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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGTGCAGCAGTTTGGAATACCTCACCTCTTCGATTTGCCGATACGGCCAACTgtaagctcaatcccacctatcttgtacaaggataaaagtgagtgcaatgatcacagtttggtataatttacag

Basic information

species Oryza sativa
transcript LOC_Os01g52170.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g52170.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G129208_T02 (Zea mays), 5'ss of exon 10
GTTGTGCAGCAGTTTGGAATACCTCACCTCTTCGATTTGCCGATACGGCCAACTgtaagctcaatc----ccacctatcttgtac-aaggataaaagtgagtgc----aatgatcacagtttggtataatttacag---------------------------------------------------------------------------------------------------------------
|||||||||||||||||||||||||||||||| |||||||| ||||||||||||||||| ||| |     | || |||| || || ||||       ||  | |     || ||   | || | || |||   | |                                                                                                               
GTTGTGCAGCAGTTTGGAATACCTCACCTCTTTGATTTGCCAATACGGCCAACTgtaagttcagtaatagctacttatcatgaactaagggggtgtttggattccttggattatagtaattagataaaataatctgaatatgatacaaacatcctagattatggcatggattaaagtattccaaccaccggattattatactcattatttatactccaactaacaatgatccacctctataatgtag

upper sequence: LOC_Os01g52170.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G129208_T01 (Zea mays), 5'ss of exon 10
GTTGTGCAGCAGTTTGGAATACCTCACCTCTTCGATTTGCCGATACGGCCAACTgtaagctcaatc----ccacctatcttgtac-aaggataaaagtgagtgc----aatgatcacagtttggtataatttacag------------------
|||||||||||||||||||||||||||||||| |||||||| ||||||||||||||||| ||| |     | || |||| || || ||||       ||  | |     || ||   | || | || |||   | |                  
GTTGTGCAGCAGTTTGGAATACCTCACCTCTTTGATTTGCCAATACGGCCAACTgtaagttcagtaatagctacttatcatgaactaagggggtgtttggattccttggattatagtaattagataaaataatctgaatatgatacaaacatcc
















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|29683979|gb|CB680254.1|CB680254
EST:     TGCAGCAGTTTGGAATACCTCACCTCTTCGATTTGCCGATACGGCCAACT                         CTTTCAGCGTCTGGAGATACTGGAATTCCTGAAGTAGTGGCTGATCCACAA
genomic: TGCAGCAGTTTGGAATACCTCACCTCTTCGATTTGCCGATACGGCCAACTgtaagctcaa ... taatttacagCTTTCAGCGTCTGGAGATACTGGAATTCCTGAAGTAGTGGCTGATCCACAA
EST: gi|27577753|gb|CB000448.1|CB000448
EST:     TGCAGCAGTTTGGAATACCTCACCTCTTCGATTTGCCGATACGGCCAACT                         CTTTCAGCGTCTGGAGATACTGGAATTCCTGAAGTAGTGGCTGATCCACAA
genomic: TGCAGCAGTTTGGAATACCTCACCTCTTCGATTTGCCGATACGGCCAACTgtaagctcaa ... taatttacagCTTTCAGCGTCTGGAGATACTGGAATTCCTGAAGTAGTGGCTGATCCACAA
EST: gi|66923650|gb|CX110498.1|CX110498
EST:     TGCAGCAGTTTGGAATACCTCACCTCTTCGATTTGCCGATACGGCCAACT                         CTTTCAGCGTCTGGAGATACTGGAATTCCTGAAGTAGTGGCTGATCCACAA
genomic: TGCAGCAGTTTGGAATACCTCACCTCTTCGATTTGCCGATACGGCCAACTgtaagctcaa ... taatttacagCTTTCAGCGTCTGGAGATACTGGAATTCCTGAAGTAGTGGCTGATCCACAA
EST: gi|29613739|gb|CB618752.1|CB618752
EST:     TGCAGCAGTTTGGAATACCTCACCTCTTCGATTTGCCGATACGGCCAACT                         CTTTCAGCGTCTGGAGATACTGGAATTCCTGAAGTAGTGGCTGATCCACAA
genomic: TGCAGCAGTTTGGAATACCTCACCTCTTCGATTTGCCGATACGGCCAACTgtaagctcaa ... taatttacagCTTTCAGCGTCTGGAGATACTGGAATTCCTGAAGTAGTGGCTGATCCACAA

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: 54 (upstream exon), 62 (downstream exon)
Score: 19

GTTGTGCAGCAGTTTGGAATACCTCACCTCTTCGATTTGCCGATACGGCCAACTgtaagctcaa ... taatttacagCTTTCAGCGTCTGGAGATACTGGAATTCCTGAAGTAGTGGCTGATCCACAAGGGGATGTTGCTAAGACGTTTCAGAATCTTGGAGTTTGTGTTGTTCAGC




<











<


<