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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGGAAGTTTGGCGAAGACGGGAACAAGTATTTCCGCCATGCCACTGGGCAGATATATGCCATCTCAAAGGACCTTGCCACATACATCTCGATCAACCGgtaagcctagagaatggctgcacatgattcttcagacaaaatattcattttactgaattgttactgatactcttgtgtcccaccatataacccag

Basic information

species Oryza sativa
transcript LOC_Os09g27950.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g27950.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G133613_T02 (Zea mays), 5'ss of exon 8
TCTGGAAGTTTGGCGAAGACGGGAACAAGTATTTCCGCCATGCCACTGGGCAGATATATGCCATCTCAAAGGACCTTGCCACATACATCTCGATCAACCGgtaagcctagagaatggctgcacatgattcttcagacaaaatattcattttactgaattgttactgatactcttgtgtcccaccatataacccag-----
|||||||||| || || |||||||||||||| |||||||| ||||| ||||||||||| |||||||| |||||||| || || |||||||| ||||||| ||||     || ||   || |   |  ||||||   |      |   |   ||||    |   ||||| |   || || | |||||||| | | |     
TCTGGAAGTTCGGAGAGGACGGGAACAAGTACTTCCGCCACGCCACGGGGCAGATATACGCCATCTCCAAGGACCTCGCGACCTACATCTCCATCAACCAgtaa-----gacaaaaccttcttcttcttcttctctct---cttgagtggcactggcaggcagctgatccatatgcgttc-accatataccaccgcccag

upper sequence: LOC_Os09g27950.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA04G43340.2 (Glycine max), 5'ss of exon 9
TCTGGAAGTTTGGCGAAGACGGGAACAAGTATTTCCGCCATGCCACTGGGCAGATATATGCCATCTCAAAGGACCTTGCCACATACATCTCGATCAACCGgtaagcctagagaatggctgcacatgattcttcagacaaaatattcattttactgaattgttactgatactcttgtgtc----ccaccatataacccag----
| ||||||||||| ||||| |||||||| || ||||| ||||| ||||||||||||||||| ||||||||||| || ||||| ||||| || ||||||| ||| |  ||   | |    |  ||  | |   | | | |  |  | || |    | |     ||||    | ||||         |||| || | | |     
TTTGGAAGTTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCAAAGGATCTGGCCACTTACATTTCCATCAACCAgtatgtatatc-atttttcgtgcaacacttaactggctatcttctgatctcg--gcaccacaactgtgtattttgtacagggattaccagatgagcaattgtt

upper sequence: LOC_Os09g27950.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA13G02420.1 (Glycine max), 5'ss of exon 9
TCTGGAAGTTTGGCGAAGACGGGAACAAGTATTTCCGCCATGCCACTGGGCAGATATATGCCATCTCAAAGGACCTTGCCACATACATCTCGATCAACCGgtaagcctagagaatggctgcacatgatt--cttcagacaaaatattcattttactgaattgttactgatactcttgtgtcccaccatataacccag---
| ||||| ||||| ||||| |||||||| || ||||| ||||| ||||||||||||||||| ||||| ||||| || ||||| ||||| || ||||||| ||| |  ||     |  |      |  ||  ||||  |      |     |     |   |  |  |||  |  |        |    || | | ||   
TTTGGAAATTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCTAAGGATCTGGCCACCTACATTTCCATCAACCAgtatggatacgcttttccaattagtacttagcttcctatggttgagagtatcagaggggctaatgttgaccccatacaactgtagtgcatgatcaagaat

upper sequence: LOC_Os09g27950.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA14G33700.1 (Glycine max), 5'ss of exon 9
TCTGGAAGTTTGGCGAAGACGGGAACAAGTATTTCCGCCATGCCACTGGGCAGATATATGCCATCTCAAAGGACCTTGCCACATACATCTCGATCAACCGgtaagcctagagaatggc-tgcaca--tgattcttcagacaaaatattcattttactgaattgttactgatactcttgtgtcccaccatataacccag---
| ||||||||||| ||||| |||||||| |||||||| ||||| ||||||||||||||||| ||||| ||||| || ||||| ||||| || || |||| ||| |  || ||  |  | |||||   | | || ||    |       ||    |   |||  | ||  ||||   | | |  ||  |    |   |    
TTTGGAAGTTTGGAGAAGAGGGGAACAAATATTTCCGACATGCAACTGGGCAGATATATGCAATCTCTAAGGATCTAGCCACCTACATTTCCATTAACCAgtatggatacagttttccatgcactactaagtcatctataattgagaccagaggagctaatcttgacc-atacaactatattgcatgaatagatttaagta

upper sequence: LOC_Os09g27950.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA06G11330.1 (Glycine max), 5'ss of exon 9
TCTGGAAGTTTGGCGAAGACGGGAACAAGTATTTCCGCCATGCCACTGGGCAGATATATGCCATCTCAAAGGACCTTGCCACATACATCTCGATCAACCGgtaagcctagagaatggctgcacatgattcttcagacaaaatattcattttactgaattgttactgatactcttgtgtc----ccaccatataacccag----
| ||||||||||| ||||| |||||||| || ||||| ||||| ||||||||||||||||| |||||||||||  | ||||| ||||| || ||||||  ||| |  ||     |   | |      | ||| |    | || |||   |  | | |   | ||||    | | |          |||| || | | |     
TTTGGAAGTTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCAAAGGATTTGGCCACTTACATTTCCATCAACAAgtacgtatatcattt---ttcgtccactacttaactggatatcttctgatctcggtaccataactgtgtatttcgcacagggattaccagattagcaattgtt

upper sequence: LOC_Os09g27950.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT1G22015.1 (Arabidopsis thaliana), 5'ss of exon 9
TCTGGAAGTTTGGCGAAGACGGGAACAAGTATTTCCGCCATGCCACTGGGCAGATATATGCCATCTCAAAGGACCTTGCCACATACATCTCGATCAACCGgtaagcctagagaatggctgcacatgattcttcagacaaaata---ttcattttactga-----attgttactgat-actcttgtgtcccaccatataacccag---
| ||||| ||||| ||||| || ||||| |||||||| ||||| || || ||||| |||||||| |||||||| |||||||||||||| || | ||||| |||||     |   |    |    ||  | ||| |||||  ||   |   ||||||  |     ||   ||   |  |  | |           | | ||   |   
TTTGGAAATTTGGAGAAGAAGGTAACAAATATTTCCGACATGCTACGGGACAGATTTATGCCATATCAAAGGATCTTGCCACATACATATCTAACAACCAgtaagtgaccaactttatggtttttggattttc-gacaaggtaagatatgttttaccaagggaaatgagtatcaaccaaacataacatttgatgtttgacttcgcag

upper sequence: LOC_Os09g27950.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv07s0031g03090.t01 (Vitis vinifera), 5'ss of exon 9
TCTGGAAGTTTGGCGAAGACGGGAACAAGTATTTCCGCCATGCCACTGGGCAGATATATGCCATCTCAAAGGACCTTGCCACATACATCTCGATCAACCGgtaagcctagagaatggctgcacatgattcttcaga---caaaatattcattttactgaattgttactgatactcttgtgtcccaccatataacccag------
 |||||| ||||| || || ||||| ||||| || || ||||| || |||||||| ||||||||||||||||| || |||||||| |||||  |||||| |||||   ||| ||||| |     | | ||| ||||     | | ||||  | | |  || ||||  |     |  | | |   |   | |   | ||      
ACTGGAAATTTGGAGAGGAGGGGAATAAGTACTTTCGGCATGCAACCGGGCAGATTTATGCCATCTCAAAGGATCTGGCCACATATATCTCTGTCAACCAgtaagaacagataatggttt----tcagtctacagagtctcatagattccatcttccaaaatgtttttatatataatattttaaatttttttctctagtcactg

upper sequence: LOC_Os09g27950.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv18s0001g04150.t01 (Vitis vinifera), 5'ss of exon 9
TCTGGAAGTTTGGCGAAGACGGGAACAAGTATTTCCGCCATGCCACTGGGCAGATATATGCCATCTCAAAGGACCTTGCCACATACATCTCGATCAACCGgtaagcctagagaatggctgcacatgattcttcagacaaaatattcattttactgaattgtta---ctgatactcttgtgtcccaccatataacccag------
 |||||||||||| || || ||||||||||||||||| ||||| ||||||||||| ||||| |||||||| || || |||||||||||||||||||||| |||||  | |||  |   |  | |||     | || |    |   |||||| ||||  |   |   |  |   |||||     || |   |   |  |      
ACTGGAAGTTTGGAGAGGAGGGGAACAAGTATTTCCGGCATGCAACTGGGCAGATTTATGCAATCTCAAAAGATCTGGCCACATACATCTCGATCAACCAgtaagaattgagtttt-ttttatatgga--attagcctgtttggccatttt-ctgagctaccatatcaaaaggtcttgcaattcatcccctgggcatgattttc

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|29613544|gb|CB618557.1|CB618557
EST:     CAGATATATGCCATCTCAAAGGACCTTGCCACATACATCTCGATCAACCG                         GCCTATATTGCACAAATATGCAAACGAAGACGTTTCACTTGGCGCATGGTT
genomic: CAGATATATGCCATCTCAAAGGACCTTGCCACATACATCTCGATCAACCGgtaagcctag ... tataacccagGCCTATATTGCACAAATATGCAAACGAAGACGTTTCACTTGGCGCATGGTT
EST: gi|29613575|gb|CB618588.1|CB618588
EST:     CAGATATATGCCATCTCAAAGGACCTTGCCACATACATCTCGATCAACCG                         GCCTATATTGCACAAATATGCAAACGAAGACGTTTCACTTGGCGCATGGTT
genomic: CAGATATATGCCATCTCAAAGGACCTTGCCACATACATCTCGATCAACCGgtaagcctag ... tataacccagGCCTATATTGCACAAATATGCAAACGAAGACGTTTCACTTGGCGCATGGTT
EST: gi|86503029|gb|CI145662.1|CI145662
EST:     CAGATATATGCCATCTCAAAGGACCTTGCCACATACATCTCGATCAACCG                         GCCTATATTGCACAAATATGCAAACGAAGACGTTTCACTTGGCGCATGGTT
genomic: CAGATATATGCCATCTCAAAGGACCTTGCCACATACATCTCGATCAACCGgtaagcctag ... tataacccagGCCTATATTGCACAAATATGCAAACGAAGACGTTTCACTTGGCGCATGGTT
EST: gi|25803713|gb|CA759674.1|CA759674
EST:     CAGATATATGCCATCTCAAAGGACCTTGCCACATACATCTCGATCAACCG                         GCCTATATTGCACAAATATGCAAACGAAGACGTTTCACTTGGCGCATGGTT
genomic: CAGATATATGCCATCTCAAAGGACCTTGCCACATACATCTCGATCAACCGgtaagcctag ... tataacccagGCCTATATTGCACAAATATGCAAACGAAGACGTTTCACTTGGCGCATGGTT

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: 34 (upstream exon), 62 (downstream exon)
Score: 3

TCTGGAAGTTTGGCGAAGACGGGAACAAGTATTTCCGCCATGCCACTGGGCAGATATATGCCATCTCAAAGGACCTTGCCACATACATCTCGATCAACCGgtaagcctag ... tataacccagGCCTATATTGCACAAATATGCAAACGAAGACGTTTCACTTGGCGCATGGTTTATCGGTTTAGACGTGGAGCACATTGACGACAGAGACATGTGCTGTGGA




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