Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAACATTTGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTCACAGgtttggactcttggatcactaaccaaatatatttatccttgagaaaacatactgagcccaaacacaactacacaagtcttacttgagttttgttttgcttggttaag

Basic information

species Oryza sativa
transcript LOC_Os03g50620.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g50620.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G131324_T01 (Zea mays), 5'ss of exon 6
GATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAACATTTGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTCACAGgtttggactcttggatcactaaccaaatatatttatccttgagaaaacatactgagcccaaacacaactacacaagtcttacttgagttttgttttgcttggttaag
||||||||||||||| ||||| ||||||||||| |||||||| || ||  ||||||| ||||||||||||||||| ||||| ||||||||||||||||||||||| | || || ||        |||| |  || ||  |||  | | ||| ||| || |||         || |  | |   |  ||||  |||| | || |  ||
GATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGCACCTGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACAGgtttgaa-tcatgaat------ataaattttcttgtcaatga--agatatattgaaccaaaa---------accaagcctgagtacgtttgttttttcatgatccag

upper sequence: LOC_Os03g50620.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G154716_T01 (Zea mays), 5'ss of exon 8
GATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAACATTTGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTCACAGgtttggactcttggatcactaaccaaatatatttatccttgagaaaacatactgagcccaaacacaactacacaagtcttacttgagttttgttttgcttggttaag
||||||||||||||| ||||| ||||||||||| |||||||| || ||  |||||||||||| |||||||||||| ||||| |||||||||||||||| |||||| | || || ||        | | || ||  |      ||| | ||| ||| || |||| |||        | |  | |   ||| | |||| | || |  ||
GATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGCACCTGAAACGGAAAATTTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACGGgtttgaa-tcatgaat--------agaaattttcttgacaatgaatatatattgaaccaaaacccaa--------gcccgagtacggttat-tttttcatgatccag

upper sequence: LOC_Os03g50620.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA08G39880.1 (Glycine max), 5'ss of exon 6
GATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAACATTTGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTCACAGgtttg-gactcttggatcactaaccaaatatatttatccttgagaaaacatactgagcccaaacacaactacacaagtcttacttgagtt-ttgttttgcttggttaag----------------------
||| ||||| |   | ||||||||||| ||    || ||||| ||||||||||||||||||||||| |  ||||||||||| ||| | ||||||||||||||||| |    || | | |  ||  |  |   ||||   |   |      |  |   || | | ||  |     |     || || | || || | ||  |||  |                         
GATAGAACTATATTCACATGTCCCAGTGCTTAAGAATTTTGTGGAACATTTGAAACGGAAAAATTTTAGTGTTTGTGCTGTTTACTTACTTGATTCACAGgtttgtggtagtttgttgagaaaatattttcttttaagttattggctctctcatattcctatagacttcctgttattgtatattttaattattatctttgttgactctaataatattaaaatgttttccag

upper sequence: LOC_Os03g50620.2 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv00s0174g00200.t01 (Vitis vinifera), 5'ss of exon 5
GATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAACATTTGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTCACAGgtttg--gactcttggatcactaaccaaatatatttatccttgagaaaacatactgagcccaaacacaactacacaagtcttacttgagttttgttttgcttggttaag
||| || || ||  | ||||| ||| | || || || ||||| || |||||||| || || |||||||| ||||||||||||||||| |||||||||||||||||  || | ||    |     |  ||| |  ||||  |   ||     || ||     |   | |  |       | ||  |     ||| |  |    |      
GATAGAGCTTTTTTCGCATGTTCCAATGCTTCGGAATTTTGTGGACCATTTGAAGCGTAAGAATTTCAATGTTTGTGCTGTGTACCTGCTTGATTCACAGgtttgtagaattttctcccttgggcataattttattattttaatgactggttattgcttgtattgagagttcttttttttttcttcttcctttttaatatcag------

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|86530562|gb|CI170768.1|CI170768
EST:     TGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTCACAG                         TTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCT
genomic: TGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTCACAGgtttggactc ... cttggttaagTTTGTTAGTGATGTGACAAAATACATCAGTGGTTGCATGGCTTCTCTTTCT
EST: gi|58611474|gb|CK039186.1|CK039186
EST:     TGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTCACAG                         TTTGTTAGTGATGTGACAAAATACATC
genomic: TGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTCACAGgtttggactc ... cttggttaagTTTGTTAGTGATGTGACAAAATACATC
EST: gi|426369|gb|D22232.1|D22232
EST:     TGAAACGGAAAAATTTCAACGNTTGTGCTGTGTACCTTCTTGATTCACAG                         TTTGTTAGTGATGT
genomic: TGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTCACAGgtttggactc ... cttggttaagTTTGTTAGTGATGT