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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_Os04g41470.1
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|29614534|gb|CB619547.1|CB619547
EST:     GGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAGTTTTGCTG                         GCTGTGTCTTGGTCCATGGTCGGAGCATGGAGAACGGACTGGTGGATTTTA
genomic: GGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAGTTTTGCTGgtatgtaatc ... tataacgcagGCTGTGTCTTGGTCCATGGTCGGAGCATGGAGAACGGACTGGTGGATTTTA
EST: gi|66920746|gb|CX107594.1|CX107594
EST:     GTATGCATGCACATTACATGCACACCTCCATGCAAATTTGAGTTTTGCTG                         GCTGTGTCTTGGTCCATGGTCGGAGCATGGAGAACGGACTGGTGGATTTTA
genomic: GGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAGTTTTGCTGgtatgtaatc ... tataacgcagGCTGTGTCTTGGTCCATGGTCGGAGCATGGAGAACGGACTGGTGGATTTTA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 74 (upstream exon), 74 (downstream exon)
Score: 34

CTAATTCAAAGCCTTGTCCTAAGTGCAAGCGGCCCATTGAAAAAAACCAGGGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAGTTTTGCTGgtatgtaatc ... tataacgcagGCTGTGTCTTGGTCCATGGTCGGAGCATGGAGAACGGACTGGTGGATTTTATGCCTGTAACCGTTATGAGGCAGCAAGGCAGGAAGGAGCG




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