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'   		18  
 5'  3'   		19  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTGAAATAGCAATAACTAAGTTGCTACTGAAGTCATATTACAATATAGTGCGGAAAAATGTTGAGGACTTCGTTCCAAAGGCAATCATGCATTTTCTGgtccgtgatcgttgtctcacttttctcattattactcgctttgcataggatggtgatttatttggcacattatttcgattataactaatgtttctggaca...

Basic information

species Oryza sativa
transcript LOC_Os01g69130.2
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g69130.2 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G180335_T03 (Zea mays), 5'ss of exon 9
GCTTGAAATAGCAATAACTAAGTTGCTACTGAAGTCATATTACAATATAGTGCGGAAAAATGTTGAGGACTTCGTTCCAAAGGCAATCATGCATTTTCTGgtccgtgatcgttgtctcacttttctcattat-tactcgctttgcataggatggtgatttatttggcacattatttcg-attataa-ctaatgtttctggaca
 |||||||||||||| || ||||||||| ||||||||||||||||||| ||  |||||||||| ||||||||| | ||||| ||||| |||||||| |||||  | ||   |  | ||   ||   | |||| | | |  |     |  |   |  ||   | ||  || ||   | | ||  ||  || |  | || |    
ACTTGAAATAGCAATTACAAAGTTGCTATTGAAGTCATATTACAATATTGTCAGGAAAAATGTGGAGGACTTCATACCAAAAGCAATTATGCATTTCCTGgtatgagagattcttatccaattgtcctttatgtgcgcattccatctctgtatgcaatccttgtgctacttttaatggcatggtaggcttagatgtcagt---

upper sequence: LOC_Os01g69130.2 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G129155_T01 (Zea mays), 5'ss of exon 17
GCTTGAAATAGCAATAACTAAGTTGCTACTGAAGTCATATTACAATATAGTGCGGAAAAATGTTGAGGACTTCGTTCCAAAGGCAATCATGCATTTTCTGgtccgtgatcgttgtctcacttttctcattattactcgctttgcataggatggtgatttatttggcacattatttcgattataactaatgtttctggaca-
|||||||||||| || || ||||||||| ||||||||||||||||||| ||  |||||||||| ||||||||  | ||||| ||| | ||||||||  ||||  |||||   | ||  | | | ||  |   ||  |  | |   |   ||  | | |    ||| |   | |     |     |||| | |      |  
GCTTGAAATAGCGATCACAAAGTTGCTATTGAAGTCATATTACAATATTGTCAGGAAAAATGTGGAGGACTTAATACCAAAAGCAGTTATGCATTTCTTGgtatgtgattcatatccgattgtcctt-tcggtatgcaatctttgtgctatttttaatggcatggtaggctttagatgtcggtgctaaagctaaacagcta

upper sequence: LOC_Os01g69130.2 (Oryza sativa), 5'ss of exon 17
lower sequence: AT2G14120.3 (Arabidopsis thaliana), 5'ss of exon 18
GCTTGAAATAGCAATAACTAAGTTGCTACTGAAGTCATATTACAATATAGTGCGGAAAAATGTTGAGGACTTCGTTCCAAAGGCAATCATGCATTTTCTGgtccgtgatc-gttgtctcacttttctcattattactcgctttgcataggatggtgatttatttggcacattatt--tcgattataactaatgtttctggaca--------------------------------
  |||| || |  ||||| ||| |  || |||| || || ||  | || ||  |||| ||||| |||||||| || ||||| ||||||||||||||||||||  ||| ||   | |   | | |||| ||| |  || ||    |||   ||||| ||| ||    |  | | |   |||||| |   | | |   ||    |                                
AGTTGAGATTGAGATAACAAAGCTATTATTGAAATCCTACTATGACATTGTAAGGAAGAATGTCGAGGACTTGGTCCCAAAAGCAATCATGCATTTTCTGgttagtgttccactcttctagtcttctgattgt--ctagccaaacatcttatggtcattgatgacacttagtgtgggtcgattctttgtgaggggactaataactctattccatataattgtgaataaaacacag

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|88200886|gb|CI198738.1|CI198738
EST:     TGCGGAAAAATGTTGAGGACTTCGTTCCAAAGGCAATCATGCATTTTCTG                         GTTAACCACACAAAACGGGAGCTGCATAATTACCTTATAACTAAGCTTTAT
genomic: TGCGGAAAAATGTTGAGGACTTCGTTCCAAAGGCAATCATGCATTTTCTGgtccgtgatc ... tcgcttgcagGTTAACCACACAAAACGGGAGCTGCATAATTACCTTATAACTAAGCTTTAT
EST: gi|25806989|gb|CA762950.1|CA762950
EST:     TGCGGAAAAATGTTGAGGACTTCGTTCCAAAGGCAATCATGCATNTTCTG                         GTTAACCACACAAAACGGGAGCTGCATAATTACCTTATAACTAAGCTTTAT
genomic: TGCGGAAAAATGTTGAGGACTTCGTTCCAAAGGCAATCATGCATTTTCTGgtccgtgatc ... tcgcttgcagGTTAACCACACAAAACGGGAGCTGCATAATTACCTTATAACTAAGCTTTAT
EST: gi|29625093|gb|CB630104.1|CB630104
EST:     TGCGGAAAAATGTTGAGGACTTCGTTCCAAAGGCAATCATGCATTTTCTG                         GTTAACCACACAAAACGGGAGCTGCATAATTACCTTATAACTAAGCTTTAT
genomic: TGCGGAAAAATGTTGAGGACTTCGTTCCAAAGGCAATCATGCATTTTCTGgtccgtgatc ... tcgcttgcagGTTAACCACACAAAACGGGAGCTGCATAATTACCTTATAACTAAGCTTTAT
EST: gi|58683601|gb|CK072288.1|CK072288
EST:     TGCGGAAAAATGTTGAGGACTTCGTTCCAAAGGCAATCATGCATTTTCTG                         GTTAACCACACAAAACGGGAGCTGCATAATTACCTTATAACTAAGCTTTAT
genomic: TGCGGAAAAATGTTGAGGACTTCGTTCCAAAGGCAATCATGCATTTTCTGgtccgtgatc ... tcgcttgcagGTTAACCACACAAAACGGGAGCTGCATAATTACCTTATAACTAAGCTTTAT
EST: gi|88224742|gb|CI224591.1|CI224591
EST:     TGCGGAAAAATGTTGAGGACTTCGTTCCAAAGGCAATCATGCATTTTCTG                         GTTAACCACACAAAACGGGAGCTGCATAATTACCTTATAACTAAGCTTTAT
genomic: TGCGGAAAAATGTTGAGGACTTCGTTCCAAAGGCAATCATGCATTTTCTGgtccgtgatc ... tcgcttgcagGTTAACCACACAAAACGGGAGCTGCATAATTACCTTATAACTAAGCTTTAT

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: 75 (upstream exon), 29 (downstream exon)
Score: 33

GCTTGAAATAGCAATAACTAAGTTGCTACTGAAGTCATATTACAATATAGTGCGGAAAAATGTTGAGGACTTCGTTCCAAAGGCAATCATGCATTTTCTGgtccgtgatc ... tcgcttgcagGTTAACCACACAAAACGGGAGCTGCATAATTACCTTATAACTAAGCTTTATAG




<











<


<