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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAAATCTTCGAGGGGCATTCTCACTATGTTATGCAAGTCACATTTAACCCGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAGgtttgcgattttgttccttacatttgcttggcatagtttttgcatttctaacatttcttggtctggatttgaatgtggtgcccttatttaatttcag

Basic information

species Oryza sativa
transcript LOC_Os02g11830.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G124886_T04 (Zea mays), 5'ss of exon 6
TCAAATCTTCGAGGGGCATTCTCACTATGTTATGCAAGTCACATTTAACCCGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAGgtttgcgat-tttgttccttaca---tttgcttggcatagtttttgcatt-tctaacattt-----------cttggtctggatttgaatgtggtgcccttattt-----aatttcag
|||||| || || ||||||||||||||||| |||||||| ||||||||||| |||||||| || || |||||||||||||| || ||||||||| |||||||||| | | | |   | ||| |   | || |||||     | ||||||| | |   |              |||  ||     ||||  ||| |  |||  |||     ||| ||||
TCAAATATTTGAAGGGCATTCTCACTATGTGATGCAAGTTACATTTAACCCAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgtttgtgttatctccgctttaaaaattctggttggccacaatgttgcattatttggtaccgacaggcgacagctttttcatagcttgatggtgatatcctattttttgtcaatatcag

upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G141587_T01 (Zea mays), 5'ss of exon 6
TCAAATCTTCGAGGGGCATTCTCACTATGTTATGCAAGTCACATTTAACCCGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAGgtttgcg-attttgttccttaca---tttgcttggcatagtttttgcatttctaacatttcttggtctg-----gatttgaatgtggtgcccttatttaatttcag---
|||||| ||||| ||||||||||||||||| |||||||| ||||||||||| ||||||||||| || |||||||||||||| || ||||||||| |||||||||| | | | | | | ||| |   | || ||||      | ||| |||  |     |  || |  |        |||||  ||| |  ||| ||||   |  |    
TCAAATATTCGAAGGGCATTCTCACTATGTGATGCAAGTTACATTTAACCCAAAAGATACCAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgtttgtgtaatctctgctttaaaagttctggttggtcacaatgttgtattatttgtcgtcattagctttttcatagtttgatggtgatatcctaatttctgtctatcag

upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA07G03890.1 (Glycine max), 5'ss of exon 6
TCAAATCTTCGAGGGGCATTCTCACTATGTTATGCAAGTCACATTTAACCCGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAGgtttgcgattttgttccttaca---tttgcttggcatagtttttgc--atttctaacatttcttggtctggatttgaatgtggtgcccttatttaatttcag-------
 || || || ||||| |||||||| ||||| |||||||| |||||||| || ||||| || || || ||||| ||||| || |||||||||||  ||||||| | |   | |  | ||| |    | ||    ||||  | ||||   ||||| ||       || |    |||  || ||  ||   | || | || |          
CCAGATATTTGAGGGACATTCTCATTATGTCATGCAAGTGACATTTAATCCTAAAGACACAAACACCTTTGCCAGTGCATCTCTTGATCGCACCATAAAGgtatacatgtgttcttcttgctagttgtgtcctgcattttctttgtttatttccaaacacctatgataaaaattaaaaagtaatgtattaatgttatcttttcttgcag

upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 6
TCAAATCTTCGAGGGGCATTCTCACTATGTTATGCAAGTCACATTTAACCCGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAGgt----ttgcgattttgttccttacatttgcttggcatagtttttgcatttctaacatttcttggtctggatttgaatgtggtgcccttatttaatttcag
 || || || || || |||||||| ||||| |||||||| |||||||| || ||||| || || || ||||||||||| || |||||||| ||| |||||||    ||  | | ||||||||     || | |   |||  |  ||||||  |  ||  | |||   |   |||  |                        
CCAGATATTTGAAGGCCATTCTCATTATGTCATGCAAGTAACATTTAATCCCAAAGACACAAACACCTTTGCTAGTGCATCTCTTGATCGGACAATAAAGgtagaattatgttcttgttcctggttgtttcctatgata--taatgcattaatg-cacctgttgtcttctcttttcag-----------------------

upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 6
TCAAATCTTCGAGGGGCATTCTCACTATGTTATGCAAGTCACATTTAACCCGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAGgtttgcgattttgttccttacatt-----tgcttggcatagtttttgc--atttctaacatttcttggtctggatttgaatgtggtgcccttat-ttaatttcag------
 || || || ||||| |||||||| ||||| |||||||| |||||||| || ||||| || || || ||||| ||||| || |||||||||||  ||||||| |     | ||||| |  |  |     ||    | ||  | ||||   ||||| |    |   || |    |||| || ||  ||   | || |||  ||||       
CCAGATATTTGAGGGACATTCTCATTATGTCATGCAAGTGACATTTAATCCTAAAGACACAAACACCTTTGCCAGTGCATCTCTTGATCGCACCATAAAGgtatatacatgtgttcttctcgctagttgtgtcctgaattttctttgtttatttccatacatctatgataaaaatttaaaagtaatgtattaatgttatcttcaattgcag

upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 6
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 5'ss of exon 6
TCAAATCTTCGAGGGGCATTCTCACTATGTTATGCAAGTCACATTTAACCCGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAGgtttgcgattttgttccttacatttgcttggcatagtttttgcattt-ctaacatttcttggtctggatttgaatgtggtgcccttatttaatttcag
||| || |||||||| || || |||||||| ||||||||||||||||| || ||||| ||||| |||||||| ||||| || |||||||| ||  |||||||    ||  | ||  || |||||       |||  |  ||   |   || |     ||   |||   |||  |||   ||  | | || |       
TCAGATATTCGAGGGACACTCACACTATGTGATGCAAGTCACATTTAATCCAAAAGACACCAACACTTTTGCCAGTGCATCCCTTGATCGTACCATAAAGgtgc-tgaaatggt--ctaacattgaaacatcattatggtttagtccgcttagtccgctcattctacgtttacatgca-tgttcatcttcag------

upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 6
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 10
TCAAATCTTCGAGGGGCATTCTCACTATGTTATGCAAGTCACATTTAACCCGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAGgtttgcgattttgttccttacatttgcttggca--tagtttttgcatttctaacatttcttggtctggatttgaatgtggtgcccttatttaatttcag--------------
|||||| ||||| || ||||| || ||||||||||||||||| || ||||| ||||| |||||||||||||||||||| || ||||| || ||  |||| ||  |    || ||     || |||   |  ||  |  || || |||| | ||  |  | |  |  | |  | ||  |  ||   |  | ||  | ||               
TCAAATTTTCGAAGGCCATTCCCATTATGTTATGCAAGTCACTTTCAACCCCAAAGACACCAATACTTTTGCTAGTGCATCCCTTGACCGTACCATAAAAgtaaga---ttagtcttcaacttttaagttacaccttcttctttcattcccaatttcccattatgagaagcttaacatt-tgttttcctgtatctacatcttttcttacctag

upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 6
lower sequence: AT3G15980.3 (Arabidopsis thaliana), 5'ss of exon 6
TCAAATCTTCGAGGGGCATTCTCACTATGTTATGCAAGTCACATTTAACCCGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAGgtttgcgat---tttgttccttacatttgcttggcatagtttttgc-----atttctaacatttcttggtctggatttgaatgtggtgcccttatttaatttcag
||| || || ||||| ||||| |||||||| ||||||||   |||||| || ||||||||||| |||||||| |||||||| |||||||| ||  ||||||| ||  |    |     |  |    ||   |||| |||||    |     | || ||| |    ||  |||     | | | |  |||  || || |  |||||
TCAGATATTTGAGGGACATTCGCACTATGTGATGCAAGTGGTATTTAATCCAAAAGATACCAACACTTTTGCCAGTGCTTCGCTTGATCGTACCATAAAGgtgtgtaagaggtccaagcactgagcttttatggcttagttagcacgaggtacttttaaaagggttt--tcttagactaattttcatgc--ttgttcatattcag

upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 6
TCAAATCTTCGAGGGGCATTCTCACTATGTTATGCAAGTCACATTTAACCCGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAGgtttg---cgattttgttccttacatttgcttggcatagtttttgcatttctaacatttctt--ggtctggatttgaatgtggtgcccttatttaatttcag-------
||| ||||| ||||| || ||||| ||||| |||||||| |||||||| || ||||||||||| |||||||||||||| || || ||||||||  | ||||| ||    |  |||  |  |  ||  |  ||  |    |||||  |    |     ||| |   || ||  | ||    |  ||| || ||   || ||         
TCAGATCTTTGAGGGCCACTCTCATTATGTGATGCAAGTGACATTTAATCCAAAAGATACCAACACTTTTGCTAGTGCATCTCTGGATCGCACCATTAAGgtatgatctggattttctgttggcaacttgttaactgcatttttttaccaattttgcttcatcaagtatgagtgtgctatttatgctctgatgatatctccttttccag

upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 6
TCAAATCTTCGAGGGGCATTCTCACTATGTTATGCAAGTCACATTTAACCCGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAGgtttgcgattttgttccttacatttgcttggcat-agtttttgcatttctaacatt-tcttggtctggatttgaatgtggt-gcccttatttaatttcag
||| || || || |||||||||||||| || |||||||| |||||||| || ||||| ||||| || ||||| ||||| || || ||||||||  ||||||| || |      |   |     |  | ||   | |  ||    || | |  || | || |  | | |||       | || |   ||||| | | |  |
TCAGATTTTTGAAGGGCATTCTCACTACGTGATGCAAGTGACATTTAATCCAAAAGACACCAACACCTTTGCAAGTGCCTCCCTCGATCGCACTATAAAGgtgtgagtggaaatgtttcttgataacctgttgtgaacttgaagatgtgtttcaatgtcctaatgttgatccttccatagttgattttattgattgtgtg

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|300215876|gb|HO088502.1|HO088502
EST:     CGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAG                         GTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCA
genomic: CGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAGgtttgcgatt ... ttaatttcagGTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCA
EST: gi|29680637|gb|CB676912.1|CB676912
EST:     ATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAG                         GTATGGAGTCTTGGTTCCCNTGATCCTAATTTCACATTAGATGGCCATTCA
genomic: ATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAGgtttgcgatt ... ttaatttcagGTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCA
EST: gi|29613909|gb|CB618922.1|CB618922
EST:     CGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAG                         GTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCA
genomic: CGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAGgtttgcgatt ... ttaatttcagGTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCA
EST: gi|29671007|gb|CB667282.1|CB667282
EST:     CGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAG                         GTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCA
genomic: CGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAGgtttgcgatt ... ttaatttcagGTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCA
EST: gi|29613910|gb|CB618923.1|CB618923
EST:     CGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAG                         GTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCA
genomic: CGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAGgtttgcgatt ... ttaatttcagGTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCA
EST: gi|29680636|gb|CB676911.1|CB676911
EST:     CGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAG                         GTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCA
genomic: CGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAGgtttgcgatt ... ttaatttcagGTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCA
EST: gi|29671006|gb|CB667281.1|CB667281
EST:     CGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAG                         GTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCA
genomic: CGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAGgtttgcgatt ... ttaatttcagGTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCA

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: 70 (upstream exon), 73 (downstream exon)
Score: 40

TCAAATCTTCGAGGGGCATTCTCACTATGTTATGCAAGTCACATTTAACCCGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAGgtttgcgatt ... ttaatttcagGTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCAAAAGGTGTCAATTGTGTTGATTACTTTACTGGTGGTGATCGCCCATACT




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