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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTACCATTGCCAGAACTCGTTAAATTCGTCTTTTTTGCAAACTTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTATCAGgtgggaagagtaattttaaatccttctatattcaatgttagaatggagggcacatactaattttcgtttcatgcctcttcag

Basic information

species Oryza sativa
transcript LOC_Os02g40090.4
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g40090.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G089630_T04 (Zea mays), 5'ss of exon 3
TTTACCATTGCCAGAACTCGTTAAATTCGTCTTTTTTGCAAACTTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTATCAGgtgggaagagtaattttaaatccttctatattcaatgttagaatggagggcacatactaattttcgtt-tcatgcctctt-cag
| |||| || || ||||| || ||||||| ||||||||| ||| | || ||||||||||||||||| || |||||||||||||||||||||||||||||||||   | || || ||  |    |||||||   | | |  ||||  |      ||||| |   |   | || ||||| || |||
TCTACCGTTACCTGAACTAGTAAAATTCGCCTTTTTTGCGAACCTGTCTATTGTTGGGATGAATGTAAGCTTGATGTGGAACTCTGTTGGATTCTATCAGgtgcagacagaaacttcga--tattctataagta-tatcggaattaaacttgtatactgacgctgtctgtcttgcctttttcag

upper sequence: LOC_Os02g40090.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM5G823629_T03 (Zea mays), 5'ss of exon 2
TTTACCATTGCCAGAACTCGTTAAATTCGTCTTTTTTGCAAACTTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTATCAGgtgggaagagtaattttaaatccttctatattcaatgttagaatggagggcacatactaatttt-cgtttcatgcc-tcttcag
||||||||| |||||||| || || || | ||||||||||||| | || || || || ||||| ||||||||||||||||||||||||||||||||||||||| |   || || |||      |||||||   | | || || |  |  | | ||||||||  |  || || |||| | |||||
TTTACCATTACCAGAACTAGTAAAGTTTGCCTTTTTTGCAAACCTGTCGATCGTCGGAATGAACGTTAGTTTGATGTGGAACTCTGTTGGATTCTATCAGgtgagggcagaaactttgg--tattctataagta-tattggagttaaacgtatatactaatgctgtgtatcttgcccttttcag

upper sequence: LOC_Os02g40090.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA16G27820.1 (Glycine max), 5'ss of exon 2
TTTACCATTGCCAGAACTCGTTAAATTCGTCTTTTTTGCAAACTTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTATCAGgtgggaagagt--aattttaaatccttctatattcaatgttagaatggagggcacatactaattttcgtttcatgcctcttcag
|||||| |||||||| ||  | ||||| ||  |  |||| ||||| || |||||||| |||||||||||| | ||||||||||| |||||||||||||| ||| |  | |   |  ||||  |  |  |  ||||| |  |    |     |   ||| | | |||    | |  | |   |||
TTTACCCTTGCCAGATCTTCTAAAATTTGTTCTCGTTGCTAACTTCTCTATTGTTGGAATGAATGTTAGTCTAATGTGGAACTCAGTTGGATTCTATCAAgtgagttgggctgagctttatctattggttcattcactaatgccttcagaagttaatattcacttt----ttagccattgacag

upper sequence: LOC_Os02g40090.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA04G39590.1 (Glycine max), 5'ss of exon 2
TTTACCATTGCCAGAACTCGTTAAATTCGTCTTTTTTGCAAACTTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTATCAGgtgggaagagtaattttaa-atccttctatatt------caatgttagaatggagggcacatactaattttcgtttcatgcctcttcag-------------
| | ||| |  | ||  |  | ||||| ||||| |||||||| || || ||||||||||||||||| ||||| ||||||||||||||||| |||||||||||      |    |||||  | |||   | |||      |    ||| |||  |    | |||   ||||    |   |    ||| |              
TCTTCCAGTATCTGATATAATCAAATTTGTCTTATTTGCAAATTTCTCCATTGTTGGGATGAATGTGAGTTTAATGTGGAACTCTGTTGGTTTCTATCAGgtaactttaaggcttttagtagcctataacattttgaaccgtctttataataaactaaagataaatatttataataattcttccttgaaattaaattgtcag

upper sequence: LOC_Os02g40090.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA02G08700.1 (Glycine max), 5'ss of exon 3
TTTACCATTGCCAGAACTCGTTAAATTCGTCTTTTTTGCAAACTTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTATCAGgtgggaagagt--aattttaaatccttctatattcaatgttagaatggagggcacatactaattttcgtttcatgcctcttcag
|||||| |||||||| ||  | ||||| ||  | ||||| ||||| || |||||||| |||||||||||| | ||||||||||| |||||||||||||| ||| |  | |   |  ||||  |  |  |  ||||| |  | |  |  ||     ||| | | |||    | |  | |   |||
TTTACCCTTGCCAGATCTTCTAAAATTTGTTCTCTTTGCTAACTTCTCTATTGTTGGAATGAATGTTAGTCTAATGTGGAACTCAGTTGGATTCTATCAAgtgagttgggctgagctttatctattggttaattcattaat-gccttcagaagttatattcacttt----ttagccattgacag

upper sequence: LOC_Os02g40090.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA08G15250.1 (Glycine max), 5'ss of exon 2
TTTACCATTGCCAGAACTCGTTAAATTCGTCTTTTTTGCAAACTTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTATCAGgtgggaagagtaattttaaatcct-tct------atattcaatgttagaatgg---agggcacatactaattttcgtttcatgcctcttcag-----------------
  | || || || || ||  | ||||| ||||| |||||||| || || ||||| || |||||||| |||||||||||||||||||| || |||||||||||   ||   || ||||   |  | |||       |||  | | |||  |  |     | || | |    | ||  |    |  |  | |                   
CCTTCCCTTACCTGATCTTATCAAATTTGTCTTATTTGCAAATTTCTCTATTGTCGGCATGAATGTGAGTTTGATGTGGAACTCTGTCGGTTTCTATCAGgtaacaactatattttttttttttatctttgaaagtatcaagttttaacactgccagtgacaaagataggtatttatactgtttccttcctttgaaatgaaaacttcag

upper sequence: LOC_Os02g40090.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA05G31940.1 (Glycine max), 5'ss of exon 4
TTTACCATTGCCAGAACTCGTTAAATTCGTCTTTTTTGCAAACTTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTATCAGgtgggaagagtaattttaaatccttcta---tattcaatgttagaatgg---------agggcacatactaattttcgtttcatgcctcttcag-------------
  | || || || || ||| | ||||| ||||| |||||||| || || ||||| || ||||| || |||||||||||||| ||||| || |||||||||||    ||| |  ||  ||||  ||  |   |||  ||| |||  |  |         | || |  || | ||  | ||||| |  ||||| |              
CCTTCCCTTACCTGATCTCATCAAATTTGTCTTATTTGCAAATTTCTCTATTGTCGGCATGAACGTGAGTTTGATGTGGAATTCTGTCGGTTTCTATCAGgtaactagattttttacaaattttttgaaagtatcaaattttaacactgccagtgacaaaggtaggtatttatagt-gtttcct-tctcttgaaatgaaaacttcag

upper sequence: LOC_Os02g40090.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA06G15280.1 (Glycine max), 5'ss of exon 3
TTTACCATTGCCAGAACTCGTTAAATTCGTCTTTTTTGCAAACTTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTATCAGgtgggaagagtaattttaa-atccttctatattc---aatgttagaatggagggcacatactaattttcgtttca--tgcctcttcag-------------
| | |||||  | ||  |  | ||||| ||||| |||||||| || || ||||||||||||||||| ||||| ||||||||||||||||| |||||||||||      |    |||||  | |||   | |||    |   |    || |    | |    |||| ||  |   |  |    ||| |              
TCTTCCATTATCTGATATAATCAAATTTGTCTTGTTTGCAAATTTCTCCATTGTTGGGATGAATGTGAGTTTAATGTGGAACTCTGTTGGTTTCTATCAGgtaactttaaggcttttagtagcctataacattttgaaccctctttatagtaaactctagataatatttataataattattccttgaaataaaattgtcag

upper sequence: LOC_Os02g40090.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA10G36620.1 (Glycine max), 5'ss of exon 2
TTTACCATTGCCAGAACTCGTTAAATTCGTCTTTTTTGCAAACTTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTATCAGgtgggaagagt--aattttaaatccttctatattcaatgttagaatggagggcacatactaattttcgtttcatgcctcttcag
|||||| || ||||| ||  | ||||| || || ||||| ||||| || |||||||| |||||||| ||| | ||||||||||| |||||||||||||| ||| |  |  |  |||||| | |  |  |  |       |||         | |  ||  ||||||| | | |  | |   |||
TTTACCCTTACCAGAGCTTCTAAAATTTGTTTTCTTTGCTAACTTCTCCATTGTTGGAATGAATGTCAGTCTAATGTGGAACTCAGTTGGATTCTATCAAgtgagttgtattgaattttcactattggtccaaggtccattaatgcattcagaagtta--aattttcttcttaaccattggcag

upper sequence: LOC_Os02g40090.4 (Oryza sativa), 5'ss of exon 3
lower sequence: AT1G34020.1 (Arabidopsis thaliana), 5'ss of exon 3
TTTACCATTGCCAGAACTCGTTAAATTCGTCTTTTTTGCAAACTTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTATCAGgtgggaagagtaattttaaatccttctatattcaatgttagaatggagggcacatactaattttcgtttcatgcctcttcag
| | || ||  | || ||  | | |||  |  | ||||| || || || |||||||| |||||||| ||| | ||||||||||||||||| || ||||||||   |    | || |  |   ||   ||  | ||    |   |   |   |  |  | ||| || | |  |  ||  ||||
TCTTCCGTTTACGGAGCTTTTGAGATTTATTCTGTTTGCTAATTTCTCCATTGTTGGAATGAATGTCAGTCTTATGTGGAACTCTGTTGGTTTTTATCAGgtattagacatcatct--agctctgtaattgtgaaaagaaatgtattgctgattttatgattgtcctgtttttgcttgtcag

upper sequence: LOC_Os02g40090.4 (Oryza sativa), 5'ss of exon 3
lower sequence: AT4G09810.1 (Arabidopsis thaliana), 5'ss of exon 3
TTTACCATTGCCAGAACTCGTTAAATTCGTCTTTTTTGCAAACTTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTATCAGgtgggaagagtaattttaaatccttctatattcaatgttagaatggagggcacatactaattttcgtttcatgcctcttcag
| | |||||  |||| ||  |||| ||  |  | ||||| || || || |||||||| |||||||||||| | ||||||||||||||||| || ||||||||        |   |||   |  || | ||     | ||    | | |  |  ||  |   ||   ||| |||| |   |||
TCTTCCATTTACAGAGCTTCTTAAGTTTATTCTGTTTGCTAATTTTTCGATTGTTGGAATGAATGTTAGTCTTATGTGGAACTCTGTTGGGTTTTATCAGgtaaatgtgtttgctttttgtg-ttatgtaacgtttcttgttgttg-gttctaatggtgtcttctcttttatgcttaa-cag

upper sequence: LOC_Os02g40090.4 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv18s0072g00080.t01 (Vitis vinifera), 5'ss of exon 2
TTTACCATTGCCAGAACTCGTTAAATTCGTCTTTTTTGCAAACTTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTATCAGgtgggaagagtaattttaaatccttctatattcaatgttagaatggagggcacatactaattttcgtttcatgcctc-ttcag-------
| | ||  | ||||| ||  | ||||| || || ||||| ||||| || |||||||| |||||||||||||| ||||||||||| || || |||||||||||        || | | |   |  | | | || ||  ||| | |  |  | | ||| |       ||| |||  ||  || |        
TCTCCCCCTTCCAGAGCTTCTGAAATTTGTATTATTTGCGAACTTCTCTATTGTTGGAATGAATGTTAGTTTAATGTGGAACTCAGTAGGGTTCTATCAGgta-------tattctgattgctctgtgtgtttaagcttacattttattgta-ataattgcagaagttacatctctaatttaactgtcag

upper sequence: LOC_Os02g40090.4 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv07s0031g01860.t01 (Vitis vinifera), 5'ss of exon 3
TTTACCATTGCCAGAACTCGTTAAATTCGTCTTTTTTGCAAACTTATCAATTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTATCAGgt-------gggaagag-taattttaaat---ccttctatattcaatgttagaatggagggcacatactaattttcgtttcatgcctcttcag------
| ||||| |  | || ||  | | ||| || || |||||||| || ||||||||||| ||||| || ||||| |||||||||||||| ||||||||||||||       |||||  | | | |||   |   |||| |    |||   ||    |  | |  |||   ||  ||   | || |    |||         
TCTACCAGTATCTGAGCTTCTGAGATTTGTTTTGTTTGCAAATTTGTCAATTGTTGGAATGAACGTGAGTTTAATGTGGAACTCTGTGGGATTCTATCAGgtcagttttgggaactgctgactttttgttctccttttgctctcatattttttttcaaagttacaagttatgttctttctcttcaaactttgatgtcag

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|29639689|gb|CB644698.1|CB644698
EST:     TTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTATCAG                         ATTGCCAAGTTGTGTATTATTCCAGTCTTGTGCATTCTGGAAATCCTGTTT
genomic: TTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTATCAGgtgggaagag ... gcctcttcagATTGCCAAGTTGTGTATTATTCCAGTCTTGTGCATTCTGGAAATCCTGTTT
EST: gi|88398814|gb|CI601150.1|CI601150
EST:     TTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTATCAG                         ATTGCCAAGTTGTG
genomic: TTGTTGGGATGAATGTTAGTTTGATGTGGAACTCTGTTGGATTCTATCAGgtgggaagag ... gcctcttcagATTGCCAAGTTGTG