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

CATCAACTCCGCCGTCGGCTCCCTCCTCGTCAGCTTCACCGTCTACATCATCCCCGCCCTCGCGCACATGATCACCTTCCGCTCCGCGCACGCTCGTGAGgtatagtaaaaatcttggcatctttttaatcactgcgctttttttttaaccttttggtttcacttttatcatgcgagtttactagtgtaggacttgcatg...

Basic information

species Oryza sativa
transcript LOC_Os03g14080.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g14080.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G149481_T04 (Zea mays), 5'ss of exon 5
CATCAACTCCGCCGTCGGCTCCCTCCTCGTCAGCTTCACCGTCTACATCATCCCCGCCCTCGCGCACATGATCACCTTCCGCTCCGCGCACGCTCGTGAGgtatagtaaaaatcttggcatctttttaatcactgcgctttttttttaaccttttggt-ttcacttttatcatgcgagtttactagtgtagg--acttgcatg-
|||||||||||||||||||||||||||||||||||||||||||||||||||||| || || |||||||||||||| ||||| |||||    || |||||||||  ||| |  |  |  |  |  |  |  ||||   ||||| ||   || ||||  |   || |  | |  |   | || |    || | |  || |   |  
CATCAACTCCGCCGTCGGCTCCCTCCTCGTCAGCTTCACCGTCTACATCATCCCGGCGCTGGCGCACATGATCACGTTCCGGTCCGCAACAGCCCGTGAGgta--gtatattttattactcccatgcatgcacta--cttttattaatacgttttattacccaatgctttttttttacttcatcgatgaaagctacctagctac

upper sequence: LOC_Os03g14080.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA12G03490.1 (Glycine max), 5'ss of exon 7
CATCAACTCCGCCGTCGGCTCCCTCCTCGTCAGCTTCACCGTCTACATCATCCCCGCCCTCGCGCACATGATCACCTTCCGCTCCGCGCACGCTCGTGAGgtatagtaaaaatcttggcatctttttaatcactgcgctttttttttaaccttttggtttcacttttatcatgcgagtttactagtgtaggacttgcatg---
|||||||||| |||| ||||| ||||| |||||||||||||| ||||| |||||||||||||| |||||  ||||||||   ||  |    ||  |  |||||   || | ||  |    |  | | ||  | ||  ||   |   | ||    |  ||| || | |||    |     ||||||  |   | | |       
CATCAACTCCACCGTTGGCTCTCTCCTTGTCAGCTTCACCGTTTACATTATCCCCGCCCTCGCCCACATCTTCACCTTCAAATCACCCTCTGCCAGACAGgtaccatatatatagttattttgtatcaaa-attgtcctacgtacctcacggactactttaacatatatatccct--cctactagacttaaattggttccttc

upper sequence: LOC_Os03g14080.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA06G00690.1 (Glycine max), 5'ss of exon 7
CATCAACTCCGCCGTCGGCTCCCTCCTCGTCAGCTTCACCGTCTACATCATCCCCGCCCTCGCGCACATGATCACCTTCCGCTCCGCGCACGCTCGTGAGgtatagtaaaaatcttggcatctttttaatcactgcgctttttttttaaccttttggtt-tcacttttatcatgcgagtttactagtgtaggacttgcatg---
|||||||||| |||| || || || || |||||||||||||| |||||||||||||||||||| |||||| ||||||||   ||  |    || ||  |||||   || |   ||    ||   || || |   | || |  |    |    ||   |  |  | |  |  |     | | |||   | |  ||| |||     
CATCAACTCCACCGTTGGATCTCTACTTGTCAGCTTCACCGTTTACATCATCCCCGCCCTCGCCCACATGTTCACCTTCAAATCACCCTCTGCCCGACAGgtac--tatattcctatatattaattcaacccaagtgcatgctacaaagtaattaattaattgcgtacaaaaaaaatgctaact--cggactactcgcaattca

upper sequence: LOC_Os03g14080.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA04G00640.1 (Glycine max), 5'ss of exon 7
CATCAACTCCGCCGTCGGCTCCCTCCTCGTCAGCTTCACCGTCTACATCATCCCCGCCCTCGCGCACATGATCACCTTCCGCTCCGCGCACGCTCGTGAGgtatagtaaaaatcttggcatctttttaatcactgcgctttttttttaaccttttggtttca---cttttatcatgcgagtttactagtgtaggacttgcatg----
|||||||||| |||| || || || || |||||||||||||| |||||||||||||||||||| |||||| ||||||||   ||  |    || ||   ||||     |  || ||    || ||  |  ||      |||  |||||||  |||      |   ||   |   | ||||   | ||  ||| | | ||||||    
CATCAACTCCACCGTTGGATCTCTTCTTGTCAGCTTCACCGTTTACATCATCCCCGCCCTCGCCCACATGTTCACCTTCAAATCACCCGCTGCCCGACGGgtacgt--actatattcaattcattcaaccca----attttaattttaactatttacaaagaaagctagaacagttcgagaaaaataaagtatg-catgcatgtggg

upper sequence: LOC_Os03g14080.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA11G11310.1 (Glycine max), 5'ss of exon 7
CATCAACTCCGCCGTCGGCTCCCTCCTCGTCAGCTTCACCGTCTACATCATCCCCGCCCTCGCGCACATGATCACCTTCCGCTCCGCGCACGCTCGTGAGgtatagtaaaaatcttggcatctttttaatcactgcgctttttttttaaccttttggtttcacttttatcatgcgagtttactagtgt-aggacttgcatg
|||||||||| |||| ||||| ||||| |||||||||||||| |||||||||||||||||||| |||||  |||||||| | ||  |     |  |  ||||||  || | |||    |||   |||  ||  |     | | | |||  || |    || | |  |   ||   | ||    |   | |  ||||   | 
CATCAACTCCACCGTTGGCTCTCTCCTTGTCAGCTTCACCGTTTACATCATCCCCGCCCTCGCCCACATCTTCACCTTCAGATCACCCTCTTCCAGACAGgtattatatatatcgcatcattcatttcttccttcattatatatattacactgtctaatttattccttcaatat-acttagtaaacatcaatacttatttt

upper sequence: LOC_Os03g14080.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv03s0038g02140.t01 (Vitis vinifera), 5'ss of exon 7
CATCAACTCCGCCGTCGGCTCCCTCCTCGTCAGCTTCACCGTCTACATCATCCCCGCCCTCGCGCACATGATCACCTTCCGCTCCGCGCACGCTCGTGAGgtatagtaaaaatcttggcatctttttaatcactgcgctttttttttaaccttttggtttcacttttatcatgcgagtttactagtgtaggacttgcatg----
|||||||||| ||||||| || ||||| || || ||||| ||||| ||||||||||| || || |||||  ||||||||   || |||   || ||||||||| |     | | |     |  |  |  |  || | |      || ||     || ||||| |     |||  |  |||  ||   |     ||   |     
CATCAACTCCACCGTCGGATCTCTCCTTGTGAGTTTCACTGTCTATATCATCCCCGCTCTGGCCCACATCTTCACCTTCAAATCAGCGGCTGCCCGTGAGgtaaaactccactttc----ttatcctgctacctacacaccagattgaaaggcatgctttcaataagtgcatttgctttttttaccattatttttttttattaa

upper sequence: LOC_Os03g14080.1 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ21839 (Selaginella moellendorffii), 5'ss of exon 7
CATCAACTCCGCCGTCGGCTCCCTCCTCGTCAGCTTCACCGTCTACATCATCCCCGCCCTCGCGCACATGATCACCTTCCGCTCCGCGCACGCTCGTGAGgtatagta-----aaaatcttggcatctttttaatcactgcgctttttttttaaccttttggtttcacttttatcatgcgagtttactagtgtaggacttgcatg
 ||||||||||| |||||  | |||||||||| |||||| ||||| ||||||||| | ||||| ||||||||||| |   |  | ||   |||  | | ||||   |      ||||||| |   |  |   | |   | | ||  |  |||  |||||||  | | |    || |    | ||| || |  |    ||      
AATCAACTCCGCGGTCGGGGCGCTCCTCGTCACCTTCACTGTCTATATCATCCCCTCGCTCGCACACATGATCACGTATAGAACAGCCTTCGCCAGGGCGgtaagtttctcgcaaaatctcgtttttctggaagttcttccactcctcgttt--ccttttgagtgc-cggagatgagattatttttcttgcttgtttctctag--

upper sequence: LOC_Os03g14080.1 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ18760 (Selaginella moellendorffii), 5'ss of exon 7
CATCAACTCCGCCGTCGGCTCCCTCCTCGTCAGCTTCACCGTCTACATCATCCCCGCCCTCGCGCACATGATCACCTTCCGCTCCGCGCACGCTCGTGAGgta--tagtaaaaatcttggcatctttttaatcactgcgctttt-----tttttaaccttttggt-ttcacttttatcatgcgagtt--tactagtgt-aggacttgcatg--------------------------------
 || ||||||||||| ||||| || ||||||| |||||| ||||||||||| ||   |||||| || ||| |||| ||| |  | ||    || || ||||||  || | |||  |||  |  |||| |        ||  | |      || || |    |  | ||||   || || || |   |  |  |    | ||||||                                      
TATAAACTCCGCCGTGGGCTCTCTACTCGTCACCTTCACAGTCTACATCATTCCTTGCCTCGCACATATGCTCACTTTCAGGACTGCCTTTGCACGAGAGgtacgtacttaaatgcttttccactttctctcgtggacgaatctacgaacttgtagctagctactgttcatccttttcgtgtgttctagtgttcacatcaggactgatggatcgatccttggttttttttgtttgtcaaacag

upper sequence: LOC_Os03g14080.1 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ34222 (Selaginella moellendorffii), 5'ss of exon 7
CATCAACTCCGCCGTCGGCTCCCTCCTCGTCAGCTTCACCGTCTACATCATCCCCGCCCTCGCGCACATGATCACCTTCCGCTCCGCGCACGCTCGTGAGgtatagtaaaaatcttggcatctttttaatcactgcgctttttttttaaccttttggtttcacttttatc-atgcgagtttactagtgtaggacttgcatg--
 ||||||||||| |||||  | |||||||||| |||||| ||||| ||||||||| | ||||| ||||||||||| |   |  | ||   |||  | | ||||   |     ||     ||||  ||  ||     | | ||    |   | |||  ||| | |   |   ||| || |||  |  |       ||   ||  
AATCAACTCCGCGGTCGGGGCGCTCCTCGTCACCTTCACTGTCTATATCATCCCCTCGCTCGCACACATGATCACGTATAGAACAGCCTTCGCCAGGGCGgtaagtttc---tcgcaaaatctcgtttttctggaagttcttccactgctcgtttcctttgagtgccaaagatgagattttttttcttgcttgtttctctgag

upper sequence: LOC_Os03g14080.1 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ36050 (Selaginella moellendorffii), 5'ss of exon 7
CATCAACTCCGCCGTCGGCTCCCTCCTCGTCAGCTTCACCGTCTACATCATCCCCGCCCTCGCGCACATGATCACCTTCCGCTCCGCGCACGCTCGTGAGgtatag---taaaaatcttggcatctt-tttaatcactgcgctttt---tttttaaccttttggt-ttcacttttatcatgcgagtt--tactagtgt-aggacttgcatg--------------------------------
 || ||||||||||| ||||| || ||||||| |||||| ||||||||||| ||   |||||| || ||| |||| ||| |  | ||    || || ||||||      ||||    ||  ||  || | |  |    |    |      || || |    |  | ||||   || || || |   |  |  |    | ||||||                                      
TATAAACTCCGCCGTGGGCTCTCTACTCGTCACCTTCACAGTCTACATCATTCCTTGCCTCGCACATATGCTCACTTTCAGGACTGCCTTTGCACGAGAGgtacgcacttaaatgcttttccactttatctcgtggacgaatctacgaacttgtagctagctactgttcatccttttcgtgtgttctagtgttcacatcaggactgatggatcgatccttggttttttttgtttgtcaaacag

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|86492945|gb|CI135578.1|CI135578
EST:     CGCTCCGCGCACGCTCGTGAG                         AACGCCGTGGAGCCGCCGCCGCGGTTCGTGGGGCGATGGACGGGCACGTTC
genomic: CGCTCCGCGCACGCTCGTGAGgtatagtaaa ... taaactgcagAACGCCGTGGAGCCGCCGCCGCGGTTCGTGGGGCGATGGACGGGCACGTTC