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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTACATTTCATCGTTTTGACAAATTCAACCTTAAGTACAATCCGTGTGGCCAAAGTAGGCTCAGAGAGATTTTCCTCAAACAGGACAATCTTATCCAAGgtatcgcttgtttcaattattttgttgacacttttgtgcatcttaccttttttgttgttgctaaacgggcttgcagtttctcctaaaatgtttgtccttg...

Basic information

species Oryza sativa
transcript LOC_Os05g28180.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g28180.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G416667_T01 (Zea mays), 5'ss of exon 9
AGTACATTTCATCGTTTTGACAAATTCAACCTTAAGTACAATCCGTGTGGCCAAAGTAGGCTCAGAGAGATTTTCCTCAAACAGGACAATCTTATCCAAGgtatcgcttgtttcaattattttgtt-----gacacttttgtgcatcttaccttttttgttgttgctaaacgggcttgcagtttctcctaaaatgtttgtccttg
|| |||||||||||||||||||||||||| || || |||||||| ||||||||||||||||||||||| |||||||||||||| || |||||||| |||||||| | |||||  || |  | | ||      |    ||| |  ||    |||||| ||    | |         ||   || | |  ||  ||| |  |  || 
AGCACATTTCATCGTTTTGACAAATTCAATCTAAAATACAATCCATGTGGCCAAAGTAGGCTCAGAGAAATTTTCCTCAAACAAGATAATCTTATTCAAGgtattggttgttataagtcctatattccttaaaagtcttttttgattgggccttttatgcaaattcc---tttatttattgtatat--tatcatgctcattgttc

upper sequence: LOC_Os05g28180.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA03G07460.1 (Glycine max), 5'ss of exon 9
AGTACATTTCATCGTTTTGACAAATTCAACCTTAAGTACAATCCGTGTGGCCAAAGTAGGCTCAGAGAGATTTTCCTCAAACAGGACAATCTTATCCAAGgtatcgcttgtttcaattattttgttgacacttttgtgcatcttaccttttttgttgttgctaaacgggcttgcagtttctcctaaaat-gtttgtccttg-
||||| |||||||| ||||| || ||||| ||||| |||||||| ||||| ||||||||||| || ||||| || || || ||||| ||||| || ||||||| |  || |||    |||     || | || |    | | |      || |  |     | || |||   | | | ||   |    | ||    | ||  
AGTACTTTTCATCGCTTTGATAAGTTCAATCTTAAATACAATCCTTGTGGTCAAAGTAGGCTGAGGGAGATATTTCTGAAGCAGGATAATCTCATACAAGgtaacattt-ttttgggtataacactgtc-ctatcacacctgtgtttacttgtaatcaaattcaaaggggcagaaatatcctatggttttgtgcagctttct

upper sequence: LOC_Os05g28180.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA01G29470.1 (Glycine max), 5'ss of exon 10
AGTACATTTCATCGTTTTGACAAATTCAACCTTAAGTACAATCCGTGTGGCCAAAGTAGGCTCAGAGAGATTTTCCTCAAACAGGACAATCTTATCCAAGgtatcgcttgtttca----attattttgttgacacttttgtgcatcttaccttttttgttgttgctaaacgggcttgcagtttctcctaaaatgtttgtccttg
||||| |||||||| ||||| || ||||| ||||| |||||||| || || |||||||||||||| ||||| || || || ||||| ||||| || ||||||| |  || |||      || |   |  |  ||| | |||   | | | |   ||    || ||| ||    |     ||||     |  || |||       
AGTACTTTTCATCGCTTTGATAAGTTCAATCTTAAATACAATCCTTGCGGTCAAAGTAGGCTCAGGGAGATATTTCTTAAGCAGGATAATCTCATTCAAGgtaacatttttttttgggtataacagtcctatcacctgtgttactttaatcaaattcaaagtggctgaaatatcccatggttttgtgcagtatttttact----

upper sequence: LOC_Os05g28180.2 (Oryza sativa), 5'ss of exon 6
lower sequence: AT2G38280.2 (Arabidopsis thaliana), 5'ss of exon 9
AGTACATTTCATCGTTTTGACAAATTCAACCTTAAGTACAATCCGTGTGGCCAAAGTAGGCTCAGAGAGATTTTCCTCAAACAGGACAATCTTATCCAAGgta-tcgcttgtttcaattatt-ttgttgacactttt-gtgcatct--taccttttttgttgttgctaaacgggcttgcagtttctcctaaaatgtttgtccttg
||||| |||||||||||||| || |||||||| ||||| || || ||||| ||||||||||| || ||||||||||| |||||||| ||||| |||||||||| | |  |  | || | | | || ||  |  |||| || ||| |  | | |   || |     || |   | ||  || ||  |        ||||       
AGTACCTTTCATCGTTTTGATAAGTTCAACCTAAAGTATAACCCTTGTGGTCAAAGTAGGCTTAGGGAGATTTTCCTTAAACAGGATAATCTCATCCAAGgtaattgaatactccagtcactcttattaccgtttttagttcatttgatgcatcagttatgcactctcagttgcctgacatttattttcgtttggtttaag----

upper sequence: LOC_Os05g28180.2 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv08s0105g00570.t01 (Vitis vinifera), 5'ss of exon 9
AGTACATTTCATCGTTTTGACAAATTCAACCTTAAGTACAATCCGTGTGGCCAAAGTAGGCTCAGAGAGATTTTCCTCAAACAGGACAATCTTATCCAAGgtatcgcttgtttcaattat-tttgttga--cacttttgtgcatcttac-cttttttgttgttgctaaacgggcttgcagtttctcctaaaatgtttgtccttg
|| ||||||||||||||||| || ||||| || ||||||||||| || || |||||||||||||| || |||||||| || ||||| ||||||||||||||||| || || ||    ||| ||| ||     |   ||| | |       ||     |    |  | |||  | ||        | | |||   ||  |     
AGCACATTTCATCGTTTTGATAAGTTCAATCTCAAGTACAATCCCTGCGGTCAAAGTAGGCTCAGGGAAATTTTCCTTAAGCAGGATAATCTTATCCAAGgtatggcgtgcttgttatatgtttattaggttaagcttgaggaaaaagtgctaaacagacccttttgaacaagtttttttcaatttccaaatacttcatt----

upper sequence: LOC_Os05g28180.2 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S168_82V6.1 (Physcomitrella patens), 5'ss of exon 9
AGTACATTTCATCGTTTTGACAAATTCAACCTTAAGTACAATCCGTGTGGCCAAAGTAGGCTCAGAGAGATTTTCCTCAAACAGGACAATCTTATCCAAGgtatcgcttgtttcaat---tattttgttgacacttttgtgcatcttaccttttttgttgttgctaaacgggcttgcagtttctcctaaaatgtttgtccttg
| ||| ||||||||||| ||||| |||||||| || |||||||| |||||||| |||||||| || ||||||||||| || || |||||||||||| ||||||  |||  | ||||     ||||| |  ||| |    || |   ||  | || |  | | |    ||    |    || | |   |  ||||| ||     
AATACGTTTCATCGTTTCGACAAGTTCAACCTGAAATACAATCCTTGTGGCCAGAGTAGGCTAAGGGAGATTTTCCTGAAGCAAGACAATCTTATCAAAGgtagtgctcttatcaaaaagcattttctcaacattcgaatg-acgctagatcttgtactctggagccacattttgcttgtatttgaaaggatgttggttga--

upper sequence: LOC_Os05g28180.2 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S307_76V6.1 (Physcomitrella patens), 5'ss of exon 9
AGTACATTTCATCGTTTTGACAAATTCAACCTTAAGTACAATCCGTGTGGCCAAAGTAGGCTCAGAGAGATTTTCCTCAAACAGGACAATCTTATCCAAGgtatcgcttgtttcaattattttgttgacacttttgtgcatcttaccttttttgtt--gttgctaaacgggcttgcagtttctcctaaaat-gtttgtccttg
|  ||||| || |||||||| || |||||||||||||||||||| || ||||||||  | || || |||||||| || ||||| ||||| ||||| |||||| |   ||   ||| ||   ||    | || |||   | ||| ||   |  |  |     | ||  |    || ||  |  |  |||||| |||||| ||  
AACACATTCCACCGTTTTGATAAGTTCAACCTTAAGTACAATCCATGCGGCCAAAGCCGACTAAGGGAGATTTTTCTGAAACAAGACAACCTTATTCAAGgt-taaattacatcatttcagttacacaaacatttacacctctaacacatgatacttcacagatattcaacttttca--tggtgttaaaatagtttgtactat

upper sequence: LOC_Os05g28180.2 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ17267 (Selaginella moellendorffii), 5'ss of exon 8
AGTACATTTCATCGTTTTGACAAATTCAACCTTAAGTACAATCCGTGTGGCCAAAGTAGGCTCAGAGAGATTTTCCTCAAACAGGACAATCTTATCCAAGgtatcgcttgtttcaattattttgttgacacttttgtgcatcttaccttttttgttgttgc-taaacgggcttgcagtttctcctaaaatgtttgtccttg
| ||| || ||| | || || ||||| ||| | || |||||||| ||||| |||||||||||| |||| || ||| | || ||||||||||| || ||||||||        | ||||  |  |   |  ||||    | ||||   ||||   |  || |     | || || |||                        
AATACTTTCCATAGATTCGATAAATTTAACTTAAAATACAATCCTTGTGGGCAAAGTAGGCTCCGAGAAATATTCTTGAAGCAGGACAATCTGATTCAAGgtatg-------ttaatttctccgcctattcttt----cttctttttttttccatcattacgcttgctggtttacag------------------------

upper sequence: LOC_Os05g28180.2 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ30909 (Selaginella moellendorffii), 5'ss of exon 8
AGTACATTTCATCGTTTTGACAAATTCAACCTTAAGTACAATCCGTGTGGCCAAAGTAGGCTCAGAGAGATTTTCCTCAAACAGGACAATCTTATCCAAGgtatcgcttgtttcaattattttgttgacacttttgtgcatcttaccttttttgttgttgctaaacgggcttgcagtttctcctaaaatgtttgtccttg
| ||| || ||| | || || ||||| ||| | || |||||||| ||||| |||||||||||| |||| || ||| | || ||||||||||| || ||||||||        | ||||  |  |   |  ||||  |   | || || |  ||    |||||     || || |||                        
AATACTTTCCATAGATTCGATAAATTTAACTTAAAATACAATCCTTGTGGGCAAAGTAGGCTCCGAGAAATATTCTTGAAGCAGGACAATCTGATTCAAGgtatg-------ttaatttctccgcctattctttcttctttttttccatcattacgcttgct-----ggtttacag------------------------

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|29675537|gb|CB671812.1|CB671812
EST:     CCAAAGTAGGCTCAGAGAGATTTTCCTCAAACAGGACAATCTTATCCAAG                         GTCGTTTTCTTGCCGAGCTAACAAAGCAAGTTTTCTCCGACCTTACAGCAA
genomic: CCAAAGTAGGCTCAGAGAGATTTTCCTCAAACAGGACAATCTTATCCAAGgtatcgcttg ... tttaaactagGTCGTTTTCTTGCCGAGCTAACAAAGCAAGTTTTCTCCGACCTTACAGCAA