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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGTTAGGGATATCCATATGGAGAACTTCAGTGTTACTGTTGGTGGTCGTGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATGgtgagttacagcataggtttcttcttgagctgttgttcacttcgtagctggcatgaataacttaggaatgaagaatgaaacatttgtaatcgtatatgtc...

Basic information

species Oryza sativa
transcript LOC_Os02g58020.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58020.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G013890_T01 (Zea mays), 5'ss of exon 3
GCTGTTAGGGATATCCATATGGAGAACTTCAGTGTTACTGTTGGTGGTCGTGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATGgtgagttacagcatag-gtttcttcttgagctgttgttcacttcgtagctgg--catgaataacttaggaatgaagaatg-----aaacatttgtaatcgtatatgtc-----------------------------------------------
|||||||||||||| |||||||||||||||||||| |||||||||||||||||||| ||||||||   |||| ||||||||||||||||||||||||||||||||| ||    | | ||||  |  |   | || | | |    || || ||  | ||   | |||     |  ||  |      | | || | |||  || |  ||                                                
GCTGTTAGGGATATACATATGGAGAACTTCAGTGTCACTGTTGGTGGTCGTGATCTAATTCAAGAAGCCACTATAACACTTGCTTTTGGGAGGCACTATGgtgagt-actctgtggtgtttggtagttttcagtagataaaactgtggccggggcctgggaagcttgcatgttcagtttatttatacatatctataaaagttttcgttgaaatgctaccctacaagttttggaatttcttatttacttgtttcag
















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|29623430|gb|CB628441.1|CB628441
EST:     TGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATG                         GTCTTGTTGGAAGAAATGGTACAGGGAAAACCTCTTTTCTCAGAGCTATGG
genomic: TGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATGgtgagttaca ... cacacttcagGTCTTGTTGGAAGAAATGGTACAGGGAAAACCTCTTTTCTCAGAGCTATGG
EST: gi|157651259|gb|EX450893.1|EX450893
EST:     TGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATG                         GTCTTGTTGGAAGAAATGGTAC
genomic: TGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATGgtgagttaca ... cacacttcagGTCTTGTTGGAAGAAATGGTAC
EST: gi|29664091|gb|CB660366.1|CB660366
EST:     TGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATG                         GTCTTGTTGGAAGAAATGGTACAGGGAAAACCTCTTTTCTCAGAGCTATGG
genomic: TGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATGgtgagttaca ... cacacttcagGTCTTGTTGGAAGAAATGGTACAGGGAAAACCTCTTTTCTCAGAGCTATGG
EST: gi|29644366|gb|CB649373.1|CB649373
EST:     TGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATG                         GTCTTGTTGGAAGAAATGGTACAGGGAAAACCTCTTTTCTCAGAGCTATGG
genomic: TGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATGgtgagttaca ... cacacttcagGTCTTGTTGGAAGAAATGGTACAGGGAAAACCTCTTTTCTCAGAGCTATGG
EST: gi|66915780|gb|CX102628.1|CX102628
EST:     TGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATG                         GTCTTGTTGGA
genomic: TGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATGgtgagttaca ... cacacttcagGTCTTGTTGGA
EST: gi|29627492|gb|CB632503.1|CB632503
EST:     TGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATG                         GTCTTGTTGGAAGAAATGGTACAGGGAAAACCTCTTTTCTCAGAGCTATGG
genomic: TGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATGgtgagttaca ... cacacttcagGTCTTGTTGGAAGAAATGGTACAGGGAAAACCTCTTTTCTCAGAGCTATGG
EST: gi|117239285|gb|CT849366.1|CT849366
EST:     TGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATG                         GTCTTGTTGGAAGAAATGGTACAGGGAAAACCTCTTTTCTCAGAGCTATGG
genomic: TGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATGgtgagttaca ... cacacttcagGTCTTGTTGGAAGAAATGGTACAGGGAAAACCTCTTTTCTCAGAGCTATGG
EST: gi|157651253|gb|EX450887.1|EX450887
EST:     TGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATG                         GTCTTGTTGGAAGAAATGGTAC
genomic: TGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATGgtgagttaca ... cacacttcagGTCTTGTTGGAAGAAATGGTAC

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: 69 (upstream exon), 75 (downstream exon)
Score: 61

GCTGTTAGGGATATCCATATGGAGAACTTCAGTGTTACTGTTGGTGGTCGTGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATGgtgagttaca ... cacacttcagGTCTTGTTGGAAGAAATGGTACAGGGAAAACCTCTTTTCTCAGAGCTATGGCGATGCATGCGATTGATGGGATTCCCAAGAACTGCCAGATATTGCATGT




<











<


<