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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTAATTCAAAGCCTTGTCCTAAGTGCAAGCGGCCCATTGAAAAAAACCAGGGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAGTTTTGCTGgtatgtaatcataatctctctgtttatgctcttcatagcacttgcagtctcatatggcttgtatgtacttgttctatataacgcag

Basic information

species Oryza sativa
transcript LOC_Os04g41470.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM5G876621_T02 (Zea mays), 5'ss of exon 8
CTAATTCAAAGCCTTGTCCTAAGTGCAAGCGGCCCATTGAAAAAAACCAGGGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAGTTTTGCTGgtatgtaatcataatctctctgtttatgctcttcatagcacttgcagtctcatatggcttgtatgtacttgttctatataac-gcag
||||||||||||||||||| || ||||| ||||| ||||||||||| ||||||||||||||||| |||||||| || ||||||||||||||||| |||||||| | | || || | | |   ||| |  ||||  |||  ||||||     ||    |   |   |   ||  |||| | ||  |||
CTAATTCAAAGCCTTGTCCCAAATGCAAACGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAGTTCTGCTGgtaagcattcttactttatgcattt-tattcttattagtgcttgcaa----atgaaacaaattgatggctgcgctatcttactacag

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G006428_T01 (Zea mays), 5'ss of exon 8
CTAATTCAAAGCCTTGTCCTAAGTGCAAGCGGCCCATTGAAAAAAACCAGGGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAGTTTTGCTGgtatgtaatcataatctctctgtttatgctcttcatagcacttgcagtctcatatggcttgtatg-tacttgttctat-ataacgcag
||||||||||||||||||| || ||||||||||| ||||||||||| ||||||||||||||||| |||||||| || ||||||||||||||||| |||||||| | | ||    |   | | |  ||  | ||| ||  | ||  ||   || ||||     ||| || |||| |||| |||   |||
CTAATTCAAAGCCTTGTCCCAAATGCAAGCGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAGTTCTGCTGgtaggcattc---tttcttttatacattttattcttattagttttag---caaatggaaaacatgatagttgtactatcatactacag

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AT1G65430.1 (Arabidopsis thaliana), 5'ss of exon 8
CTAATTCAAAGCCTTGTCCTAAGTGCAAGCGGCCCATTGAAAAAAACCAGGGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAGTTTTGCTGgtatgtaatcataatctctctgtttatgct---cttcatagcacttgcagtctca--tatggcttgtatgtacttgttcta-tataacgcag----------
| ||||| ||||| ||||| || ||||| ||||| || || ||||||||||| || ||||| ||||| ||||| || ||||| ||||||||||| |||||||| ||  | ||||  |   || |||  |        |||      | |||      | |    | | | |||||  | || | |||| | |          
CAAATTCCAAGCCCTGTCCAAAATGCAAACGGCCAATAGAGAAAAACCAGGGTTGTATGCATATTACGTGCACCCCACCATGTAAATTTGAGTTCTGCTGgtaagt--tgataaagtggttgattaaacaaaatgctataatgtcagaagttatgcttttattctctctatacttcctgtaatctaactctgaattggattc

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv00s0207g00090.t01 (Vitis vinifera), 5'ss of exon 8
CTAATTCAAAGCCTTGTCCTAAGTGCAAGCGGCCCATTGAAAAAAACCAGGGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAGTTTTGCTGgtatgtaatcataatctc--tctgtttatgctc-------ttcatagcacttgcagtctcatatggcttgtatgtacttgttctatataacgcag-----
||||||| ||||||||||| ||||| |||||||| || ||||||||||| || || ||||| || ||||||||||| ||||| |||||||||||||||||||| ||    ||| |||   |||   ||  |||       || |       ||   | |  |     ||||||  |||||       || |         
CTAATTCCAAGCCTTGTCCAAAGTGTAAGCGGCCAATCGAAAAAAACCAAGGTTGTATGCATATCACATGCACACCGCCATGTAAATTTGAGTTTTGCTGgtaagtttatatactcttgttctagatagactcacatgtatttaggaggtctggtctttattccattttgtatccacttggcaacactagcattatcaag

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 8
lower sequence: PP1S9_199V6.1 (Physcomitrella patens), 5'ss of exon 9
CTAATTCAAAGCCTTGTCCTAAGTGCAAGCGGCCCATTGAAAAAAACCAGGGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAGTTTTGCTGgtatgtaatc-ataatctctct---gtttatgctcttc-atagcacttg---cagtctcatatggcttgtatgtac----ttgttctatataacgcag------------------------------------------------------------------------------------------------
| ||    || || ||||| || || ||  |||| || ||||| || || || |||||||||||||| |||||||| || ||||||||||||||||||||||| |||||  ||||| ||  |    | ||   || |  || |  | ||   || ||| |  |   || |||  ||     |  |  |  | |||  |                                                                                                
CGAACAGCAAACCCTGTCCCAAATGTAAAAGGCCAATCGAAAAGAATCAAGGCTGCATGCACATTACTTGCACACCACCTTGCAAATTTGAGTTTTGCTGgtaagtaatggataatttcaattgaatctaaagtcatggatggatcatgattcattcttaccttaattttatagacacagctacttaagtttacgttgcttcactctgagtatgttgacaccagtggttggtaagtctatcacttataagcaaccaaatttattcactcagttttatttatgcgtttttgacag

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 8
lower sequence: PP1S178_72V6.3 (Physcomitrella patens), 5'ss of exon 8
CTAATTCAAAGCCTTGTCCTAAGTGCAAGCGGCCCATTGAAAAAAACCAGGGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAGTTTTGCTGgta---tgtaatcataatctctctgtttatgctcttcatagcacttgc---agtctcatatggcttgtatgtacttgt-----tctatataacgcag-----------------------------------------------------------------------
| ||    || || || ||||| || ||| | || |||||||||||||| || |||||||| ||||| |||||||| || |||||||||||||||||||||||   |||||  || ||   |   ||  |    || |    ||||       | |  ||    |  |||||    ||     |   ||||| |                                                                          
CAAACAGCAAACCCTGCCCTAAATGTAAGAGACCGATTGAAAAAAACCAAGGCTGCATGCATATTACTTGCACACCACCTTGCAAATTTGAGTTTTGCTGgtaagttgtaaatattattcttactttagttaaattaaagttacttaattggatttagtactattaatatgtgaaagtcaccatgcttataaggtcatcaactcagctgctgcaattcatgttgcctcattctcaagtgtagcttttgaaccttgacttctttggcag

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 8
lower sequence: PP1S114_2V6.1 (Physcomitrella patens), 5'ss of exon 8
CTAATTCAAAGCCTTGTCCTAAGTGCAAGCGGCCCATTGAAAAAAACCAGGGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAGTTTTGCTGgta----------tgtaatcataat-------ctctctgtttatgctcttcatagc---acttgcagtctcatatggcttgtatgtacttgtt---ctatataacgcag------------------------------------------------------------------------------------------
| ||    || ||||| || ||||| ||| |||| ||||| |||||||| || |||||||| || || ||||| || || ||||||  |||||||||||||||          ||||||  |||         | | | |||   ||  |   ||     ||||    |  ||     | |    | ||  ||   ||    |  ||||                                                                                          
CAAACAGCAAACCTTGCCCCAAGTGTAAGAGGCCAATTGAGAAAAACCAAGGCTGCATGCATATCACTTGCACTCCACCTTGCAAACATGAGTTTTGCTGgtaaacaatttaatgtaattttaaaaaaatagttttttattttcccttattgaagttaagcttgttaacgaatgaaattcggtcttgctcattaagctcatcagtgcagctgcggcagtccatgctattgtattttaacgctttgagtgtctggtttggaaatagtgtcacttacaagagttcactgatactataacag

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 8
lower sequence: PP1S156_28V6.1 (Physcomitrella patens), 5'ss of exon 8
CTAATTCAAAGCCTTGTCCTAAGTGCAAGCGGCCCATTGAAAAAAACCAGGGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAGTTTTGCTGgtatgt------aatcataatctctct------gtttatgctcttcatagcacttgcagtctcat-----atggcttgtatgtacttgttctatataacgcag----------------------------------------------------------------
| ||    || || || || || || ||  |||| ||||| |||||||| || || ||||||||||| ||||||||||| ||||||||||||||||||||||| ||       ||  || |   |||       |  |||   || |   ||||  |   |||||     |||| |  || ||  |||||   | || |                                                                    
CAAACAGCAAACCCTGCCCCAAATGTAAAAGGCCAATTGAGAAAAACCAAGGGTGTATGCACATTACTTGCACACCTCCTTGCAAATTTGAGTTTTGCTGgtaagtctaatagattttattgggtctcgaggaatgaatgggtttaaattcactctccaactcatcgataatggttcttaagtttttgttgctt-tagcctgaatgggttgaaagctggtcattgataagacacttacttatgagcaacccacttttgtttctaaag

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 8
lower sequence: EFJ17699 (Selaginella moellendorffii), 5'ss of exon 8
CTAATTCAAAGCCTTGTCCTAAGTGCAAGCGGCCCATTGAAAAAAACCAGGGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAGTTTTGCTGgtatgtaatcataatctctctgtttatgctcttcatagcacttgcagtctcatatggcttgtatgtacttgttctatataacgcag
| ||||| || |||||||| ||||| ||  | || || ||||||   || ||||||||||| || || || || ||||| ||||| ||||||||||||||||| ||  |     | |||| | | |||        |    | | ||                                       
CCAATTCCAAACCTTGTCCAAAGTGTAAAAGACCGATCGAAAAATCTCAAGGATGCATGCATATAACGTGTACGCCTCCGTGCAAGTTTGAGTTTTGCTGgtaggtgttttctttttctc-gctgatgactgattgatgtgtggtag---------------------------------------

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 8
lower sequence: EFJ16231 (Selaginella moellendorffii), 5'ss of exon 8
CTAATTCAAAGCCTTGTCCTAAGTGCAAGCGGCCCATTGAAAAAAACCAGGGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAGTTTTGCTGgtatgtaatcataatctctctgtttatgctcttcatagcacttgcagtctcatatggcttgtatgtacttgttctatataacgcag
| ||||| || |||||||| ||||| ||  | || || ||||||   || ||||||||||| || || || || ||||| ||||| ||||||||||||||||| || ||  |  | |||| | | |||        |    | | ||                                       
CCAATTCCAAACCTTGTCCAAAGTGTAAAAGACCGATCGAAAAATCTCAAGGATGCATGCATATAACGTGTACGCCTCCGTGCAAGTTTGAGTTTTGCTGgtaggtgatttttttttctc-gctgatgtctgattgatgtgtggtag---------------------------------------

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|29681156|gb|CB677431.1|CB677431
EST:     GGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAGTTTTGCTG                         GCTGTGTCTTGGTCCATGGTCGGAGCATGGAGAACGGACTGGTGGATTTTA
genomic: GGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAGTTTTGCTGgtatgtaatc ... tataacgcagGCTGTGTCTTGGTCCATGGTCGGAGCATGGAGAACGGACTGGTGGATTTTA