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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtattctgctcctacattgctattgctctattctttatgatgttcttttgtgagcttacttagtatttctgaataaatgacactgatatcgaattccagATTAAGAGTCATTTCAAGGACATCGGTGTTCCAGCTGATGTAAAATACATTGATCCGACATATATGGTCCGGGCCTGTCGTGCGAATGCATCTGATGCTA

Basic information

species Oryza sativa
transcript LOC_Os09g24910.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g24910.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G127717_T01 (Zea mays), 3'ss of exon 12
--------tgtattctgctcctacattgctattgctctattctttatgatgttcttttgtgagcttacttagtatttctgaataaatgacactgatatcgaattccagATTAAGAGTCATTTCAAGGACATCGGTGTTCCAGCTGATGTAAAATACATTGATCCGACATATATGGTCCGGGCCTGTCGTGCGAATGCATCTGATGCTA
        | |||  | |||  || ||||| ||| | || | | |  ||  |||||||   |  |||| || ||||        | || || |  ||||   || ||||| ||||  ||||||||||||||||||||||| |||||| |||||||||||||||| ||||||||||| |||||||| || || ||||||||||||||||
gttgaccctttatggttctctaactttgctcttgttgtaatttgtg-gacattctttttccactttacatattattc-------agtggcatttgtatcaccttacagATCAAGAAGCATTTCAAGGACATCGGTGTTCCCGCTGATCTAAAATACATTGATCCAACATATATGGTTCGGGCCTGCCGGGCAAATGCATCTGATGCTA

upper sequence: LOC_Os09g24910.2 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv14s0108g00540.t01 (Vitis vinifera), 3'ss of exon 12
--tgtattctgctcctacattgctattgctctattctttatgatgttcttttgtgagcttacttagtatttctgaataaatgacactgatatcgaattc-cagATTAAGAGTCATTTCAAGGACATCGGTGTTCCAGCTGATGTAAAATACATTGATCCGACATATATGGTCCGGGCCTGTCGTGCGAATGCATCTGATGCTA
  | || |||  || ||||  ||      | |||| | |   ||  ||||   |   ||| | |  | ||  |||          || | |     |   ||||| ||||  ||||| | |   || || |||||||||||||| |||||||||||||| || |||||| | || || ||||| || ||||||||||||||| 
gttatagtctcatcttacaaggcagcacttgtattttcttccattctcttccatattcttgcattttcttgatgatagtgatgggctcacacttcttcaacagATCAAGAAACATTTTAGGAGGATTGGCGTTCCAGCTGATGTTAAATACATTGATCCCACTTATATGATTCGAGCGTGTCGAGCAAATGCATCTGATGCTG

upper sequence: LOC_Os09g24910.2 (Oryza sativa), 3'ss of exon 12
lower sequence: PP1S114_31V6.1 (Physcomitrella patens), 3'ss of exon 11
tgtattctgctcctacattgctattgctctattctttatgatgttcttttgtgagctt---acttagtat--ttctgaataaatgacactgatatcgaattccagATTAAGAGTCATTTCAAGGACATCGGTGTTCCAGCTGATGTAAAATACATTGATCCGACATATATGGTCCGGGCCTGTCGTGCGAATGCATCTGATGCTA
       || |     |||||| |    | || ||  |||      ||| |  |||||   | || | |   ||  |   |  | | | || | ||| ||  ||| | ||||| |||||||||||||| || || ||||| ||||| || ||||||||||| || || ||| | || || ||||| || ||||| |||||    |
---cgagtgatttaggattgctgtactccgatgctcaatggcaaa-tttcgaaagcttcgaattttgaacgatttcggggaccttaaaatg-tgtcgtatcgcagGTAAAGAGACATTTCAAGGACATTGGAGTACCAGCGGATGTGAAGTACATTGATCCTACCTACATGATTCGAGCATGTCGAGCCAATGCTTCTGACCGAA

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|86838031|gb|CI343299.1|CI343299
EST:     GGTGTCCACATGCAACAGAAG                         ATTAAGAGTCATTTCAAGGACATCGGTGTTCCAGCTGATGTAAAATACATT
genomic: GGTGTCCACATGCAACAGAAGgtatgttttc ... cgaattccagATTAAGAGTCATTTCAAGGACATCGGTGTTCCAGCTGATGTAAAATACATT
EST: gi|86493701|gb|CI136334.1|CI136334
EST:     CATCAGGAAATGTAATACTTAGTGACTTTGGTGTCCACATGCAACAGAAG                         ATTAAGAGTCATTTCAAGGACATCGGTGTTCCAGCTGATGTAAAATACATT
genomic: CATCAGGAAATGTAATACTTAGTGACTTTGGTGTCCACATGCAACAGAAGgtatgttttc ... cgaattccagATTAAGAGTCATTTCAAGGACATCGGTGTTCCAGCTGATGTAAAATACATT
EST: gi|86884674|gb|CI313053.1|CI313053
EST:     AATACTTAGTGACTTTGGTGTCCACATGCAACAGAAG                         ATTAAGAGTCATTTCAA-GACATCGGTGTTCCAGCTGATGTAAAATACATT
genomic: AATACTTAGTGACTTTGGTGTCCACATGCAACAGAAGgtatgttttc ... cgaattccagATTAAGAGTCATTTCAAGGACATCGGTGTTCCAGCTGATGTAAAATACATT
EST: gi|86504245|gb|CI146878.1|CI146878
EST:     CATCAGGAAATGTAATACTTAGTGACTTTGGTGTCCACATGCAACAGAAG                         ATTAAGAGTCATTTCAAGGACATCGGTGTTCCAGCTGATGTAAAATACATT
genomic: CATCAGGAAATGTAATACTTAGTGACTTTGGTGTCCACATGCAACAGAAGgtatgttttc ... cgaattccagATTAAGAGTCATTTCAAGGACATCGGTGTTCCAGCTGATGTAAAATACATT
EST: gi|87018028|gb|CI275842.1|CI275842
EST:     CATCAGGAAATGTAATACTTAGTGACTTTGGTGTCCACATGCAACAGAAG                         ATTAAGAGTCATTTCAAGGACATCGGTGTTCCAGCTGATGTAAAATACATT
genomic: CATCAGGAAATGTAATACTTAGTGACTTTGGTGTCCACATGCAACAGAAGgtatgttttc ... cgaattccagATTAAGAGTCATTTCAAGGACATCGGTGTTCCAGCTGATGTAAAATACATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttgtgagcttacttagtatttctgaataaatgacactgatatcgaattccagATTAAGAGTCATTTCAAGGACATCGGTGTTCCAGCTGATGTAAAATACATTGATCCGACATATATGGTCCGGGCCTGTCGTGCGAATGCATCTGATGCTA
                                    cactgat  putative branch site (score: 3)
                   tatttctgaataaat  TA-rich tract