTGATTCTGGGTCTACAAAgtaattgaactttcctgttggctgctgttgtaatgccttgacttaaaatttagtctagaacattaattgatcagagaatacgggcctcatcatttgccct...

Basic information

species Oryza sativa
transcript LOC_Os02g57180.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57180.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G143651_T01 (Zea mays), 5'ss of exon 8
CTGCAACTATGATTGGCACAGAAGATCGGATTTTGAATAGATGGGCACAGTTTGCCAAAAATTGGGGTTTCCTCCCTCTTGTTGATTCTGGGTCTACAAAgtaattgaactttcctgttggctgctgttgtaatgccttgacttaaaatttagtctagaacattaattgatcagagaatacgggcctca----tcatttgccct-------------------------------
|||| || |||||||||||||||||||| ||  |||| ||||||||||| ||||| || ||||||||||||||||| ||||||| |  ||| ||||| |||||| |    || ||||||| |   | |  | |||||| ||| | ||| | |||  ||  ||| || ||| |      |       | |    |  ||||||                                 
CTGCTACCATGATTGGCACAGAAGATCGAATCCTGAACAGATGGGCACAATTTGCAAAGAATTGGGGTTTCCTCCCGCTTGTTGGTGGTGGATCTACTAAgtaagt---tttgcctgttgac---tctcctgatgcct-gacctgaaaatgagttcagggcatgaaatgacctccttttgttcatgttagaagttctttgccagcagttaaattacgtaatgttcccttttgcag

upper sequence: LOC_Os02g57180.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA13G18950.1 (Glycine max), 5'ss of exon 8
CTGCAACTATGATTGGCACAGAAGATCGGATTTTGAATAGATGGGCACAGTTTGCCAAAAATTGGGGTTTCCTCCCTCTTGTTGATTCTGGGTCTACAAAgtaattgaactttcctgttggctgctgttgtaatgccttgacttaaaatttagtctagaacattaattgatca-gagaatacgggcctcatcatttgccct--------------------------------------------
||||    |||||||| ||||| |||||||||||||||  |||||| || ||||| ||||| |  || || || ||  |  |||    ||||   ||||||||  |  |  |   | | |||   |  | | |        |||    |||  | |   ||   | |  ||   |    ||| ||      | | |  |                                              
CTGCTGTAATGATTGGTACAGAGGATCGGATTTTGAATCCATGGGCTCATTTTGCTAAAAAGTATGGCTTTCTTCCGTTGTTTGGAGATGGGAGCACAAAgtatgtataaatctat-taggcaattactatgaacttcaatctttttttttctttttttaccaaagtgaattgtgttgttactggttctgacttctttcagctttgaaattcattttttttatctgacaaatgcaattattgcag
















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|11442907|gb|BF430806.1|BF430806
EST:     TTTGCTAAAAATTGGGGTTTCCTCCCTCTTGTTGATTCTGGGTCTACAAA                         GATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCT
genomic: TTTGCCAAAAATTGGGGTTTCCTCCCTCTTGTTGATTCTGGGTCTACAAAgtaattgaac ... gtttttgcagGATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCT
EST: gi|58690755|gb|CK079442.1|CK079442
EST:     TTTGCTAAAAATTGGGGTTTCCTCCCTCTTGTTGATTCTGGGTCTACAAA                         GATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCT
genomic: TTTGCCAAAAATTGGGGTTTCCTCCCTCTTGTTGATTCTGGGTCTACAAAgtaattgaac ... gtttttgcagGATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCT
EST: gi|29673109|gb|CB669384.1|CB669384
EST:     TTTGCCAAAAATTGGGGTTTCCTCCCTCTTGTTGATTCTGGGTCTACAAA                         GATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCT
genomic: TTTGCCAAAAATTGGGGTTTCCTCCCTCTTGTTGATTCTGGGTCTACAAAgtaattgaac ... gtttttgcagGATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCT
EST: gi|29673108|gb|CB669383.1|CB669383
EST:     TTTGCCAAAAATTGGGGTTTCCTCCCTCTTGTTGATTCTGGGTCTACAAA                         GATTCAGCCTGTTTATGTTGTGGAATGT-GCTGCTGCTA
genomic: TTTGCCAAAAATTGGGGTTTCCTCCCTCTTGTTGATTCTGGGTCTACAAAgtaattgaac ... gtttttgcagGATTCAGCCTGTTTATGTTGTGGA-TGTTGCTGCTGCTA
EST: gi|29671358|gb|CB667633.1|CB667633
EST:     TTTGCCAAAAATTGGGGTTTCCTCCCTCTTGTTGATTCTGGGTCTACAAA                         GATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCT
genomic: TTTGCCAAAAATTGGGGTTTCCTCCCTCTTGTTGATTCTGGGTCTACAAAgtaattgaac ... gtttttgcagGATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCT
EST: gi|29671359|gb|CB667634.1|CB667634
EST:     TTTGCCAAAAATTGGGGTTTCCTCCCTCTTGTTGATTCTGGGTCTACAAA                         GATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCT
genomic: TTTGCCAAAAATTGGGGTTTCCTCCCTCTTGTTGATTCTGGGTCTACAAAgtaattgaac ... gtttttgcagGATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCT
EST: gi|8856604|gb|AU093922.1|AU093922
EST:     TTGGGGTTTCCNCCCCNCTTGTTGA-TCTGGGTCTAC-AA                         GATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCT
genomic: TTGGGGTTTCC-TCCCTCTTGTTGATTCTGGGTCTACAAAgtaattgaac ... gtttttgcagGATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCT
EST: gi|88730417|gb|CI754030.1|CI754030
EST:     TTGATTCTGGGTCTACAAA                         GATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCT
genomic: TTGATTCTGGGTCTACAAAgtaattgaac ... gtttttgcagGATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCT

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: 68 (upstream exon), 75 (downstream exon)
Score: 52

CTGCAACTATGATTGGCACAGAAGATCGGATTTTGAATAGATGGGCACAGTTTGCCAAAAATTGGGGTTTCCTCCCTCTTGTTGATTCTGGGTCTACAAAgtaattgaac ... gtttttgcagGATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCTCAAGGATGACGGCACCAGCATGGGAAAGACCTACGAACTTGGTGGACCA




<











<


<