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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGAAGACTTCCAAATGAAATGGGCCTTTGAAACTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAGgtattttgattgcctgactagctattctgtgtcttttagcatggattattgccttcccaacttcatattattgtttgttgcgcttgtcatatccaatag

Basic information

species Oryza sativa
transcript LOC_Os10g35960.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g35960.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G085747_T02 (Zea mays), 5'ss of exon 8
TTTGAAGACTTCCAAATGAAATGGGCCTTTGAAACTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAGgtattttgattgcctgactagctattctgtgtcttttagcatggattattgccttcccaacttcatat--tattgtttgttgcgcttgtcatatccaatag--
|||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| ||||||||||||||||| |||||||  |||||     ||||  ||||  ||   || |       |   ||  ||  |||  || ||||  |||||||||  | |||| || |||  || |   
TTTGAAGACTTCCAAATGAAATGGGCCTTTGAGACTCTTCAGAGGTATCGGAACCGATTTTGCATGTTCAATGATGACGTACAGgtatcctgattcttaaacta-ttattacgtaatttattctggaaagctttttctgaccagttttatatattattgtttgacgggcttatcctatttaaaatag

upper sequence: LOC_Os10g35960.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G085747_T05 (Zea mays), 5'ss of exon 7
----------------TTTGAAGACTTCCAAATGAAATGGGCCTTTGAAACTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAGgtattttgattgcctgactagctattctgtgtcttttagcatggattattgccttcccaacttcatat--tattgtttgttgcgcttgtcatatccaatag--
                |||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| ||||||||||||||||| |||||||  |||||     ||||  ||||  ||   || |       |   ||  ||  |||  || ||||  |||||||||  | |||| || |||  || |   
AGTGATAAAATCACAGTTTGAAGACTTCCAAATGAAATGGGCCTTTGAGACTCTTCAGAGGTATCGGAACCGATTTTGCATGTTCAATGATGACGTACAGgtatcctgattcttaaacta-ttattacgtaatttattctggaaagctttttctgaccagttttatatattattgtttgacgggcttatcctatttaaaatag
















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|58687567|gb|CK076254.1|CK076254
EST:     CTCTTCAGAGGTATCGTAACCGATTTTGTATGTTCAATGATGACGTGCAG                         GGGACAGCAGGAGTTGCTCTAGCTGGCCTACTT
genomic: CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAGgtattttgat ... tatccaatagGGGACAGCAGGAGTTGCTCTAGCTGGCCTACTT
EST: gi|58673493|gb|CK062179.1|CK062179
EST:     CTCTTCAGAGGTATCGTAACCGATTTTGTATGTTCAATGATGACGTGCAG                         GGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
genomic: CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAGgtattttgat ... tatccaatagGGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
EST: gi|58665242|gb|CK053928.1|CK053928
EST:     CTCTTCAGAGGTATCGTAACCGATTTTGTATGTTCAATGATGACGTGCAG                         GGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
genomic: CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAGgtattttgat ... tatccaatagGGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
EST: gi|58694574|gb|CK083261.1|CK083261
EST:     CTCTTCAGAGGTATCGTAACCGATTTTGTATGTTCAATGATGACGTGCAG                         GGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
genomic: CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAGgtattttgat ... tatccaatagGGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
EST: gi|58659006|gb|CK047686.1|CK047686
EST:     CTCTTCAGAGGTATCGTAACCGATTTTGTATGTTCAATGATGACGTGCAG                         GGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
genomic: CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAGgtattttgat ... tatccaatagGGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
EST: gi|29664101|gb|CB660376.1|CB660376
EST:     CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAG                         GGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
genomic: CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAGgtattttgat ... tatccaatagGGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
EST: gi|29624067|gb|CB629078.1|CB629078
EST:     CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAG                         GGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
genomic: CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAGgtattttgat ... tatccaatagGGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
EST: gi|29656255|gb|CB652530.1|CB652530
EST:     CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAG                         GGGACAGCANGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTG
genomic: CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAGgtattttgat ... tatccaatagGGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTG
EST: gi|29687359|gb|CB683634.1|CB683634
EST:     CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAG                         GGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
genomic: CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAGgtattttgat ... tatccaatagGGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
EST: gi|58604291|gb|CK014819.1|CK014819
EST:     CTCTTCAGAGGTATCGTAACCGATTTTGTATGTTCAATGATGACGTGCAG                         GGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
genomic: CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAGgtattttgat ... tatccaatagGGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
EST: gi|29624065|gb|CB629076.1|CB629076
EST:     CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAG                         GGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
genomic: CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAGgtattttgat ... tatccaatagGGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
EST: gi|29678813|gb|CB675088.1|CB675088
EST:     CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAG                         GGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA
genomic: CTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAGgtattttgat ... tatccaatagGGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAA

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), 74 (downstream exon)
Score: 43

TTTGAAGACTTCCAAATGAAATGGGCCTTTGAAACTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAGgtattttgat ... tatccaatagGGGACAGCAGGAGTTGCTCTAGCTGGCCTACTTGGAGCTGTGAGAGCACAAGGTCGACCCCTCTCTGATTTTACTAAGCAGAAGATAGTTGTGGTGGGAG




<











<


<