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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATGCGTTGGACTTGGATAATGCGATGGCATATGACAATGCTGTTTCTGCTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAGgtgtcttacaagccatatgaattaatatacttactctgaagtgtattcttactcatttgaaatcatggtgttgctacctgtcctgctgattaattaaact...

Basic information

species Oryza sativa
transcript LOC_Os03g49420.2
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g49420.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G033619_T02 (Zea mays), 5'ss of exon 16
CAATGCGTTGGACTTGGATAATGCGATGGCATATGACAATGCTGTTTCTGCTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAGgtgtcttacaagccatatgaattaatatacttactctgaagtgtattcttactcatttgaaat-catggtgttgctacctgtcctgctgattaattaaact-----
 |||||  |||| ||||||||||| ||||| |||||||||||||||||||||||||| |||||||| |  ||||||||||||  |||||||| |||||||||        | |||||   |   ||||  ||  |||    | |||  |    ||| |    | | |  |   ||    |    |      |||||  | |     
TAATGCCCTGGATTTGGATAATGCAATGGCCTATGACAATGCTGTTTCTGCTCTTGGAAAAATATGCCGATTTCATCGTGATATCATTGATGTATCTCAGgtactc----aaccatacttaggcatatggttcttctagcttatatcatgg--catctagcctgcttcattcagccttgtagtatataatataattccatttctga

upper sequence: LOC_Os03g49420.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GLYMA05G28950.1 (Glycine max), 5'ss of exon 19
CAATGCGTTGGACTTGGATAATGCGATGGCATATGACAATGCTGTTTCTGCTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAGgtgtcttacaagccatatgaattaatatacttactctgaagtgt--attcttactcat--ttgaaatcatggtgttgctacctgtcctg---ctgattaattaaact--------------------------------------------------
 |||||  |  | |  |||||||  ||||||||||||||||||||||| ||| | || ||||| || || |||||||||||  | |||||| |  | |||||    ||||     |  |  || |||   |  || ||  || |   |||||  | ||  |||  || ||  || | | |    | |||   ||||||  ||    |                                                  
TAATGCTCTTCATTCAGATAATGTAATGGCATATGACAATGCTGTTTCCGCTTTGGGAAAAATTTGCCAATTTCATCGTGACAGTATTGATTCTGCCCAGgt-cagtacatattttccg--tttataacttgcctttgtggttttggttcttgattatgtttgtcattattatgat-caattctttctgagtctgatttgttgtttttaggttgagatgatggttaatatttttgtaatgttctgtcatgtttgcag

upper sequence: LOC_Os03g49420.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GLYMA08G12120.1 (Glycine max), 5'ss of exon 17
CAATGCGTTGGACTTGGATAATGCGATGGCATATGACAATGCTGTTTCTGCTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAGgtgtcttacaagccatatgaattaatatacttactctgaagtgtattcttactcatttgaaatcatggtgttgctacctgtcctgctgattaattaaact-------------------------------------------------------
 |||||  |  | |  |||||||  ||||||||||||||||| ||||| ||||| || ||||| || || |||||||||||  | |||||| |  | |||||    ||||     |     || ||| |||| || |   |  | |  ||  |||||     |     | ||   | |  | ||     |   ||    |                                                       
TAATGCTCTTCATTCAGATAATGTAATGGCATATGACAATGCCGTTTCCGCTCTGGGAAAAATTTGCCAATTTCATCGTGACAGTATTGATTCTGCCCAGgt-cagtacatattttccctgtttata-acttgcttttgtggttttgattcttcattatgtttgtcattattatgatcaattctttgagtctgttttgttgtttttaggttgagatgatagttaatatttttgtaatgttctgttatgtttgcag

upper sequence: LOC_Os03g49420.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GLYMA19G29010.1 (Glycine max), 5'ss of exon 17
CAATGCGTTGGACTTGGATAATGCGATGGCATATGACAATGCTGTTTCTGCTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAGgtgtcttacaagcca----tatgaattaatatacttactctgaagtgtattcttactcatttgaaatcatggtgttgctacctgtcctgct-gattaattaaact
 |||||  |  |    |||||    ||||||||||||||||| || || |||||||| |||||||| || || ||||||||| ||||  ||||| | ||||| | ||||||        |     |      | |   |   ||   | |||||  | | ||  |||| || |  || | ||  |     | ||  || ||    
AAATGCACTACATGCTGATAACATAATGGCATATGACAATGCCGTCTCAGCTCTTGGAAAAATATGCCAATTCCATCGTGATAGCATAAATGCAGCACAGgtattttacaatttggtgctccatgtctccgcagtcttttaaaatgctgttcttgtttactt--aatcttgcttgtgatcccaatgtcatttgaaaaagtat---

upper sequence: LOC_Os03g49420.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GLYMA16G04400.1 (Glycine max), 5'ss of exon 17
CAATGCGTTGGACTTGGATAATGCGATGGCATATGACAATGCTGTTTCTGCTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAGgtgtcttacaagccatatgaattaatatacttactctgaagtgtattcttactcatttgaaatcatggtgttgctacctgtcctgctgattaattaaact-----
 |||||  |  | |  |||||    ||||||||||||||||||||||| |||||||| |||||||| || || ||||||||| ||||  ||||| | ||||| | |||||     |      |        |  |   || ||   |  |  |  |||     | |  | |||||     ||||  | |  | || ||       
AAATGCACTACATTCTGATAACATAATGGCATATGACAATGCTGTTTCAGCTCTTGGAAAAATATGCCAATTCCATCGTGATAGCATAAATGCAGCACAGgtattttacatttggtgccccatgtctctgctgtttgaaaatgctgttcttgttgttta----cttaatcttgcttgtgatcctaat-accatttgaaacagtat

upper sequence: LOC_Os03g49420.1 (Oryza sativa), 5'ss of exon 16
lower sequence: Vv08s0007g07240.t01 (Vitis vinifera), 5'ss of exon 17
CAATGCGTTGGACTTGGATAATGCGATGGCATATGACAATGCTGTTTCTGCTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAGgtgtcttacaagccat-atgaattaatatac-ttactctgaagtgtatt-cttactcatttgaaatcatggtgttgctacctgtcctgctgattaattaaact
 |||||   ||| |  |||||||  ||||| ||||| ||||||||||| || ||||| |||||||| ||||| ||||| ||| | || |||||    ||||| | | | |   ||| ||   ||  | |   || ||     || || | | |    |  |    ||         ||   |     |||   |||| |    
TAATGCACGGGATTCAGATAATGTAATGGCTTATGATAATGCTGTTTCCGCACTTGGAAAAATATGCCAGTTCCATCGCGATAGTATAGATGCCGTGCAGgtatat-atatctcatcattccttgctttgggttgcttctgtgtatactacctttatacgtagcttcccctcccctcttttttaggcgcttcctaatcatg--

upper sequence: LOC_Os03g49420.1 (Oryza sativa), 5'ss of exon 16
lower sequence: Vv06s0004g00500.t01 (Vitis vinifera), 5'ss of exon 17
CAATGCGTTGGACTTGGATAATGCGATGGCATATGACAATGCTGTTTCTGCTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAGgt-gtcttacaagccatatgaattaatatacttactctgaagtgtatt---cttactcatt-tgaaatcatggtgttgctacctgtcctgctgattaattaaact
 |||||  || |    |||||||  ||||||||||| ||||||||||||||||| || ||||| || ||||||||||||||  | |||||| || ||||||| || | ||    |  |   || |  |||  ||  |  | ||  |||    ||  ||||  |  | ||||| | || | ||        || |  ||||     
TAATGCACTGCAACCAGATAATGTAATGGCATATGATAATGCTGTTTCTGCTCTAGGAAAAATTTGCCAGTTTCATCGTGACAGTATTGATTCAGCTCAGgtagtttcacttttctcaaccat-atcatatctaagcacaggttgattatattttgtcatcatctactcatg-tattccaacaaaattgcctaaaaaattgg---

upper sequence: LOC_Os03g49420.1 (Oryza sativa), 5'ss of exon 16
lower sequence: EFJ38876 (Selaginella moellendorffii), 5'ss of exon 17
CAATGCGTTGGACTTGGATAATGCGATGGCATATGACAATGCTGTTTCTGCTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAGgtgtcttacaagccatatgaattaatatacttactctgaagtgtattcttactcatttgaaatcatggtgttgct-acctgtcctgctgattaattaaact
|  ||||  | |   ||||||    ||||||   || |||||||| ||||||||||| |||||||||||||| ||  | ||| |||| |||||  | ||||||| |         | ||  |   |   ||| ||||    ||||||  |  ||| ||    |    ||||| || | | |                    
CGCTGCGCGGCAACAGGATAACATCATGGCAACCGATAATGCTGTGTCTGCTCTTGGAAAAATATGTCAGTTCCAAAGAGATAGCATCGATGCTACACAGgtgtgt--------gtgtgtgtgtgtgctctt-ctctattatgtattgatcatcactttgtgt----gtgtttctcatcag--------------------

upper sequence: LOC_Os03g49420.1 (Oryza sativa), 5'ss of exon 16
lower sequence: EFJ15568 (Selaginella moellendorffii), 5'ss of exon 17
CAATGCGTTGGACTTGGATAATGCGATGGCATATGACAATGCTGTTTCTGCTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAGgtgtcttacaagccatatgaattaatatacttactctgaagtgtattcttactcatttgaaatcatggtgttgct-acctgtcctgctgattaattaaact
|  ||||  | |   ||||||    ||||||   || |||||||| ||||||||||| |||||||||||||| ||  | ||| |||| |||||  | |||||||             ||  |   | | ||| |||||   |||| |  |  ||| ||    |    ||||| || | | |                    
CGCTGCGCGGCAACAGGATAACATCATGGCAACCGATAATGCTGTGTCTGCTCTTGGAAAAATATGTCAGTTCCAAAGAGATAGCATCGATGCTACACAGgtgt------------gtgtgtgtgtgttctt-ctctgttatgtactgatcatcactttgtgt----gtgtttctcatcag--------------------

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|29681491|gb|CB677766.1|CB677766
EST:     CTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAG                         GTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAG
genomic: CTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAGgtgtcttaca ... atattaacagGTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAG
EST: gi|29679232|gb|CB675507.1|CB675507
EST:     CTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAG                         GTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAG
genomic: CTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAGgtgtcttaca ... atattaacagGTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAG
EST: gi|29629241|gb|CB634252.1|CB634252
EST:     CTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAG                         GTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAG
genomic: CTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAGgtgtcttaca ... atattaacagGTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAG
EST: gi|27576974|gb|CA999668.1|CA999668
EST:     CTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAG                         GTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAG
genomic: CTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAGgtgtcttaca ... atattaacagGTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAG
EST: gi|29629841|gb|CB634850.1|CB634850
EST:     CTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAG                         GTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAG
genomic: CTCTTGGGAAAATATGTCAGTTTCATCGTGATGGCATTGATGCATCTCAGgtgtcttaca ... atattaacagGTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAG